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Smolecule.A_PARITY|Smolecule.A_CHIRALITY"abbrevgroups".
"abbrevgroupsAllowed".
AbstractStructureChecker detecting abbreviations ("COOH", "Ala",
"NO2", etc.) in a Molecule instance represented in abbreviated group form."absLabelVisible" or "absLabel".
StructureFixer implementation which removes absolute stereo property from the molecule.StructureFixer interfacetrue if molecule is accepted by the filter.
Action implementation which performs config element add
"addRemoveHatomsEnabled".
MDSet object.
PropertyChangeListener for element property changes
PropertyChangeListener for a specific element property change
Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[], int)
Hydrogenize.addHAtoms(MoleculeGraph, MolAtom[], int)
Hydrogenize.addLonePairs(MoleculeGraph, MolAtom[])
str parameter to the inactive tasks list.
ProgressWriter.Logger to retrieve suppressed (error) messages.
Molecule object to the actual cell
of the viewer.
Molecule object to the actual cell
of the viewer and resets the view only if required.
ParametrizedMetric node to the DOM tree.
ParametrizedMetrics node to the DOM tree.
JChemProperties table.
PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class
PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with
the given name is changed
PropertyChangeListener for a specific property.
PropertyChangeListener for a specific property.
MDSimilarityResultWriter object.
RxnMolecule.addComponent(Molecule, int)
RxnMolecule.addComponent(Molecule, int, boolean)
TransferableDescriptor to the MTransferable
Registry.
ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean, boolean)
instead.
TransferableDescriptor to the registry, and constructing it
by the given parameters.
CheckerRunner implementation with advanced fixing capabilities.CheckerRunner with more advanced fixing capabilities.
AbstractStructureChecker detecting atoms withalias labels.AlignmentMolecule form a Molecule
based on the settings.AlignmentAPIRing.aliphaticAtomCount()
Ring.aliphaticBondCount()
Ring.aliphaticRingCount()
Ring.aliphaticRingCount(int)
Ring.aliphaticRings()
Ring.aliphaticRings(int)
"animate".
"animDelay".
"animFPS".
"animSync".
DispOptConsts.AUTOMATIC_FOG
Ring.aromaticAtomCount()
Ring.aromaticBondCount()
DefaultStructureCheckerResult for identifying aromaticity problems,
thus errorType property is StructureCheckerErrorType.AROMATICITYStructureCheckerErrorType.AROMATICITY by default.
AbstractStructureChecker detecting aromatization problems.Ring.aromaticRingCount()
Ring.aromaticRingCount(int)
Ring.aromaticRings()
Ring.aromaticRings(int)
CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean)
To keep the same functionality use with TRUE boolean parameters.
MDocSource implementation for an array of documents or molecules.Stereochemistry.asymmetricAtomCount()
Stereochemistry.asymmetricAtoms()
"atomFont".
"atomMappingVisible".
"atomNumbersVisible".
"atomPropertiesVisible".
"atomSet".
"atomSetColor".
"atomsize".
"atomStrings".
"atomSymbolsVisible".
AtomChecker detecting atom maps.AtomProperty class provides access to chemical properties of
Molecule atoms by atom index.AtomChecker detecting atoms having an query property
set.AtomChecker detecting atoms with atom value.AbstractStructureChecker detecting attached data in the molecule.MolAtom.setExtraLabel(java.lang.String)
Labels with R-group ID: "1" for R1, "2" for R2, ...
MolAtom.setExtraLabel(java.lang.String)
Labels with R-group ID: "1" for R1, "2" for R2, ...
MolAtom.setAtomMap(int).
MolAtom.setAtomMap(int).
MolAtom.addRgroupAttachmentPoint(int, int).
MolAtom.setExtraLabel(java.lang.String).
MolAtom.setExtraLabel(java.lang.String).
"autoscale".
"autoTabScale".
AutoMapper finds the best mapping from reactant side atoms
to product side atoms of a reaction."automaticFogEnabled".
"background".
"bgloadEnabled".
"bgload".
"ballRadius".
CheckerRunner interface/BasicCheckerRunner instance which will can execute StructureChecker instances read from
configurationReader
BCUT descriptor.BCUT descriptor generator object.
BCUT descriptor class."bondDraggedAlong".
"bondLengthVisible".
"bondSet".
"bondSetColor".
"bondSpacing".
BondChecker for the detection of unpreferred bond angles in 2D
molecule layouts.BondChecker detecting bonds with unpreferred lengths in 2D molecule
layouts."border".
"buttonmenubar".
"cacheMols".
freqCount[] absolute frequency
counts per cells.
freqCount[] absolute frequency
counts per cells.
calcDissimilarity().
PluginWorkUnit.getResult().
ReusablePluginWorkUnit.getResult().
CallbackIface.
CallbackIface.callback(String, Object)
to the context.
CallbackIface.
CallbackIface.
CallbackIface.
CallbackIface.
AbbrevGroupRecognizer.testLine(String)
must be used instead
JTFRecognizer.canBeJTFHeader(String)
must be used instead
PDBRecognizer.testRecord(String)
must be used instead
true if repeatedly running the same plugin object
while getting the results on the GUI is allowed, false otherwise.
Ring.carboaliphaticRingCount()
Ring.carboaromaticRingCount()
Ring.carboRingCount()
Ring.carboRingCount(int)
Ring.carboRings()
Ring.carboRings(int)
CustomDescriptor class.MolBond instead"cell".
CFGenerator class generates topological fingerprints
of molecular graphs.CFGenerator which can be used to
generate chemical fingerprints for an arbitrary number of molecules.
MoleculeGraph insteadRing.chainAtomCount()
Ring.chainBondCount()
true if molecule should be processed,
false otherwise.
List of StructureCheckerResult
which contains all the identified problems
UserSettings.getPropertiesDescriptionChangedByOtherApp() method
to retreive the return value of this method. If you really
need it.
StructureChecker instances automaticallyStructureFixer instances.CheckerRunnerImpl instance which will can execute StructureChecker instances read from
configurationReader
ChemicalFingerprint class implements topological fingerprints as a
type of MolecularDescriptors.Stereochemistry.chiralCenterCount()
Stereochemistry.chiralCenters()
"chiralitySupport".
String
Cleaner.clean(MoleculeGraph, int, String)
Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor)
AbstractStructureFixer which cleans the molecule in 2d"clean2dOpts".
"clean3dOpts".
"cleanDim".
"cleanOpts".
ConcurrentProcessor instance, awaits termination of associated
worker threads and releases any resource this processor has reserved.
ConcurrentProcessor.cleanup(long) with Long.MAX_VALUE.
false
i - j cut-bond.
ClipboardHandler the
functionalities in this class will be unsupported after Marvin
5.4
The class will be removed in 5.5other.
other.
MolBond.cloneBond(MolAtom a1, MolAtom a2).
ConfigElement.clone()
Returns a clone of the element, or null if clone not supported
next()
MolExportModule and the underlying stream.
MolExportModule and, optionally, the underlying stream.
DatabaseProperties.setUsePreparedStatement(boolean).
ConnectionHandler.close()
MolAtom insteadCodeAssistFactory to set up CodeAssistFragmenter.collect(java.lang.String, java.lang.String, java.lang.String, java.lang.String, java.lang.String[])
to initiate data collecting and use Fragmenter.setDataInLabel(boolean) and
Fragmenter.setAttachmentPointType(int) to set attachment data storage options.
MolAtom.setSetSeq(int).
MolAtom.setSetSeq(int).
"colorScheme".
"cols".
CompactMarkushViewer.
compareQueries( MolecularDescriptor target ) but
for each target.
ChemJEP object.
ChemJEP object.
ChemJEP object.
ComponentElement of a simple
(not structured) GraphicComponent.
ComponentElement.
- ComponentElement(GraphicComponent, int, int, int) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Creates a new instance of
ComponentElement of a complex (structured) GraphicComponent.
- ComponentElement(GraphicComponent, int, int, Integer) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Creates a new instance of
ComponentElement.
- ComponentElement(ComponentElement) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Copies the given
ComponentElement.
- componentHidden(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Hides windows if the parent frame is hidden.
- componentMoved(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Does nothing.
- componentResized(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Does nothing.
- componentShown(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Shows windows if the parent frame is hidden.
- COMPOSITE -
Static variable in class chemaxon.jchem.db.DatabaseConstants
-
- COMPOSITE_DRIVER -
Static variable in class chemaxon.jchem.db.DatabaseConstants
- JDBC driver for Composite database
- CompositeInputProducer - Class in chemaxon.util.concurrent.marvin
- Input producer composed of an array of input producers.
- CompositeInputProducer() -
Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
- Constructor.
- CompositeInputProducer(InputProducer[]) -
Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
- Constructor.
- CompositeWorkUnit - Class in chemaxon.util.concurrent.marvin
- Work unit composed of an array of work units, to be called in a linear fashion
in a single thread, one after the other in the specified order.
- CompositeWorkUnit() -
Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
- Constructor.
- CompositeWorkUnit(WorkUnit[]) -
Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
- Constructor.
- CompositeWorkUnitFactory - Class in chemaxon.util.concurrent.marvin
- Work unit factory composed of an aray of work unit factories.
- CompositeWorkUnitFactory(WorkUnitFactory[]) -
Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
- Constructor.
- composition(int) -
Method in class chemaxon.calculations.ElementalAnalyser
- Gets the elemental analysis, the relative percent composition of a pure
chemical substance by element (w/w%).
- COMPRESS -
Static variable in class chemaxon.formats.MdlCompressor
- Compression flag.
- compressedData -
Variable in class chemaxon.descriptors.PFParameters
- Buffer for compressed data, used in
MolecularDescriptor.toData(
final int[] ).
- computeSurface(MacroMoleculeComponent.MoleculeVisualizer) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Activates the container cell of the
MoleculeVisualizer, and
computes its Connolly surface.
- computeSurface(String) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Computes the given type of surface in the active cell of the viewer.
- ConcurrentProcessor - Interface in chemaxon.util.concurrent
- Executes jobs in parallel and returns their results iterator-style.
- ConcurrentProcessors - Class in chemaxon.util.concurrent.processors
- Creates
ConcurrentProcessor instances. - ConcurrentReactorProcessor - Class in chemaxon.reaction
- Executes a chemical reaction: creates products from reactants with
reaction center data.
- ConcurrentReactorProcessor() -
Constructor for class chemaxon.reaction.ConcurrentReactorProcessor
-
- ConcurrentStandardizerProcessor - Class in chemaxon.reaction
- Performs standardization of molecules in concurrent mode.
- ConcurrentStandardizerProcessor() -
Constructor for class chemaxon.reaction.ConcurrentStandardizerProcessor
-
- CONFIG_DIR -
Static variable in class chemaxon.jep.Evaluator
- Default directory for storing configuration files.
- ConfigBuilderPanel - Class in chemaxon.alchemist.configbuilder
- Configuration Builder Panel for list based configuration editing
- ConfigBuilderPanel(String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with default options.
- ConfigBuilderPanel(String, Action, Action) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with default options.
- ConfigBuilderPanel(String, AlchemistProfile) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with default options.
- ConfigBuilderPanel(String, AlchemistProfile, Action, Action) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with default options.
- ConfigBuilderPanel(Configuration) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with default options.
- ConfigBuilderPanel(Configuration, Action, Action) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with default options.
- ConfigBuilderPanel(Configuration, AlchemistProfile) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with specified configuration and profile
- ConfigBuilderPanel(Configuration, AlchemistProfile, Action, Action) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Constructs a config builder panel with specified configuration and profile
with file load and save support.
- ConfigBuilderPanel.LeftListModel - Class in chemaxon.alchemist.configbuilder
- Is a
SynchronizedAbstractFilterListModel implementation. - ConfigBuilderPanel.LeftListModel() -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanel.LeftListModel
-
- ConfigBuilderPanelFactory - Class in chemaxon.alchemist.configbuilder
- Factory for various
ConfigBuilderPanel instances - ConfigBuilderPanelFactory() -
Constructor for class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
-
- ConfigElement - Class in chemaxon.alchemist.configbuilder
- This is the abstract ConfigElement.
- ConfigElement() -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element.
- ConfigElement(String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id
- ConfigElement(String, String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id and name
- ConfigElement(String, String, Icon) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id, name and icon
- ConfigElement(String, String, Icon, String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id, name, icon
and tooltip
- ConfigElement(String, String, Icon, String, String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id, name, icon
and tooltip
- ConfigElement(String, String, Icon, ImageIcon, String, String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id, name, icon, disabled icon
and tooltip
- ConfigElementEditor - Interface in chemaxon.alchemist.configbuilder
- This interface defines the method any object that would like to be
an editor of any
ConfigElement needs to implement. - ConfigElementFactory - Class in chemaxon.alchemist.configbuilder
- This class is responsible for creating config item objects
defined by configuration xml, and bundle file
- ConfigElementFactory(String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates a
ConfigElementFactory based on configPath
- ConfigElementFactory(String, LicenseSupport) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates a
ConfigElementFactory based on configPath
- ConfigElementFactory(Configuration) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates a
ConfigElementFactory based on Configuration
- ConfigElementFactory(Configuration, LicenseSupport) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates a
ConfigElementFactory based on Configuration
- configFilePath -
Variable in class chemaxon.descriptors.MDParameters
- location of the configuration file
- ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader
- This interface is provided for classes which can read the configuration of
CheckerRunner. - CONFIRM_TRANSFER -
Static variable in class chemaxon.marvin.view.ViewParameterConstants
- Identifier of parameter:
"confirmTransfer".
- CONFORMATION_PLUGIN_GROUP -
Static variable in class chemaxon.license.LicenseManager
- Identifier of plugin: Conformation Plugin Group
- ConformerPlugin - Class in chemaxon.marvin.calculations
- Plugin class for conformer calculation.
- ConformerPlugin() -
Constructor for class chemaxon.marvin.calculations.ConformerPlugin
- Constructor.
- CONJUGATED -
Static variable in class chemaxon.struc.MolBond
- Conjugation state of the bond.
- connect() -
Method in class chemaxon.util.ConnectionHandler
- Deprecated. since JChem 5.4, use
ConnectionHandler.connectToDatabase() to avoid having to catch useless exceptions.
- connect_NE() -
Method in class chemaxon.util.ConnectionHandler
- Deprecated. since JChem 5.2 use
ConnectionHandler.connect()
- ConnectionHandler - Class in chemaxon.util
- A JavaBean for connecting to relational databases using JDBC.
- ConnectionHandler() -
Constructor for class chemaxon.util.ConnectionHandler
- Creates new ConnectionHandler
- ConnectionHandler(Connection) -
Constructor for class chemaxon.util.ConnectionHandler
- Creates a new ConnectionHandler and sets the connection to an externally created Connection
(e.g. from a connection pool).
- ConnectionHandler(ConnectionHandler) -
Constructor for class chemaxon.util.ConnectionHandler
- Creates new ConnectionHandler based on the settings of an other
ConnectionHandler.
- connectToDatabase() -
Method in class chemaxon.util.ConnectionHandler
- Connects to the database.
- constant -
Variable in class chemaxon.marvin.services.ServiceArgument
- field indicates constant argument
- containerFrame -
Variable in class chemaxon.marvin.space.MSpaceEasy
-
- contains(float, float, float) -
Method in class chemaxon.marvin.space.BoundingBox
- Tells whether the given location is inside the box.
- contains(MObject) -
Method in class chemaxon.struc.MDocument
- Searches an object in the document.
- contains(MDocument) -
Method in class chemaxon.struc.MDocument
- Tests whether the document contains all objects of another document.
- contains(MolAtom) -
Method in class chemaxon.struc.Molecule
- Checks if the molecule graph contains the specified atom.
- contains(MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Checks if the molecule graph contains the specified atom.
- contains(MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Checks if the molecule graph contains the specified bond.
- contains(MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Does the molecule graph contain the specified fragment?
- contains(MProp) -
Method in class chemaxon.struc.MPropertyContainer
- Tests whether the container contains the specified property object.
- contains(MProp) -
Method in class chemaxon.struc.prop.MCollectionProp
- Tests whether the collection contains the specified property.
- contains(MolAtom) -
Method in class chemaxon.struc.RgMolecule
- Checks if the root structure or an R-group contains the specified node.
- contains(MolBond) -
Method in class chemaxon.struc.RgMolecule
- Checks if the root structure or an R-group contains the specified edge.
- contains(MolAtom) -
Method in class chemaxon.struc.RxnMolecule
- Checks if a reactant, agent or product structure contains the specified
node.
- contains(MolBond) -
Method in class chemaxon.struc.RxnMolecule
- Checks if a reactant, agent or product structure contains the specified
edge.
- contains(int) -
Method in class chemaxon.util.IntArray
- Tests if the specified object is a component in this IntArray.
- containsAllAtomsOf(Sgroup) -
Method in class chemaxon.struc.Sgroup
- Checks if the S-group contains the atoms of another S-group.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MPolyline
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.MObject
- Checks if the object contains the specified atom reference.
- containsComponent(GraphicComponent) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the component is in the cell.
- containsComponent(GraphicComponent) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if the component exists in the scene.
- containsCoordinateBond(MoleculeGraph) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Decides whether a molecule graph contains coordinate bonds.
- containsHydrogens() -
Method in class chemaxon.util.MolHandler
- True if the molecule contains explicit Hydrogen atoms,
false otherwise.
- containsLadderTypePolymer() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Decides whether the structure of this sgroup contains a
ladder-type repeating unit.
- containsMulticenterSgroup(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Decides whether a molecule contains Multicenter S-groups.
- containsOnlyOne(Class) -
Method in class chemaxon.struc.MDocument
- Tests whether the document contains only one object of the specified
class.
- containsPoint(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- containsPoint(DPoint3, CTransform3D) -
Method in class chemaxon.struc.MObject
-
- containsPropertyKey(String) -
Method in class chemaxon.struc.MolAtom
- Returns true if this atom has a mapping for the specified property key.
- containsPseudoAtom(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if molecule contains pseudo atom.
- containsSRUSgroup(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Decides whether a molecule contains SRU S-groups.
- contract(int) -
Method in class chemaxon.struc.Sgroup
- Sets the state to
Sgroup.XSTATE_C.
- contract(int) -
Method in interface chemaxon.struc.sgroup.Expandable
- Contracts the S-group.
- contract(int) -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Contracts this S-group.
- contract(int) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Contracts this S-group.
- ContractGroupFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which contracts the abbreviated groups in the molecule - ContractGroupFixer() -
Constructor for class chemaxon.fixers.ContractGroupFixer
-
- contractOrExpandSgroups(int, String, boolean) -
Method in class chemaxon.marvin.view.MDocStorage
- Contract or expand S-groups in the specified cell.
- contractOrExpandSgroupsAll(boolean) -
Method in class chemaxon.marvin.view.MDocStorage
- Contract or expand S-groups in all molecules.
- contractSgroups() -
Method in class chemaxon.struc.Molecule
- Contracts all S-groups.
- Control - Class in chemaxon.marvin.space.monitor
- Transformation on a
GraphicComponent that changes the coordinates, and not just the view. - Control() -
Constructor for class chemaxon.marvin.space.monitor.Control
- Creates a new instance of Control
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.Control
- Does control on x-y events.
- control(int) -
Method in class chemaxon.marvin.space.monitor.Control
- Does control on z event.
- control(int) -
Method in class chemaxon.marvin.space.monitor.DihedralControl
- One part of the molecule being in one of the end of the torsion bond
will be rotated around the bond.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.DihedralControl
- Does nothing.
- control -
Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
-
- control(int) -
Method in class chemaxon.marvin.space.monitor.DihedralMonitor
- Passes the control event to the control.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
- Changes the location say translates the component of the control
in the global coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
- Changes the location say translates the component of the control
in the global coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Changes the orientation say rotates the component of the control
in the global coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Changes the orientation that is rotates the component of the control
in the global coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.LocalLocationControl
- Changes the location say translates the component of the control
in its local coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.LocalLocationControl
- Changes the location say translates the component of the control
in its local coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
- Changes the orientation say rotates the component of the control
in its local coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
- Changes the orientation say rotates the component of the control
in its local coordinate system.
- control -
Variable in class chemaxon.marvin.space.monitor.Monitor
-
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Causes the monitor's controll to take action with 2 parameters.
- control(int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Causes the monitor's controll to take action with 1 parameter.
- control(int) -
Method in class chemaxon.marvin.space.monitor.ResizeControl
- Resizes the component in z direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.ResizeControl
- Resizes the component in x, y direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- CONV_SELFREF -
Static variable in class chemaxon.struc.MProp
- Conversion of self referring property.
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) -
Method in class chemaxon.checkers.result.SgroupCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) -
Method in interface chemaxon.checkers.result.StructureCheckerResult
- This method converts the entities contained in this result according to the convertData.
- convert() -
Method in class chemaxon.formats.MdlCompressor
- Compression/decompression
- convert(byte[], int) -
Static method in class chemaxon.formats.MdlCompressor
- (Un)compress the specified molfile or SDfile.
- convert(String, int) -
Static method in class chemaxon.formats.MdlCompressor
- (Un)compress the specified molfile or SDfile.
- convert() -
Method in class chemaxon.formats.MolConverter
- Convert the next molecule.
- convert(double[][]) -
Static method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- convert(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Creates an MDL mol or compressed mol representation of the molecule.
- convert(Molecule) -
Method in class chemaxon.marvin.io.MolExportModule
- Convert a molecule to a string or byte array.
- convert(String) -
Method in interface chemaxon.naming.NameConverter
- Convert a name into the corresponding structure.
- ConvertAliasToGroupFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts the aliases to contracted abbreviated groups in the molecule - ConvertAliasToGroupFixer() -
Constructor for class chemaxon.fixers.ConvertAliasToGroupFixer
-
- convertBase64Gzip2Text(String) -
Static method in class chemaxon.util.HTMLUtil
- Converts gzip compressed data with base64 encoding to text.
- convertCoordinateBondsToData(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Converts coordinate bonds to data sgroups (attached data)
with field name MRV_COORDINATE_BOND.
- convertForAppletParameter(String) -
Static method in class chemaxon.util.HTMLTools
- Converts a string to a format that can be used as a
value of an applet parameter
in an HTML page.
- convertForJavaScript(String) -
Static method in class chemaxon.util.HTMLTools
- Converts a string to a format that can be used as a
value of JavaScript variable in an HTML page.
- convertForJavaScript(String) -
Static method in class chemaxon.util.HTMLUtil
- Converts a string to a format that can be used as a
value of JavaScript variable in an HTML page.
- convertMultiCenterSgroupsToData(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Converts the multicenter sgroups to data sgroups in the molecule.
- convertPageSettingsToData(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Converts page setting of multipage molecular document to data sgroups (attached data)
with field name MRV_PAGE_XXX.
- ConvertPseudoToGroupFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts the pseudo informations to
contracted abbreviated groups in the molecule - ConvertPseudoToGroupFixer() -
Constructor for class chemaxon.fixers.ConvertPseudoToGroupFixer
-
- convertResult(StructureCheckerResult) -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- This method provides the possibility to convert back the affected properties of the result
if there was any convert in the molecule structure before check.
- convertResult(StructureCheckerResult) -
Method in class chemaxon.checkers.runner.SketchCheckerRunner
- This method converts the result by changing the atoms and bonds back to the original
instead of the cloned ones
- ConvertToAtomFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts the aliases to atom with
atom number contained in the alias information - ConvertToAtomFixer() -
Constructor for class chemaxon.fixers.ConvertToAtomFixer
-
- ConvertToCarbonFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts pseudo atoms to carbon atoms - ConvertToCarbonFixer() -
Constructor for class chemaxon.fixers.ConvertToCarbonFixer
-
- convertToFrags() -
Method in class chemaxon.struc.Molecule
- Converts this molecule to its disconnected fragments, expanding all
S-groups and keeping disconnected Multicenter S-groups in the same fragment,
but ungroupping and separating fragments in all other types of S-groups.
- convertToSmilingFormat(Molecule) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tries to convert a molecule to a SMILES related format.
- convertToSmilingFormat(MProp) -
Static method in class chemaxon.formats.MFileFormatUtil
- Try to convert a property to text with a SMILES related format argument.
- convertToString(MDocument, String, int) -
Static method in class chemaxon.formats.MolExporter
- Converts the document to text format.
- convertToString(MProp, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Converts the property to text format.
- convertToString(MPropertyContainer, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Convert key of MPropertyContainer to string.
- convertToString(String, int) -
Method in class chemaxon.struc.MDocument.Prop
- Deprecated. As of release 5.7, replaced by
MolExporter.convertToString(MDocument, String, int)
- convertToString(String, int) -
Method in class chemaxon.struc.MProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String).
Instead MProp.CONV_SELFREF flag use fmt + ":-selfrefprops" string in fmt.
- convertToString(String) -
Method in class chemaxon.struc.MProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MBooleanProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MDoubleProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MHashProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MIntegerProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MListProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MMoleculeProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
Instead MProp.CONV_SELFREF flag use fmt + ":-selfrefprops" string in fmt.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MObjectProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MStringProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertTransform(CTransform3D, boolean) -
Method in class chemaxon.struc.graphics.MRectangle
-
- COORDDEP -
Static variable in class chemaxon.struc.MProp
- Coordinate dependent property.
- COORDINATE -
Static variable in class chemaxon.struc.MolBond
- Coordinate bond flag.
- COORDINATE_BOND_ARROW_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_OFFSET -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_STYLES -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_HASHED_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_SOLID_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLE -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"coordinateBondStyle".
- COORDINATE_BOND_STYLE_AT_MULTICENTER -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"coordinateBondStyleAtMulticenter".
- COORDINATE_BOND_STYLE_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLE_OFFSET -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLES -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- CoordinationSystemErrorChecker - Class in chemaxon.checkers
- Detects errors of multicenter coordination systems.
- CoordinationSystemErrorChecker() -
Constructor for class chemaxon.checkers.CoordinationSystemErrorChecker
- Default constructor
- COORDS_UPDATE -
Static variable in interface chemaxon.struc.sgroup.Expandable
- Performs coordinate update during the unbinding of atoms.
- COPY_AS_FORMAT -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Default format to be selected on Copy as dialog.
- COPY_AS_IMAGE_BITMAP -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_AS_IMAGE_EMF -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_AS_OLE -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_AS_TEXT -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_OPTIONS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Deprecated. since 5.3.3 has no sense
- copyInto(int[]) -
Method in class chemaxon.util.IntArray
- Copies the components of this IntArray into the specified array.
- CopyOptConstants - Interface in chemaxon.marvin.util
- Deprecated. since 5.2.1 the whole copy-paste engine was refactored. The
constants defined in this interface either non exists in the new
implementation or its value has changed. See the constants own
description for details.
- copyProperties(Molecule, Molecule) -
Static method in class chemaxon.metabolizer.MetabolizerUtilities
-
- copyProperties(MBracket) -
Method in class chemaxon.struc.graphics.MBracket
- Copies line properties to another line object.
- copyProperties(MPolyline) -
Method in class chemaxon.struc.graphics.MPolyline
- Copies line properties to another line object.
- correctCornersRadius(double, double) -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- count() -
Method in class chemaxon.descriptors.MDSimilarityResultWriter
- Increments the counter of the results processed.
- countAllAtoms() -
Method in class chemaxon.struc.MolAtom
- Counts all atoms represented by this atom.
- countAllAtoms() -
Method in class chemaxon.struc.Sgroup
- Counts the total number of atoms recursively.
- countAllAtoms() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Counts all atoms represented by this atom.
- countEnumerations() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the number of all enumerated structures,
no arithmetic overflow because counts in
BigInteger.
- countEnumerationsMagnitude() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the magnitude (the number of decimal "digits")
of the number of all enumerated structures.
- countExpandableContractableSgroups() -
Method in class chemaxon.struc.Molecule
- Counts the expandable and contractable S-groups.
- countOrderedComponentSgroups() -
Method in class chemaxon.struc.Molecule
- Counts the ordered component S-groups.
- countRecords(MProgressMonitor, int, Runnable, int) -
Method in class chemaxon.marvin.view.MDocStorage
- Counts the total number of records and sets the size of the document
storage.
- countRecordsInFraction(double, int, MProgressMonitor) -
Method in class chemaxon.marvin.view.MDocStorage
- Deprecated.
- COVALENT_HYDRATION_ERROR_REMARK -
Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
- Covalent hydration error remark.
- covalentRadiusOf(int, int) -
Static method in class chemaxon.struc.MolAtom
- Gets the covalent radius in C-C bond length units.
- CPK_SCHEME -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- CPK color scheme in display option flags.
- CPK_SCHEME_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- CPK color scheme.
- crdMolRefresh() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- crdSafeRefresh() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- create(String) -
Method in class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates an instace of class extending
ConfigElement and identified
by configElementId in configuration XML
- create(Class<?>) -
Method in class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates an instance of
configElementClass class.
- create(Element) -
Method in class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates
ConfigElement instance based on bundle informations
- create(String) -
Static method in class chemaxon.descriptors.MDHypothesisCreator
- Creates a hypothesis of the given type.
- create(String) -
Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
- Creates a similarity calculator object according to the user defined parameters.
- create(String, int, int) -
Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
- Creates a similarity calculator object according to the user defined parameters.
- create(Element, Standardizer, String) -
Static method in class chemaxon.fragmenter.CutBondReviser
- Creates a CutBondReviser object corresponding to the given DOM element node.
- create(List) -
Method in class chemaxon.fragmenter.ExhaustiveFragmenter
- Creates the molecule fragments by removing the previously found cut-bonds
and fragmenting the input molecule.
- create(List) -
Method in class chemaxon.fragmenter.Fragmenter
- Creates the molecule fragments by removing the previously found cut-bonds
and fragmenting the input molecule.
- create(byte[]) -
Static method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- create(String, String) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
- create(String, PSymbols) -
Static method in class chemaxon.pharmacophore.PMap
- Creates a PMap object from a pharmacophore point list string.
- create(int, InputProducer) -
Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- create(int, InputProducer, WorkUnitFactory) -
Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- create(String) -
Static method in class chemaxon.util.DotfileUtil
- Opens a dotfile for writing.
- CREATE_OR_REPLACE_RESULT_TABLE -
Static variable in class chemaxon.jchem.db.JChemSearch
- Constant for the generation of result tables.
- createArgument(T) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value
- createArgument(String, T) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value
- createArgumentAs(T, Class<T>) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value and type
- createArgumentAs(String, T, Class<T>) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value and type
- createArray(String, String, int, int) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates an array property.
- createArrayXSD(String, String, int, int) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates an array property from the XSD type.
- createAtomIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an atom iterator for the specified molecule of the factory
according to the atom related behavior set in the factory.
- createAtomNeighbourIterator(MolAtom) -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an iterator to get the atom neighbours of the specified
atom.
- createBHtab() -
Method in class chemaxon.struc.MoleculeGraph
- Creates the bond table extended with implicit hydrogen atoms.
- createBHtab() -
Method in class chemaxon.struc.RxnMolecule
- Creates the graph union's bond table extended with implicit hydrogen
atoms.
- createBondIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs a bond iterator for the specified molecule of the factory
according to bond related behavior set in the factory.
- createBondNeighbourIterator(MolAtom) -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an iterator to get the bonds connecting to the specified
atom.
- createBracket(Sgroup, DPoint3[], int) -
Static method in class chemaxon.marvin.util.CleanUtil
-
- createChemicalTermsTextPane() -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
- createChemicalTermsTextPane(boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
- createChemicalTermsTextPane(boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(boolean, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
- createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
- createChemicalTermsTextPane(String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
- createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
- createChemicalTermsTextPane(String, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, boolean, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
- createChemicalTermsTextPane(String, String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String, boolean, String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createCHtab() -
Method in class chemaxon.struc.MoleculeGraph
- Creates the connection table extended with implicit hydrogen atoms.
- createCHtab() -
Method in class chemaxon.struc.RxnMolecule
- Creates the graph union's connection table extended with implicit
hydrogen atoms.
- createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) -
Method in class chemaxon.struc.graphics.MTextAttributes
-
- createConstantFromString(String, Class<?>) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Creates a
ServiceArgument constant based on string value and argument type.
- createDefaultParameterPanel(String, Component) -
Static method in class chemaxon.marvin.plugin.PluginFactory
- Creates default parameter panel based on XML config.
- createDefaultParameterPanel(Class, String, Component) -
Static method in class chemaxon.marvin.plugin.PluginFactory
-
- createDehydrogenizedReadOnlyGraph() -
Method in class chemaxon.struc.MoleculeGraph
- Creates a dehydrogenized version of the molecule.
- createEMF(String, String) -
Static method in class chemaxon.util.ImageExportUtil
- Creates a .NET based EMF picture.
- createExportModule() -
Method in class chemaxon.formats.MFileFormat
- Creates the export module.
- createExportModule(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Creates an export module for the specified format.
- createFeatureMap(Molecule) -
Method in class chemaxon.pharmacophore.PMapper
- Creates the feature ID -> atom index BitSet HashMap
for the given target molecule.
- createGearch() -
Method in class chemaxon.struc.Molecule
-
- createGearch() -
Method in class chemaxon.struc.MoleculeGraph
-
- createGearch() -
Method in class chemaxon.struc.RgMolecule
-
- createGearch() -
Method in class chemaxon.struc.RxnMolecule
-
- createGearch() -
Method in class chemaxon.struc.SelectionMolecule
-
- createImage(Buffer, int, int) -
Method in class chemaxon.marvin.space.GraphicScene
-
- createImageExporterParameter(Properties, String, MDocument) -
Static method in class chemaxon.util.ImageExportUtil
- Creates the Image Exporter parameter String based on the values in the
Properties object.
- createImportMod(MolInputStream) -
Static method in class chemaxon.marvin.io.MRecordImporter
- Creates an importer for the specified molecule input stream.
- createImportMod(String) -
Static method in class chemaxon.marvin.io.MRecordImporter
- Creates an importer for the specified molecule format.
- createImportModule() -
Method in class chemaxon.formats.MFileFormat
- Creates the molecule import module.
- createInput() -
Method in class chemaxon.util.concurrent.marvin.ReusableInputProducer
-
- createJCSObserver() -
Static method in class chemaxon.jchem.db.JChemSearch
- Construct and return a new
JCSObserver instance with default
settings.
- createLabels(MDSet) -
Method in class chemaxon.descriptors.MDSimilarityResultWriter
- Creates labels.
- createLicenseManagerPanel() -
Static method in class chemaxon.license.LicenseManager
- Creates the main panel which is used for end-user license managing.
- createMD(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Creates an MolecularDescriptor based on settings stored in the database
- createMDSet(String[]) -
Method in class chemaxon.jchem.db.MDTableHandler
- Creates an MDSet based on settings stored in the database
- createMDSetComponent(int, String, String) -
Method in class chemaxon.descriptors.MDReader
- Creates and sets the given component of the internal
MDSet
object of the given type and specified parameter settings.
- createMDTable(String, String, String, String) -
Method in class chemaxon.descriptors.GenerateMD
- Creates a database table to store the
MolecularDescriptors
generated.
- createMDTable(String, String, String, String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Creates a Molecular Descriptor Table.
- createMDTable(String, String, String, String, boolean) -
Method in class chemaxon.jchem.db.MDTableHandler
- Creates a Molecular Descriptor Table.
- createMenu(ResourceBundle, String) -
Static method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.createMenu
- createMenu(ResourceBundle, String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Utility method to create a menu with a label specified as a resource.
- createMenu(ResourceBundle, String, boolean) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu with a label specified as a resource.
- createMenuItem(ResourceBundle, String, Class, boolean) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu item with a label specified as a resource.
- createMenuItem(ResourceBundle, String, boolean) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu with a label specified as a resource.
- createMenuItem(ResourceBundle, String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu with a label specified as a resource.
- createMMoleculeProp(String) -
Static method in class chemaxon.marvin.io.MPropHandler
-
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the major tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Returns the molecule form with largest distribution.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the major tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the canonical tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the modified input molecule (e.g. microspecies, major tautomeric form).
- createMol() -
Method in class chemaxon.formats.MolImporter
- Creates a target molecule object for import.
- createMol() -
Method in class chemaxon.marvin.io.formats.mdl.MolImport
- Creates a new target molecule object.
- createMol() -
Method in class chemaxon.marvin.io.MolImportModule
- Creates a new target molecule object for the import.
- createMol() -
Method in class chemaxon.marvin.io.MRecordImporter
- Creates an empty target molecule for import.
- createMol(String) -
Static method in class chemaxon.struc.RgMolecule
- Deprecated. As of Marvin 3.4,
MolImportModule.createMol() must be used.
- createMolConverter(InputStream, OutputStream, String[], int[]) -
Static method in class chemaxon.formats.MolConverter
- Creates a MolConverter instance with the attributes specified in the
parameters.
- createMolecule() -
Method in class chemaxon.struc.Sgroup
- Creates a molecule object that contains only this group.
- createMolecule(Molecule) -
Method in class chemaxon.struc.Sgroup
- Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
- createMolecule() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Creates a molecule object that contains only this group.
- createMoleculeFromInputStream(InputStream) -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Helper function to get Molecule or MacroMolecule from the given
InputStream with MolImporter.
- createMoleculeIterator(Collection<Molecule>) -
Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
- Creates a
MoleculeIterator object for iterating through collection of
molecules (Molecule objects).
- createMoleculeIterator(Molecule[]) -
Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
- Creates a
MoleculeIterator object for iterating through a molecule
array (Molecule[]).
- createMolIfNeeded() -
Method in class chemaxon.marvin.io.MRecordImporter
- Creates an empty target molecule for import if non-concurrent mode,
returns
null if concurrent mode.
- createMolsFrame() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- createNewCell() -
Method in class chemaxon.marvin.space.GraphicScene
- Sets an empty cell to be the active cell.
- createNext() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Creates identical attributes for the next section.
- createParameterPanel() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates the parameter panel.
- createPooledWu(int, InputProducer, WorkUnitFactory) -
Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
- For test only
- createPropertyTable(ConnectionHandler) -
Static method in class chemaxon.jchem.db.DatabaseProperties
- Creates a new property table for storing JChem's settings.
- createPropertyTable(ConnectionHandler, int) -
Static method in class chemaxon.jchem.db.DatabaseProperties
- Creates a new property table for storing JChem's settings.
- createReaction(Molecule, DPoint3[], int) -
Static method in class chemaxon.struc.RxnMolecule
- Creates a reaction.
- createReaction(MoleculeGraph, DPoint3[]) -
Static method in class chemaxon.struc.RxnMolecule
- Creates a reaction.
- createReactionObject(Molecule, String, String, String, String) -
Method in class chemaxon.reaction.Reactor
- Deprecated. Will be removed from the public API.
- createReactionObject(Molecule, String, String, String, double[]) -
Method in class chemaxon.reaction.Reactor
- Deprecated. Will be removed from the public API.
- createRecognizer(String) -
Method in class chemaxon.formats.MFileFormat
- Creates a recognizer module.
- createRecordReader(MolInputStream, String) -
Method in class chemaxon.formats.MFileFormat
- Creates the record reader.
- createRecordReader(InputStream, String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Creates a record reader for an input stream.
- createRecordReader(InputStream, String, String, String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Creates a record reader for an input stream.
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AliasChecker
-
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AtomChecker
-
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
- createResult(Molecule, List<MolBond>) -
Method in class chemaxon.checkers.BondChecker
-
- createResult(Molecule, List<E>) -
Method in class chemaxon.checkers.ComponentChecker
- Creates a
StructureCheckerResult from a List containing the components.
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.PseudoAtomChecker
-
- createResult(Molecule, List<StructureCheckerResult>) -
Method in class chemaxon.checkers.ReactionChecker
- This method a merged StructureCheckerResult from the
List
of StructureCheckerResult which contains the problems of the components in
the reaction
- createResultView(String, MolPanel) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- createRgComponentIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an rgroup definition component iterator for the specified molecule of the factory
if the molecule is an RgMolecule, an empty iterator otherwise.
- createRotationAboutBond(MolBond, double) -
Static method in class chemaxon.marvin.util.CleanUtil
- Creates a rotation transformation about a bond.
- createRowData(String) -
Method in class chemaxon.jchem.db.UpdateHandler
- Calculates row data from molecule string.
- createRowData(byte[]) -
Method in class chemaxon.jchem.db.UpdateHandler
- Calculates row data from molecule string.
- createRxnComponentIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs a reaction component iterator for the specified molecule of the factory
if the molecule is an RxnMolecule, an empty iterator otherwise.
- createSavedCoordsArray(MoleculeGraph) -
Static method in class chemaxon.marvin.util.CleanUtil
- Creates an empty array for the atomic coordinates of a structure.
- createScalar(String, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates a scalar property.
- createScalar(String, String, MProgressMonitor) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates a scalar property.
- createScalarXSD(String, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates a scalar property from the XSD type.
- createSelectionPanel(int) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Adds the basic MarvinSpace selection panel to the container.
- createSelectionPanelAndProgressBar() -
Method in class chemaxon.marvin.space.MSpaceEasy
- Adds the basic MarvinSpace selection panel to the container.
- createSmolecule() -
Method in class chemaxon.struc.MoleculeGraph
- Creates a
Smolecule represenation of this molecule.
- createSpacePanel(Molecule[]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates space panel with given molecules,
creates colored surface to each molecule.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Deprecated. Use
ResonancePlugin.createStandardizedMolecule(Molecule) instead
- createStandardizedMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Creates standardized molecule, the original input molecule is cloned
only if the original molecule should not be modified.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Deprecated. Use
TautomerizationPlugin.createStandardizedMolecule(Molecule) instead
- createStandardizedMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Creates standardized molecule, the original input molecule is cloned
only if the original molecule should not be modified.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Deprecated. Use
CalculatorPlugin.createStandardizedMolecule(Molecule) instead
- createStandardizedMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Creates standardized molecule, the original input molecule is cloned.
- createStandardizerPanel() -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- import org.exolab.castor.xml.MarshalException;
Returns a standardizer configbuilder panel with default elements
without file load and save support
- createStandardizerPanel(AlchemistProfile) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with default elements
without file load and save support
- createStandardizerPanel(String[]) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with default elements (excluding the given elements)
without file load and save support
- createStandardizerPanel(String[], AlchemistProfile) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with default elements (excluding the given elements)
without file load and save support
- createStandardizerPanel(boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with default elements
with or without file load and save support
- createStandardizerPanel(AlchemistProfile, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel withStructureCheckerConfigBuilderAlchemist. default elements
with or without file load and save support
- createStandardizerPanel(String[], boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with default elements (excluding the given elements)
with or without file load and save support,
- createStandardizerPanel(String[], AlchemistProfile, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with default elements (excluding the given elements)
with or without file load and save support,
- createStandardizerPanel(String) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- return
Returns a standardizer configbuilder panel with specified elements
without file load and save support
- createStandardizerPanel(String, AlchemistProfile) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with specified elements
without file load and save support
- createStandardizerPanel(String, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with specified elements
with or without file load and save support
- createStandardizerPanel(String, AlchemistProfile, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a standardizer configbuilder panel with specified elements
with or without file load and save support
- createStatistics -
Variable in class chemaxon.descriptors.MDGenerator
- indicates if statistical data has to be gathered during generation
- createStructureCheckerPanel() -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements
without file load and save support
- createStructureCheckerPanel(AlchemistProfile) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements
without file load and save support
- createStructureCheckerPanel(String[]) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements (excluding the given elements)
without file load and save support
- createStructureCheckerPanel(String[], AlchemistProfile) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements (excluding the given elements)
without file load and save support
- createStructureCheckerPanel(boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements
with or without file load and save support
- createStructureCheckerPanel(AlchemistProfile, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements
with or without file load and save support
- createStructureCheckerPanel(String[], boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements (excluding the given elements)
with or without file load and save support,
- createStructureCheckerPanel(String[], AlchemistProfile, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with default elements (excluding the given elements)
with or without file load and save support,
- createStructureCheckerPanel(String) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with specified elements
without file load and save support
- createStructureCheckerPanel(String, AlchemistProfile) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with specified elements
without file load and save support
- createStructureCheckerPanel(String, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with specified elements
with or without file load and save support
- createStructureCheckerPanel(String, AlchemistProfile, boolean) -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- Returns a structure checker configbuilder panel with specified elements
with or without file load and save support
- createStructureTable(ConnectionHandler, StructureTableOptions) -
Static method in class chemaxon.jchem.db.UpdateHandler
- Creates a structure table.
- createSubPanel(String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a sub-panel with a title.
- createTopLeftConstraints() -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates GridBagConstraints for the top left component.
- createViewPanel(Molecule[]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates view panel with given molecules,
places molecule properties in formatted texts.
- createViewPanel(Molecule[], int, int, int, int) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates view panel with given molecules,
places molecule properties in formatted texts.
- createWorkUnit() -
Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
- Creates a
CompositeWorkUnit object composed of work units created by the factories.
- createWorkUnit() -
Method in interface chemaxon.util.concurrent.WorkUnitFactory
-
- CRITICAL_ERROR_MSG -
Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
- Critical error message.
- cross(DPoint3, DPoint3) -
Static method in class chemaxon.struc.DPoint3
- Calculates the cross product of the two vectors
- CrossedDoubleBondChecker - Class in chemaxon.checkers
- A descendant of
BondChecker for the detection of unspecified double bonds
represented by crossed bond type. - CrossedDoubleBondChecker() -
Constructor for class chemaxon.checkers.CrossedDoubleBondChecker
- Default constructor
- CrossedDoubleBondFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts crossed double bond to wiggly - CrossedDoubleBondFixer() -
Constructor for class chemaxon.fixers.CrossedDoubleBondFixer
-
- CSMDL_IN -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.
- CSMOL_OUT -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed Molfiles and Rgfiles.
- CSRDF -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed RDfiles.
- CSRXN_OUT -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed Rxnfiles.
- CSSDF_OUT -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed SDfiles.
- ctab -
Variable in class chemaxon.struc.MoleculeGraph
- Connection table.
- CTransform3D - Class in chemaxon.struc
- 3D transformation matrix.
- CTransform3D(CTransform3D) -
Constructor for class chemaxon.struc.CTransform3D
- Copy constructor.
- CTransform3D() -
Constructor for class chemaxon.struc.CTransform3D
- Constructs an identity transformation.
- CTSPECIFIC_H -
Static variable in class chemaxon.struc.MolAtom
- Hydrogen atom connecting alone to one side of a double bond with
specified CIS or TRANS stereo information.
- CTUMASK -
Static variable in interface chemaxon.struc.StereoConstants
- Double bond stereo mask.
- CTUNKNOWN -
Static variable in interface chemaxon.struc.StereoConstants
- CIS/TRANS cannot be determined because bond angle is close to
180 degrees.
- CTUNSPEC -
Static variable in interface chemaxon.struc.StereoConstants
- Unspecified double bond.
- CubeRecognizer - Class in chemaxon.formats.recognizer
- Gaussian Cube format recognizer.
- CubeRecognizer(String) -
Constructor for class chemaxon.formats.recognizer.CubeRecognizer
- Creates a Gaussian Cube format recognizer.
- currentBond -
Variable in class chemaxon.util.iterator.IteratorFactory.BondIterator
- Current bond index pointer of the iterator.
- currentBond -
Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
- Current bond pointer of the iterator.
- currentMetricIndex -
Variable in class chemaxon.descriptors.MDParameters
- index of the parametrized metric currently in use
- cursorDown(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
- Move the cursor down.
- cursorToRowEnd(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
-
- cursorToRowStart(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
-
- cursorUp(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
- Moves the cursor up.
- CustomDescriptor - Class in chemaxon.descriptors
- The
CustomDescriptor class implements a generic molecular
descriptor class which supports third party or use defined descriptors. - CustomDescriptor() -
Constructor for class chemaxon.descriptors.CustomDescriptor
- Creates a new, empty instance of CustomDescriptor without allocating
internal storage for its value.
- CustomDescriptor(int, int) -
Constructor for class chemaxon.descriptors.CustomDescriptor
- Creates a new, empty instance of CustomDescriptor and allocates internal
storage to store values.
- CustomDescriptor(CDParameters) -
Constructor for class chemaxon.descriptors.CustomDescriptor
- Creates a new instance of CustomDescriptor according to the parameters
given.
- CustomDescriptor(String) -
Constructor for class chemaxon.descriptors.CustomDescriptor
- Creates a new instance of CustomDescriptor according to the parameters given.
- CustomDescriptor(CustomDescriptor) -
Constructor for class chemaxon.descriptors.CustomDescriptor
- Copy constructor.
- CUSTOMIZATION_ENABLED -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"customizationEnabled".
- customPaletteColors -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- CutBondReviser - Class in chemaxon.fragmenter
- Common base class for the classes that perform the revision of planned cut-bonds.
- CutBondReviser() -
Constructor for class chemaxon.fragmenter.CutBondReviser
- Default constructor.
- CXSMARTS -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Extended SMARTS.
- CXSMILES -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Extended SMILES.
- cyclomaticNumber() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the smallest number of graph edges which must be removed such
that no circuit remains.
MolecularDescriptor.toData()
DatabaseProperties.DatabaseProperties(ConnectionHandler, boolean) instead.
The constructor DatabaseProperties(conh) is equivalent to DatabaseProperties(conh, false).
null as its detail message.
"debug".
RGroupDecomposition results."defaultSaveFormat".
MPolyline.DEFAULT_ARROW_HEAD_LENGTH instead.
MPolyline.DEFAULT_ARROW_HEAD_WIDTH instead.
"defaultTool".
JChemSearch.DissimilarityMetrics.metricNames
JChemSearch.DissimilarityMetrics.metricNames, starting from 0.
StructureCheckerResultMoleculeGraph.implicitizeHydrogens(int)
with parameter MolAtom.ALL_H does the same.
JChemProperties table.
JChemProperties table,
if it exists.
JChemProperties table.
JChemProperties table.
String
"detach".
"detachable".
refresh()
or redraw() instead.
"dispQuality".
SurfaceColoring object in case of custom properties.
SurfaceColoring object in case of built-in properties.
RingStrainErrorChecker instead."downWedge".
"draggable".
GraphicCell from the Jogl rendering thread and draws the molecule.
DOTTED_TYPE or FILLED_TYPE.
three quality modes.
MESH_TYPE or TRANSPARENT_TYPE.
ServiceArguments implementing this interface
should support automatic evaluation of arguments before service call
based on context.ECFP class implements Extended-Connectivity Fingerprints (ECFPs)
as a type of MolecularDescriptors.ECFPFeatureLookup instance with the default
ECFP configuration parameters.
ECFPFeatureLookup instance with the given
ECFP configuration parameters.
ECFPFeatureLookup instance with the given
ECFP configuration parameters.
ECFPGenerator class generates ECFP fingerprints of molecular graphs.ECFPGenerator, which can be used to
generate ECFP fingerprints for an arbitrary number of molecules.
"editable".
"elements".
"2dviewerEnabled".
"3dviewerEnabled".
null.
HitColoringAndAlignmentOptions.markushDisplayMode
MarkushEnumerationPlugintrue if this decomposition is equivalent to the specified decomposition.
"escapeChar".
boolean.
boolean[].
double.
double[].
Sgroup.XSTATE_X or Sgroup.XSTATE_XC.
AbstractStructureFixer which expands all abbreviated groups in the moleculeDefaultStructureCheckerResult for identifying explicit hydrogen
problems, thus errorType property is StructureCheckerErrorType.EXPLICIT_H by default.StructureCheckerErrorType.EXPLICIT_H by default.
MolExporter.exportToBinFormat(MDocument, String)
MolExporter.exportToBinFormat(Molecule, String)
MolExporter.exportToFormat(MDocument, String)
MolExporter.exportToFormat(Molecule, String)
MolExporter.exportToObject(MDocument, String)
MolExporter.exportToObject(Molecule, String)
MolExporter.exportToObject(Molecule[], String, MolExportModule)
StructureCheckerResult that supports external
StructureChecker development."extraBonds".
"xtmpls".
"ezVisible".
MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie().
true if the hit is accepted by the filteringExpression.
0D molecules only.
MoleculeGraph.findFrag(int, int, MoleculeGraph),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
MoleculeGraph.findFragById(int, int, MoleculeGraph),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFragById(fragId, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
MoleculeGraph.findFrags(Class, int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
StructureChecker on the given molecule and after that fixes all
identified problems with the first StructureFixer which is associated with the current problem.
StructureFixer which
is associated with the StructureCheckerErrorType of the result.
StructureFixer implementations which
StructureCheckerErrorType can be fixed by the current fixerStructureFixer implementations which
error codes (identified by a unqie String) can be fixed by the current fixer"fogFactor".
double[][] 2xN table
to a 2-column tab-separated string representation of the table.
int
size units (bit count / 32).
BCUT descriptor from an external data format,
created by a previous call to toData().
toData().
CustomDescriptor from an external data format,
created by a previous call to toData().
ECFP fingerprint from an external data format
created by toData().
MolecularDescriptor object from its external
(database) representation.
PharmacophoreFingerprint from an external data
format, created by a previous call to toData().
toData().
toData().
fromIdentiferSet().
BCUT descriptor from its float array representation
(generated by toFloatArray()).
ECFP fingerprint from its float array representation.
ECFP fingerprint from a set of Integer
identifers.
ECFP fingerprint from an array of int
identifiers.
BCUT descriptor from its string representation
created by toString().
toString().
toString().
ECFP fingerprint from its string representation
created by toString().
toString().
toString().
toString().
Ring.fusedAliphaticRingCount()
Ring.fusedAliphaticRingCount(int)
Ring.fusedAliphaticRings()
Ring.fusedAliphaticRings(int)
Ring.fusedAromaticRingCount()
Ring.fusedAromaticRingCount(int)
Ring.fusedAromaticRings()
Ring.fusedAromaticRings(int)
Ring.fusedRingCount()
Collection of the base colors.
Collection of the base Molecule RGB colors and base
colors.
Collection of the base Molecule RGB colors.
Collection of black and white colorMolecularDescriptor
object.
CFGenerator and generates the descriptor for the
given molecule.
ECFPGenerator and generates the descriptor for the
given molecule.
MDSet from the given molecular structure.
MolecularDescriptor (depending
on the specific ganerator providing this service) for the given molecule.
MolecularDescriptorGenerator and
generates the descriptor for the given molecule.
RFGenerator and generates the descriptor for the
given molecule.
AlignmentMolecule form a Molecule based
on the values of the setters.
RgMolecule with the specified scaffold
(see MarkushGenerator.setQuery(chemaxon.struc.Molecule)) covering the specified targets
(see MarkushGenerator.setTargets(chemaxon.struc.Molecule[])).
Colors, which are
different enough from the specified forbidden colors.
Colors, with no
forbidden colors.
AlignmentMolecule form a Molecule based
on the values of the setters.
byte units.
int units.
GenerateMD provides a high level Application Program Interface
(API) with comprehensive functionality for the generation of various
Molecular Descriptors.- GenerateMD() -
Constructor for class chemaxon.descriptors.GenerateMD
- Creates an empty
MolecularDescripotor generator object.
- GenerateMD(int) -
Constructor for class chemaxon.descriptors.GenerateMD
- Creates an object for generating the given number of different
MolecularDescriptors (a molecular descriptor set, MDSet
) simultaneously.
- generateMetabolites(Metabolizer, File, String, String) -
Method in class chemaxon.metabolizer.MetabolizerUtilities
- This function exports all metabolites generated by the give Metabolizer object
into the outputFile with the outputFormat
- generateMetabolites(Metabolizer, OutputStream, String, String) -
Method in class chemaxon.metabolizer.MetabolizerUtilities
- This function exports all metabolites generated by the give Metabolizer object
into the outputStream with the outputFormat
- generateMetabolitesWithChildDepth(Metabolizer, File, String, String) -
Method in class chemaxon.metabolizer.MetabolizerUtilities
- This function exports all metabolites generated by the give Metabolizer object
into the outputFile with the outputFormat CHILDDEPTH property included
- generateMetabolitesWithChildDepth(Metabolizer, OutputStream, String, String) -
Method in class chemaxon.metabolizer.MetabolizerUtilities
- This function exports all metabolites generated by the give Metabolizer object
into the outputStream with the outputFormat CHILDDEPTH property included
- generateMetabolitesWithChildDepth(Metabolizer, MolExporter, String, String) -
Method in class chemaxon.metabolizer.MetabolizerUtilities
-
- generateRawDisplayList() -
Method in class chemaxon.marvin.space.SurfaceComponent
-
- generator -
Variable in class chemaxon.descriptors.MDParameters
- generates
MolecularDescriptors
- genericTautomer -
Variable in class chemaxon.jchem.db.UpdateHandler.RowData
-
- GEOMETRY_PLUGIN_GROUP -
Static variable in class chemaxon.license.LicenseManager
- Identifier of plugin: Geometry Plugin Group
- GeometryPlugin - Class in chemaxon.marvin.calculations
- Plugin class for geometric properties calculations.
- GeometryPlugin() -
Constructor for class chemaxon.marvin.calculations.GeometryPlugin
- Constructor.
- get(int, int, int) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the histogram bar height of two features ('fa'-'fb') corresponding to
the given ditance 'dist'.
- get(int) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the content of the specified hitogram bin.
- get(int, int, float) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- get(String) -
Method in class chemaxon.marvin.common.UserSettings
- Deprecated. since 5.4 use
UserSettings.getProperty(String) instead.
- get(String) -
Method in class chemaxon.struc.MPropertyContainer
- Gets a property object.
- get(int) -
Method in class chemaxon.struc.prop.MHashProp
- Gets a value.
- get(String) -
Method in class chemaxon.struc.prop.MHashProp
- Gets a value.
- get(int) -
Method in class chemaxon.struc.prop.MListProp
- Gets the specified element.
- get(int) -
Method in class chemaxon.util.IntArray
- Returns the component at the specified index.
- get3DMolecule() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the 3D molecule used in 3D surface area calculation.
- getAbsoluteCellIndex(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Determines the absolute cell index of a visible cell
- getAbsoluteCellIndex(JComponent) -
Method in class chemaxon.marvin.beans.MViewPane
- Determines in which cell the specified component is located.
- getAbsoluteLabelVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Are Absolute labels visible?
- getAbsoluteStereo() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the absolute stereo matching mode.
- getAbsoluteXY() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the X and Y coordinates of the data label in the molecule's
coordinate system, considering absolute/relative placement.
- getAbundance(int, int) -
Static method in class chemaxon.struc.PeriodicSystem
- Natural abundance of the isotope
- getAcceptorAtomCount() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the overall acceptor atom count (without multiplicity) in the molecule.
- getAcceptorCount(int) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the atomic acceptor count corresponding to the specified atom index.
- getAcceptorCount() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the overall acceptor count (with multiplicity) in the molecule.
- getActionMap() -
Method in class chemaxon.struc.graphics.MTextBox
- Returns the ActionMap used to determine what Action to fire for
particular KeyStroke binding.
- getActiveCell() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the active cell of the scene.
- getActiveCellIndex() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the index of the active cell.
- getActiveGroups() -
Method in class chemaxon.reaction.Standardizer
- Deprecated. Not used anymore.
- getAgent(int) -
Method in class chemaxon.struc.RxnMolecule
- Gets an agent.
- getAgentCount() -
Method in class chemaxon.struc.RxnMolecule
- Gets the number of agents.
- getAgents() -
Method in class chemaxon.struc.RxnMolecule
- Gets all agents in an array.
- getAlias() -
Method in class chemaxon.marvin.services.ServiceArgument
- Returns the argument alias.
- getAliasstr() -
Method in class chemaxon.struc.MolAtom
- Gets the alias string or pseudo atom type string for pseudo atoms.
- getAlignedMoleculesAsFragments() -
Method in class chemaxon.marvin.alignment.Alignment
-
- getAlignedMoleculesAsFragments() -
Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getAlignedMoleculesAsFragments() -
Method in interface chemaxon.marvin.alignment.PairwiseComparison
- After the similarity calculation the final orientations and conformations can be retrieved as a single molecule.
- getAlignedMoleculesAsFragments() -
Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getAlignedQuery() -
Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getAlignedQuery() -
Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- getAlignedQuery() -
Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getAlignedTarget() -
Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getAlignedTarget() -
Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- getAlignedTarget() -
Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getAlignedWithNewCoordinates() -
Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getAlignmenMolecule() -
Method in class chemaxon.descriptors.ShapeDescriptor
-
- getAlignScaffold() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Gets the scaffold aligning mode
- getAliphaticAtomCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the aliphatic atom count.
- getAliphaticBondCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the aliphatic bond count.
- getAliphaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the aliphatic ring count.
- getAliphaticRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the number of aliphatic rings (SSSR smallest set of smallest
rings) of a given size in the molecule.
- getAliphaticRingCountOfSize(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Deprecated. Use
TopologyAnalyserPlugin.getAliphaticRingCount(int)
- getAliphaticRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the aliphatic rings in the molecule.
- getAliphaticRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Indentifies aliphatic rings in the molecule having a given size (number
of atoms).
- getAllAtomCount() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the atom count (including implicit hydrogens).
- getAllAtomCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the atom count.
- getAllComponents(Class) -
Method in class chemaxon.marvin.space.GraphicScene
-
- getAllFragments() -
Method in class chemaxon.struc.RxnMolecule
- Gets the list of reaction fragments (product, reactant, agent components)
that build up this reaction.
- getAllMolecules() -
Method in class chemaxon.struc.MDocument
- Gets an array containing all molecule objects.
- getAllNonEmptyMolecules() -
Method in class chemaxon.struc.MDocument
- Gets an array containing all non-empty molecule objects.
- getAllObjects() -
Method in class chemaxon.struc.MDocument
- Gets all objects stored in this document and from the chemical structure of the document.
- getAllObjects() -
Method in class chemaxon.struc.Molecule
-
- getAllObjects() -
Method in class chemaxon.struc.RgMolecule
-
- getAllObjects() -
Method in class chemaxon.struc.RxnMolecule
-
- getAllOptionsAsString() -
Method in class chemaxon.sss.search.SearchOptions
- Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value
(except dissimilarity threshold in case of similarity search)
- getAllOptionsAsString(String) -
Method in class chemaxon.sss.search.SearchOptions
- Returns a string that
- describes the state of the options
- can be the input of setOptions(String)
- contains all options, including those which have their default value
(except dissimilarity threshold in case of similarity search)
- getAllPositions() -
Method in class chemaxon.naming.DocumentExtractor.Hit
-
- getAllProperties() -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns all properties in the JChem property table.
- getAngle(int, int, int) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the angle of 3 atoms.
- getAngle(int[]) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the angle of 3 atoms.
- getAnimated() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets index of animated cells of the table (or simple viewer).
- getAnimDelay() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the repeat delay for animations.
- getAnimFPS() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the frames per second for animations.
- getAppliedTaskIDs() -
Method in class chemaxon.reaction.ConcurrentStandardizerProcessor
- Returns the IDs of tasks applied to the last input molecule.
- getAppliedTaskIDs() -
Method in class chemaxon.reaction.Standardizer
- Returns the IDs of tasks applied to the last input molecule.
- getAppliedTaskIndexes() -
Method in class chemaxon.reaction.ConcurrentStandardizerProcessor
- Returns the indexes of tasks applied to the last input molecule.
- getAppliedTaskIndexes() -
Method in class chemaxon.reaction.Standardizer
- Returns the indexes of tasks applied to the last input molecule.
- getArcAngle() -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the central angle of the arc.
- getArcCenter(DPoint3, DPoint3, double) -
Static method in class chemaxon.struc.graphics.MPolyline
- Returns the arc center.
- getArcHeight() -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- getArcRadius(CTransform3D) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the arc radius.
- getArcRadius(DPoint3, DPoint3, double) -
Static method in class chemaxon.struc.graphics.MPolyline
-
- getArcWidth() -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- getAromataType() -
Method in class chemaxon.checkers.result.AromaticityCheckerResult
- Returns the type of the aromatization
- getAromaticAndAliphaticRings(int, boolean, boolean, int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Get aromatic and or aliphatic ring atom indexes.
- getAromaticAtomCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the aromatic atom count.
- getAromaticBondCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the aromatic bond count.
- getAromaticRingCharge(int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the total partial charge of the smallest aromatic ring
containing the specified atom.
- getAromaticRingCharge(int, int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the partial charge of the smallest aromatic ring
containing the specified atom.
- getAromaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the aromatic ring count.
- getAromaticRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the number of aromatic rings (SSSR smallest set of smallest
rings) of a given size in the molecule.
- getAromaticRingCountOfSize(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Deprecated. Use
TopologyAnalyserPlugin.getAromaticRingCount(int)
- getAromaticRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the aromatic rings in the molecule.
- getAromaticRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Indentifies aromatic rings in the molecule having a given size (number
of rings).
- getAromaticSystemCharge(int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the total partial charge of the aromatic system
containing the specified atom.
- getAromaticSystemCharge(int, int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the partial charge of the aromatic system
containing the specified atom.
- getAromatizationMethod() -
Method in class chemaxon.sss.search.MCES
- Gets the aromatization method.
- getAromatizedStructures() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the enumerated structures in aromatized form.
- getAromatizeMethod() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the aromatize method.
- getAromrings() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. please use getAromaticAndAliphaticRings instead.
- getAromrings(int) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. please use getAromaticAndAliphaticRings instead.
- getAromType() -
Method in class chemaxon.checkers.AromaticityErrorChecker
- Returns the aromType
- getArrayFlags() -
Method in interface chemaxon.struc.Smolecule
- Gets info about the used arrays.
- getArrowAsProperty() -
Method in class chemaxon.struc.RxnMolecule
- Gets the properties (type, endpoint coordinates) of the reaction arrow in
this reaction.
- getArrowFlags(int) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the arrow flags.
- getArrowLength(int) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the arrow head length.
- getArrowWidth(int) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the arrow head width.
- getASA() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns water accessible surface area calculated using a radius of 1.4 A for the water molecule.
- getASAHydrophobic() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns water accessible surface area of all hydrophobic (|qi|<0.125) atoms.
- getASANegative() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns water accessible surface area of all atoms with negative partial charge (strictly less than 0).
- getASAPlus() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns water accessible surface area of all atoms with positive partial charge (strictly greater than 0).
- getASAPolar() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns water accessible surface area of all polar (|qi|>=0.125) atoms.
- getAsBitSet() -
Method in class chemaxon.descriptors.DescriptorGenerator
- Returns the generated descriptor in a BitSet representation if it is available.
- getAscent(Graphics, FontMetrics) -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the ascent of this portion.
- getAsFloatArray() -
Method in class chemaxon.descriptors.DescriptorGenerator
- Returns the generated descriptor in a float array representation if it is available.
- getAsIntArray() -
Method in class chemaxon.descriptors.DescriptorGenerator
- Returns the generated descriptor in an int array representation if it is available.
- getAsMolecule() -
Method in class chemaxon.sss.search.MCES
- Gets the found MCES as a
Molecule object.
- getASSBClusters() -
Method in class chemaxon.descriptors.GenerateMD
-
- getAssociatedComponents() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns an
Iterator that can enumerate the components
associated to (depending on) this component.
- getAssociatedNonQueryFormat() -
Method in class chemaxon.formats.MFileFormat
- Gets the associated non-query format.
- getAssociatedQueryFormat() -
Method in class chemaxon.formats.MFileFormat
- Gets the associated query format.
- getAsString() -
Method in class chemaxon.descriptors.DescriptorGenerator
- Returns the generated descriptor in its native string representation.
- getAsymmetricAtomCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the number of asymmetric atoms.
- getAsymmetricAtoms() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines the asymmetric atoms.
- getAsymmetricEuclidean(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the asymmetric Euclidean distance.
- getAsymmetricEuclidean(CustomDescriptor) -
Method in class chemaxon.descriptors.CustomDescriptor
- Calculates the asymmetric Euclidean distance.
- getAsymmetricEuclidean(ECFP) -
Method in class chemaxon.descriptors.ECFP
- Calculates the asymmetric Euclidean distance.
- getAsymmetricEuclidean(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getAsymmetricFBPA(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the asymmetric FBPA convolution product based distance of
the fingerprint from an other (given as parameter).
- getAsymmetryFactor() -
Method in class chemaxon.descriptors.MDParameters
- Gets the asymmetry factor used in the current parametrized asymmetric metrics.
- getAtno() -
Method in class chemaxon.struc.MolAtom
- Gets the atomic number.
- getAtom() -
Method in class chemaxon.jep.context.AtomContext
- Returns the input atom index.
- getAtom() -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Gets the atom.
- getAtom(int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the nth atom.
- getAtom(int) -
Method in class chemaxon.struc.RgMolecule
- Gets a node in the graph union.
- getAtom(int) -
Method in class chemaxon.struc.RxnMolecule
- Gets a node.
- getAtom(int) -
Method in class chemaxon.struc.Sgroup
- Gets an atom in the S-group.
- getAtom1() -
Method in class chemaxon.struc.MolBond
- Gets the first endpoint.
- getAtom1(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the index of the first atom of the specified bond.
- getAtom2() -
Method in class chemaxon.struc.MolBond
- Gets the second endpoint.
- getAtom2(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the index of the second atom of the specified bond.
- getAtomArray() -
Method in class chemaxon.struc.MoleculeGraph
- Creates an array of atoms.
- getAtomArray() -
Method in class chemaxon.struc.Sgroup
- Gets the array of atoms in the S-group.
- getAtomCount() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getAtomCount(int) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the number of atoms with given atomic number
(including its isotopes).
- getAtomCount(int, int) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the number of atoms with given atomic number
in the molecule isotope with the specified mass number.
- getAtomCount() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the number of atoms in the input molecule.
- getAtomCount(boolean) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the number of atoms in the molecule with arbitrarily enumerating hydrogens.
- getAtomCount() -
Method in class chemaxon.pharmacophore.PMap
- Returns the number of atoms.
- getAtomCount() -
Method in class chemaxon.sss.search.MCES
- Gets the number of atoms in the found MCES.
- getAtomCount() -
Method in interface chemaxon.struc.Incomplecule
- Gets the number of atoms.
- getAtomCount() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the number of atoms.
- getAtomCount(int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the number of atoms with the given atomic number.
- getAtomCount() -
Method in class chemaxon.struc.RgMolecule
- Gets the number of nodes in the root structure.
- getAtomCount(int) -
Method in class chemaxon.struc.RgMolecule
- Gets the number of atoms with the given atomic number in the root
structure.
- getAtomCount() -
Method in class chemaxon.struc.RxnMolecule
- Returns the number of nodes in the graph union.
- getAtomCount(int) -
Method in class chemaxon.struc.RxnMolecule
- Gets the number of atoms with the given atomic number in the unified
molecule graph of the reaction.
- getAtomCount() -
Method in class chemaxon.struc.Sgroup
- Gets the number of atoms in the S-group.
- getAtomCount() -
Method in class chemaxon.util.MolHandler
- Retrieves the number of atoms in the Molecule
stored in the MolHandler object.
- getAtomFont() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the atom symbol font name.
- getAtomicNumber(String) -
Static method in class chemaxon.struc.MolAtom
- Gets the atomic number of an element.
- getAtomicNumber(String) -
Static method in class chemaxon.struc.PeriodicSystem
- Returns the atomic number of the element specified by its symbol.
- getAtomicRadius(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Atomic radius of the element Angstroms.
- getAtomicSurfaceAreaIncrement(int) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the 3D surface area increments.
- getAtomIndex(int) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the atom index in the standardized molecule,
or the atom index itself if the input molecule has not been standardized.
- getAtomIterator(boolean) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the iterator of the atoms of the molecule.
- getAtomlogPHIncrement(int) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Deprecated. Increments of implicit H-s are not calculated. Returns the same value as
logPPlugin.getAtomlogPIncrement(int)
- getAtomlogPIncrement(int) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the logP increment for the specified atom.
- getAtomMap() -
Method in class chemaxon.struc.MolAtom
- Gets the atom-atom mapping number.
- getAtomMap(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the atom-atom mapping number.
- getAtomMapMatch() -
Method in class chemaxon.sss.search.MCES
- Gets the matching mode for atom map numbers.
- getAtomMapping() -
Method in class chemaxon.sss.search.MCES
- Gets the atom mapping of the found MCES.
- getAtomMappingMethod() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the atom mapping method.
- getAtomNumbersVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 2.9.13, replaced by isAtomNumbersVisible.
- getAtomProperty() -
Method in class chemaxon.marvin.space.AtomProperty
-
- getAtomProperty() -
Method in class chemaxon.marvin.space.MoleculeComponent
- See
MoleculeIterators.AtomPropertyInterface for details.
- getAtomReverseMapping() -
Method in class chemaxon.sss.search.MCES
- Gets the reverse atom mapping of the found MCES.
- getAtoms() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getAtoms() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getAtoms(int) -
Method in class chemaxon.pharmacophore.PMap
- Returns the atom indices of the atoms having the given feature.
- getAtoms(int, int[]) -
Method in class chemaxon.pharmacophore.PMap
- Returns the atom indices of the atoms having the given feature.
- getAtoms() -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Gets the atoms.
- getAtoms() -
Method in class chemaxon.struc.MDocument.CheckerMark
-
- getAtomSelections() -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- getAtomSetColor(int) -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the color of an atom set.
- getAtomSetColor(int) -
Method in class chemaxon.struc.MDocument
- Gets an atom set color.
- getAtomSetColorMode(int) -
Method in class chemaxon.struc.MDocument
- Gets the atom set coloring mode.
- getAtomSetColors() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Determines the coloring of atoms.
- getAtomSetColors() -
Method in class chemaxon.descriptors.PFParameters
- Gets the coloring of atoms as defined in the XML configuration file.
- getAtomSetColors() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Determines the coloring of atoms.
- getAtomSetFont(int) -
Method in class chemaxon.struc.MDocument
- Gets an atom set font.
- getAtomSetIndexes(Molecule) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the individual atom color indexes.
- getAtomSetIndexes(Molecule, PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PFParameters
- Gets the individual atom colors by pharmcophore point type.
- getAtomSetIndexes(Molecule) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the individual atom colors by pharmcophore point type.
- getAtomSetNames() -
Method in class chemaxon.descriptors.MolecularDescriptor
-
- getAtomSetNames() -
Method in class chemaxon.descriptors.PFParameters
- Gets the name of atom sets (pharmacophore point type set), as defined
in the configuration file/string.
- getAtomSetNames() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getAtomSetRGB(int) -
Method in class chemaxon.struc.MDocument
- Gets an atom set color.
- getAtomSetSize() -
Method in class chemaxon.struc.MDocument
- Gets the size of the atom set.
- getAtomsize() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the atom size.
- getAtomSize() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the atom size in C-C bond length units.
- getAtomsize() -
Method in class chemaxon.marvin.MolPrinter
- Deprecated. As of Marvin 5.2.2, replaced by
MolPrinter.getAtomSize().
- getAtomSize() -
Method in class chemaxon.marvin.MolPrinter
- Returns the atom size in units of regular bond length.
- getAtomStereo(MolAtom, int) -
Static method in class chemaxon.sss.search.Search
- Determine the stereo type of an atom
- getAtomStereo(int) -
Method in interface chemaxon.struc.Smolecule
- Gets atom stereo properties as an integer.
- getAtomSymbol(int, int, int[], CTransform3D) -
Method in class chemaxon.struc.MolAtom
- Gets the string representation of the atom symbol.
- getAtomSymbol(int, int, int[], CTransform3D) -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Gets the string representation of the atom symbol.
- getAtomSymbolListAsString(MolAtom[]) -
Static method in class chemaxon.struc.Sgroup
-
- getAtomType(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the type of an atom.
- getAtomTypeMatch() -
Method in class chemaxon.sss.search.MCES
- Gets the matching mode for atom types.
- getAtropBonds() -
Method in class chemaxon.marvin.alignment.AtropIsomerDetector
- After the calculate method finished.
- getAttach() -
Method in class chemaxon.struc.MolAtom
- Gets the S-group attachment point information.
- getAttachAtoms() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the attachment points.
- getAttachedDataMatch() -
Method in class chemaxon.sss.search.SearchOptions
- Returns whether attached data (in data sgroups) should be used
when comparing structures.
- getAttachedDataPrefixes() -
Method in class chemaxon.sss.search.SearchOptions
- Returns the prefixes of the names of those data sgroups
that will be used during structure comparison or
null
if all data sgroups should be checked.
- getAttachParentSgroup() -
Method in class chemaxon.struc.MolAtom
- Gets the parent S-group of an S-group attachment point atom.
- getAttrFont(MTextAttributes) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the font for the specified attribute object.
- getAttribute(String) -
Method in class chemaxon.struc.graphics.MBracket
- Gets the value of an attribute.
- getAttribute(String) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the value of an attribute.
- getAttribute(String) -
Method in class chemaxon.struc.graphics.MRectangle
- Gets the value of an attribute.
- getAttribute(String) -
Method in class chemaxon.struc.graphics.MRoundedRectangle
- Gets the value of an attribute.
- getAttribute(String) -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the value of an attribute.
- getAttribute(String) -
Method in class chemaxon.struc.MObject
- Gets the value of an attribute.
- getAttributes(int, int, int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the common attributes of the selected text.
- getAttributes() -
Method in class chemaxon.struc.graphics.MTextDocument.Section
- Gets the attributes.
- getAutoScale() -
Method in class chemaxon.marvin.beans.MSketchPane
- Returns autoscale property.
- getAutoTabScale() -
Method in class chemaxon.marvin.beans.MViewPane
- Is tab scale automatically changed?
- getAvailableNewHits(int) -
Method in class chemaxon.jchem.db.JChemSearch
- Used with run mode =
JChemSearch.RUN_MODE_ASYNCH_PROGRESSIVE.
- getAverageNonZeroRatio() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the average percentage of cells that have non-zero value taken all
descriptors generated since the initialization of the generator into
account.
- getAveragePolarizabilityComponent() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the average polarizability component
(for
geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
- getAWTFont() -
Method in class chemaxon.struc.graphics.MFont
- Gets an AWT font instance.
- getBackground() -
Method in class chemaxon.struc.MObject
- Gets the background color of the object.
- getBackgroundColor() -
Method in class chemaxon.marvin.MolPrinter
- Returns the current background color.
- getBackgroundColor() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the background color of the scene.
- getBackgroundColor() -
Method in class chemaxon.marvin.space.monitor.Label
- Returns the background color of the label.
- getBalabanIndex() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the Balaban distance connectivity of the molecule, which is
the average distance sum connectivity.
- getBallRadius() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the ball radius in units of covalent radius.
- getBallRadius() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the ball radius for ball and stick mode.
- getBallRadius() -
Method in class chemaxon.marvin.MolPrinter
- Gets the ball radius for "ball and stick" mode.
- getBaseFont() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the base font.
- getBaseFont() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the base font.
- getBaseFontFamily() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the base font family.
- getBaseFontStyle() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the base font style.
- getBaseMap(int) -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the base map corresponding to the given map.
- getBestTabScale(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the best scale value for a molecule cell.
- getBestTabScale() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the smallest best scale value in the molecule table.
- getBFactor(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getBFactor(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getBFactorPalette() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the palette that is used when the coloring mode of the component
is b-factor coloring.
- getBicycloStereo() -
Method in class chemaxon.struc.MolAtom
- Gets the bicyclo stereo information of this atom.
- getBit(int) -
Method in class chemaxon.descriptors.CustomDescriptor
-
- getBitCount() -
Method in class chemaxon.descriptors.CFParameters
- Gets the preset bit count (number of fingerprint bits to be set to 1)
parameter.
- getBitCount() -
Method in class chemaxon.descriptors.RFParameters
- Gets the preset bit count (number of fingerprint bits to be set to 1)
parameter.
- getBitPosition() -
Method in class chemaxon.descriptors.ECFPFeature
- Gets the generated bit position for this ECFP feature.
- getBitPosition(MolAtom, int) -
Method in class chemaxon.descriptors.ECFPFeatureLookup
- Returns the corresponding bit position for the given atom neighborhood.
- getBitPosition(int) -
Method in class chemaxon.descriptors.ECFPFeatureLookup
- Returns the corresponding bit position for the given integer identifier.
- getBond(int) -
Method in class chemaxon.struc.MolAtom
- Gets the i-th bond.
- getBond(int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the nth bond.
- getBond(int) -
Method in class chemaxon.struc.RgMolecule
- Gets an edge in the graph union.
- getBond(int) -
Method in class chemaxon.struc.RxnMolecule
- Gets an edge.
- getBond(int) -
Method in class chemaxon.util.iterator.IteratorFactory.BondIterator
- Returns a bond of a specified index.
- getBond(int) -
Method in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
- Returns a bond of a specified index.
- getBondArray() -
Method in class chemaxon.struc.MoleculeGraph
- Creates an array of bonds.
- getBondConnectionInfo() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Gets a bond triplet which stores the crossing bond and flip
information.
- getBondCorrespondence() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Gets four bonds that store the crossing bond and flip
information.
- getBondCount() -
Method in class chemaxon.descriptors.CFParameters
- Gets the preset path length (number of adjacent bonds) parameter.
- getBondCount() -
Method in class chemaxon.descriptors.RFParameters
- Gets the preset path length (number of adjacent bonds) parameter.
- getBondCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the bond count.
- getBondCount(boolean) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the number of bonds in the molecule with arbitrarily enumerating hydrogens.
- getBondCount() -
Method in class chemaxon.sss.search.MCES
- Gets the number of bonds in the found MCES.
- getBondCount() -
Method in interface chemaxon.struc.Incomplecule
- Gets the number of bonds
- getBondCount() -
Method in class chemaxon.struc.MolAtom
- Gets the number of bonds/ligands.
- getBondCount() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the number of bonds.
- getBondCount() -
Method in class chemaxon.struc.RgMolecule
- Gets the number of edges in the root structure.
- getBondCount() -
Method in class chemaxon.struc.RxnMolecule
- Gets the number of edges in the graph union.
- getBondFlags(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the bond descriptor flags.
- getBondIndex(int, int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the index of the bond connecting two atoms,
-1 if the two atoms are not connected by bond.
- getBondIndex(int, int) -
Method in interface chemaxon.struc.Smolecule
- Gets the index of the bond between the specified atoms.
- getBondIterator(boolean) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the iterator of the atoms of the molecule.
- getBondMapping() -
Method in class chemaxon.sss.search.MCES
- Gets the bond mapping of the found MCES.
- getBondReverseMapping() -
Method in class chemaxon.sss.search.MCES
- Gets the reverse bond mapping of the found MCES.
- getBonds() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getBonds() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getBonds() -
Method in class chemaxon.struc.MDocument.CheckerMark
-
- getBonds(MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Returns the bonds attached to the given atom in this molecule graph.
- getBondSetColor(int) -
Method in class chemaxon.struc.MDocument
- Gets a bond set color.
- getBondSetColorMode(int) -
Method in class chemaxon.struc.MDocument
- Gets the bond set coloring mode.
- getBondSetRGB(int) -
Method in class chemaxon.struc.MDocument
- Gets a bond set color.
- getBondSetSize() -
Method in class chemaxon.struc.MDocument
- Gets the bond set size.
- getBondSetThickness(int) -
Method in class chemaxon.struc.MDocument
- Gets a bond set thickness.
- getBondSpacing() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the double bond spacing.
- getBondSpacing() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the double bond spacing.
- getBondSpacing() -
Method in class chemaxon.marvin.MolPrinter
- Returns the double bond spacing that is the distance of
the two lines representing a double bond.
- getBondTable() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the bond (edge) table.
- getBondTable() -
Method in class chemaxon.struc.RgMolecule
- Gets the bond table of the root structre.
- getBondTable() -
Method in class chemaxon.struc.RxnMolecule
- Gets the bond table for the graph union.
- getBondTo(MolAtom) -
Method in class chemaxon.struc.MolAtom
- Finds the bond that connects this atom to another atom.
- getBondType(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines the type of a bond (aromatic bonds are automatically recognized)
- getBondType(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the type of a bond.
- getBondType(int, int) -
Method in interface chemaxon.struc.Smolecule
- Gets the type of a bond between the two specified atoms.
- getBondTypeMatch() -
Method in class chemaxon.sss.search.MCES
- Gets the matching mode for bond types.
- getBondWidth() -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 4.1, replaced by
MarvinPane.getBondSpacing()
- getBondWidth() -
Method in class chemaxon.marvin.MolPrinter
- Deprecated. as of Marvin 4.1, replaced by
MolPrinter.getBondSpacing()
- getBoolean(String) -
Static method in class chemaxon.sss.search.SearchOptions
- Returns value as a boolean flag.
- getBorderColor() -
Method in class chemaxon.marvin.space.monitor.Label
- Returns the border color of the label.
- getBorderWidth() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the width of the border between cells.
- getBottom() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the y coordinate of the bottom of the cell in pixels.
- getBoundingBox() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the smallest box containing the graphic component.
- getBoundingBox() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getBoundingBox() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the
BoundingBox that is the smallest container box of the component.
- getBoundingBoxAndSetSphereRadius() -
Method in class chemaxon.marvin.space.GraphicCell
- Computes the radius of the bounding sphere in order to set the z coordinate
of the camera properly.
- getBoundingCenter() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the center of the box as a vector.
- getBoundingRadius() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the radius of the bounding sphere of the box, which is
the distance between the lower-left-front corner and the center.
- getBoundingRectangle(MoleculeGraph[]) -
Method in class chemaxon.marvin.MolPrinter
- Returns the bounding rectangle of the specified molecules using the current scale factor.
- getBoundingSphereRadius() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the radius of the bounding sphere of the component.
- getBoundRectSize() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the size of the bounding rectangle.
- getBracketCount() -
Method in class chemaxon.struc.Sgroup
- Gets the number of brackets in this S-group.
- getBracketOrientation() -
Method in class chemaxon.struc.graphics.MBracket
- Gets the orientation of the bracket.
- getBrackets() -
Method in class chemaxon.struc.Sgroup
- Gets all graphic brackets from this Sgroup
- getBreakingChars() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the breaking characters after that the text in the text
box can be broken if it doesn't fit into the text box.
- getBrightestMolId() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the id of that molecule which had the maximum number of non-zero
cells among all descriptors generated since the initialization of the
generator object.
- getBrightness() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets the brightness of the fingerprint.
- getBrightness() -
Method in class chemaxon.descriptors.ECFP
- Gets the brightness of the fingerprint.
- getBrightness() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the brightness of the fingerprint.
- getBtab() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. as of Marvin 5.4, please use
MoleculeGraph.getBondTable() instead
- getBtab() -
Method in class chemaxon.struc.RgMolecule
- Deprecated. as of Marvin 5.4, please use
RgMolecule.getBondTable() instead
- getBtab() -
Method in class chemaxon.struc.RxnMolecule
- Deprecated. as of Marvin 5.4, please use
RxnMolecule.getBondTable() instead
- getBufferedImage() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the Canvas as a BufferedImage with the same size in pixels.
- getBuiltInPalette(int) -
Static method in class chemaxon.marvin.space.SurfaceColoring
- Returns the colors of a built-in palette.
- getBuiltInPalette(Object) -
Static method in class chemaxon.marvin.space.SurfaceColoring
- Returns the colors of a built-in palette.
- getBuiltInPalettes() -
Static method in class chemaxon.marvin.space.SurfaceColoring
- Returns the string identifiers of the built-in palettes.
- getC(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the state of a checkbox in a GridBagView table.
- getCacheCapacity() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the maximum number of cached documents.
- getCachedDoc(int, String) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the specified document if it is present in the memory.
- getCachedDocIndices() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the indices of cached records.
- getCachedResults(Molecule, boolean) -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns cached results, separated from the plugin object,
so that no further enqueries needed to the plugin to get the result.
- getCachedTables() -
Static method in class chemaxon.jchem.db.JChemSearch
- Gets the names and sizes of tables currently in the cache.
- getCacheError() -
Method in class chemaxon.jchem.db.JChemSearch
- For checking for cache errors.
- getCacheID() -
Static method in class chemaxon.jchem.db.CacheRegistrationUtil
-
- getCacheLock() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the synchronization lock for caching operations.
- getCacheRegisterer(String, String, String, boolean) -
Method in class chemaxon.jchem.db.CacheRegistrationUtil
-
- getCacheRegistrationTableName() -
Method in class chemaxon.jchem.db.DatabaseProperties
- Get the cache registration table name of the currently used property table.
- getCacheRegistrationTableName(ConnectionHandler) -
Static method in class chemaxon.jchem.db.DatabaseProperties
- Get the table name containing the registration information
- getCalcMolecule() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the molecule used in the calculation.
- getCameraZ() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the z coordinate of the camera.
- getCanvasComponent() -
Method in class chemaxon.marvin.beans.MSketchPane
- Determines canvas component of MarvinSketch.
- getCanvasComponent(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Deprecated. as of Marvin 3.0, replaced by getVisibleCellComponent
- getCapacity() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the total capacity.
- getCarboaliphaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of carboaliphatic rings in the molecule (aliphatic
rings containing carbon atoms only).
- getCarboaromaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of carboaromatic rings in the molecule (aromatic
rings containing carbon atoms only).
- getCarbonVisibility() -
Method in class chemaxon.marvin.MolPrinter
- Returns the visibility style of the C labels on Carbon atoms.
- getCarboRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the carbo ring count.
- getCarboRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of carbocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- getCarboRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only).
- getCarboRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only) having the given number of atoms.
- getCell() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the container cell of the component.
- getCell(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the
GraphicCell which has the given index.
- getCellButtom() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the y coordinate of the buttom of the active cell in pixels.
- getCellCount() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the number of molecule cells in the table.
- getCellCount() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the number of cells in the scene.
- getCellDrawProperty(String) -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the value of the cell-range drawing property with the given name.
- getCellDrawProperty(String) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the draw property from the active cell or null if there is no active cell
or the property is not defined in the active cell.
- getCellDrawProperty(int, String) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the draw property from the given cell or null if not defined.
- getCellEditorValue() -
Method in class chemaxon.marvin.beans.MViewEditor
- Returns the edited molecule that is a
Molecule instance.
- getCellHeight() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the height of the cells.
- getCellIndex() -
Method in class chemaxon.marvin.space.CellOrComponentId
- Returns the internal index of the cell either this is a cell id or a component id.
- getCellLeft() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the x coordinate of the left edge of the active cell.
- getCellRight() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the x coordinate of the right edge of the active cell.
- getCellSize() -
Method in class chemaxon.descriptors.MDParameters
- Gets the number of bits of an atomic cell in the descriptor.
- getCellTop() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the y coordinate of the top of the active cell.
- getCellWidth() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the width of the cells.
- getCenter() -
Method in class chemaxon.marvin.space.monitor.Control
- Returns the center of the transformation.
- getCenter(int, int) -
Method in class chemaxon.struc.RxnMolecule
- Gets the geometrical center of a reaction component.
- getCenterAtom() -
Method in class chemaxon.descriptors.ECFPFeature
- Gets the center atom of the represented substructure.
- getCentralShown() -
Method in class chemaxon.clustering.Ward
- Indicates whether central objects are displayed.
- getChainAtomCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the chain atom count.
- getChainBondCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the chain bond count.
- getChangeSupport() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- Returns the changeSupport
- getChangingAtoms(boolean, int) -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the indexes of changing atoms.
- getChangingBondData(boolean) -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns changing bond data.
- getCharactersRead() -
Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
-
- getCharge(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getCharge(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getCharge() -
Method in class chemaxon.struc.MolAtom
- Gets the charge.
- getCharge(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the charge of an ion.
- getChargeDensity(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the total charge density of an atom
calculated with HMO,
Double.NaN for no value.
- getChargeDistribution() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the charge distribution array over pH values.
- getChargeLocation() -
Method in class chemaxon.struc.Sgroup
- Returns the charge location attribute of the S-group.
- getChargeMatch() -
Method in class chemaxon.sss.search.MCES
- Gets the matching mode for atom formal charges.
- getChargeMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get the charge matching option value
- getCheckerConfigFileName() -
Method in class chemaxon.marvin.common.UserSettings
-
- getCheckerList() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- Returns the checkerList
- getCheckerList() -
Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
-
- getCheckerList() -
Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
-
- getCheckerMarks() -
Method in class chemaxon.struc.MDocument
- Returns the array of checker marks
NOTE: checker marks will be reset on any molecule change
- getCheckSpHyb() -
Method in class chemaxon.sss.search.SearchOptions
- Get the sp-hybridization state option
- getChemicalHashedFingerprint(int[], int) -
Static method in class chemaxon.descriptors.ReactionFingerprint
- Creates chemical hashed fingerpint from reaction fingerprint.
- getChemTermColumns(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns the name of columns with values automatically calculated based on
Chemical Terms expressions.
- getChemTermForColumn(String, String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Gets the Chemical Terms expression that should be used to compute the
value for the given column.
- getChemTermsFilter() -
Method in class chemaxon.sss.search.SearchOptions
- Gets the Chemical Terms filtering expression
- getChemTermsFilterConfig() -
Method in class chemaxon.sss.search.SearchOptions
- Gets the configuration string for Chemical Terms filter.
- getChildSgroup(int) -
Method in class chemaxon.struc.Sgroup
- Gets a child S-group.
- getChildSgroupCount() -
Method in class chemaxon.struc.Sgroup
- Gets the number of child S-groups.
- getChiralCenterCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of tetrahedral stereogenic centers.
- getChiralCenters() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines the chiral center atoms.
- getChirality(int) -
Method in class chemaxon.struc.MoleculeGraph
- Computes the chirality of an atom of the Molecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- getChirality(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the chirality of an atom.
- getChiralitySupport() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets chirality support level.
- getChiralitySupport() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the chirality support parameter.
- getChiralitySupport() -
Method in class chemaxon.marvin.MolPrinter
- Returns the current chirality display mode.
- getClassifier() -
Method in class chemaxon.fragmenter.Fragmenter
- Returns the classifier object.
- getClassName() -
Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
- Returns the full class name of the service
- getClean2dOpts() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the 2D cleaning options.
- getClean3dOpts() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the 3D cleaning options.
- getCleanDim() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the number of space dimensions for cleaning.
- getClip(CTransform3D) -
Method in class chemaxon.struc.graphics.MRectangle
- Gets the clipping rectangle.
- getClipboard() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns the default Toolkit's system clipboard if available, otherwise
returns a new singleton clipboard instance.
- getClipboard() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getClipboardClearerTask() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getCloneResult() -
Method in class chemaxon.descriptors.MDReader
- Gets the current value of the cloning policy flag.
- getClusterCount() -
Method in class chemaxon.clustering.Ward
- Gets the number of clusters.
- getClusterEnumerator(boolean) -
Method in class chemaxon.clustering.LibraryMCS
- Gets a new
LibraryMCS.ClusterEnumerator object.
- getClusterEnumerator(boolean, boolean) -
Method in class chemaxon.clustering.LibraryMCS
- Gets a new
LibraryMCS.ClusterEnumerator object.
- getCoarseReactionTanimoto(ReactionFingerprint) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Returns the tanimoto distance of the reaction centers.
- getColor() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getColor() -
Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- getColor() -
Method in class chemaxon.marvin.space.ComponentElement
- Returns the color that is assigned to the ComponentElement.
- getColor() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the constant color of the component.
- getColor() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getColor() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the constant color of the surface.
- getColor() -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- getColor() -
Method in class chemaxon.marvin.space.monitor.Control
- Returns the color of the control.
- getColor() -
Method in class chemaxon.marvin.space.monitor.DihedralControl
- Returns the color of the control.
- getColor() -
Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
- Returns the color of the control.
- getColor() -
Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Returns the color of the control.
- getColor() -
Method in class chemaxon.marvin.space.monitor.LocalLocationControl
- Returns the color of the control.
- getColor() -
Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
- Returns the color of the control.
- getColor() -
Method in class chemaxon.marvin.space.monitor.ResizeControl
- Returns the color of the control.
- getColor() -
Method in class chemaxon.marvin.space.PharmacophoreArrow
- Returns the color of the component.
- getColor() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Returns the color of the PharmacophorePoint.
- getColor() -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the constant color of the surface.
- getColor() -
Method in class chemaxon.struc.MDocument.CheckerMark
-
- getColor() -
Method in class chemaxon.struc.MObject
- Gets the color of the object.
- getColor(String) -
Static method in class chemaxon.util.HTMLTools
- Converts the string to a Color Object.
- getColor3() -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the constant color of the surface.
- getColoring() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the hit coloring options.
- getColoringScheme() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getColors() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getColors() -
Method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- getColorScheme() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the color scheme.
- getColorScheme() -
Method in class chemaxon.marvin.MolPrinter
- Returns the current color scheme.
- getColorType() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getColorType() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the color type of the surface.
- getColorType() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the color type of the visualizer.
- getColumn(int) -
Static method in class chemaxon.struc.MolAtom
- The column or group of an element in the periodic system.
- getColumn(int) -
Static method in class chemaxon.struc.PeriodicSystem
- The column or group of an element in the periodic system.
- getColumnCount() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the number of columns in the scene.
- getColumnsToRegenerate(ConnectionHandler, String, int) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Return the columns should be regenerated in a table depending on a regeneration type.
- getColumnWidth() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the default column width.
- getColumnWidth(int) -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the default width of a specified column.
- getColumnWidthsString() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets a parameter string containing column widths.
- getCommandKeyStroke(int) -
Static method in class chemaxon.marvin.util.SwingUtil
- Gets the command keystroke preferred on the current platform.
- getComment() -
Method in class chemaxon.struc.Molecule
- Gets the comment.
- getComment() -
Method in class chemaxon.struc.RgMolecule
- Gets the comment of the root molecule.
- getCommonActions() -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated.
- getCommonActions() -
Method in class chemaxon.marvin.beans.MSketchPane
-
- getCommonActions() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the common actions.
- getCommonBitCount(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
-
- getCommonBitCount(ReactionFingerprint) -
Method in class chemaxon.descriptors.ReactionFingerprint
-
- getCompatibleAttributes(MTextAttributes, MFont, MTextAttributes.MFontCreator, int) -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the compatible attributes.
- getCompleteHG() -
Method in class chemaxon.sss.search.SearchOptions
- Retrieves the information if only complete structures are matching on
target homology groups.
- getComponent(Molecule, int) -
Method in class chemaxon.checkers.AtomChecker
-
- getComponent(Molecule, int) -
Method in class chemaxon.checkers.BondChecker
-
- getComponent(Molecule, int) -
Method in class chemaxon.checkers.ComponentChecker
- Gets the component from the molecule with index i.
- getComponent() -
Method in class chemaxon.marvin.plugin.gui.ParameterPanel
- Returns the parameter panel component.
- getComponent() -
Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
- Returns the parameter panel component.
- getComponent() -
Method in class chemaxon.marvin.space.ComponentElement
- Returns the component which contains this
ComponentElement.
- getComponent(int) -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the component having the given index.
- getComponent(int) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns its visualizer with the given index.
- getComponent() -
Method in class chemaxon.marvin.space.monitor.DihedralMonitor
- Returns the molecule whose atoms are monitored.
- getComponent() -
Method in class chemaxon.marvin.space.monitor.Label
- Returns the GraphicComponent of the only selected item.
- getComponent() -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Returns the GraphicComponent of the only selected item.
- getComponent(long) -
Method in class chemaxon.struc.RxnMolecule
- Gets a reactant, product or agent.
- getComponent(int, int) -
Method in class chemaxon.struc.RxnMolecule
- Gets a reactant, product or agent.
- getComponentCount(Molecule) -
Method in class chemaxon.checkers.AtomChecker
-
- getComponentCount(Molecule) -
Method in class chemaxon.checkers.BondChecker
-
- getComponentCount(Molecule) -
Method in class chemaxon.checkers.ComponentChecker
- Gets the number of the components in the molecule
- getComponentCount() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the number of components of the cell including monitors, surfaces and so on.
- getComponentCount() -
Method in class chemaxon.sss.search.MCES
- Gets the number of components in the found MCES.
- getComponentCount(int) -
Method in class chemaxon.struc.RxnMolecule
- Gets the number of reactants, products or agents.
- getComponentElement() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the previously picked but unprocessed ComponentElement or the whole
component as a ComponentElement, if no picking happened.
- getComponentElement() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the previously picked but unprocessed ComponentElement or the whole
component as a ComponentElement, if no picking happened.
- getComponentElement(MacroMoleculeComponent.MoleculeVisualizer) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the visualizer as a
ComponentElement.
- getComponentElement() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the previously picked but unprocessed
ComponentElement or the whole
component as a ComponentElement, if no picking happened.
- getComponentFlags(long) -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction component type flags from the ID.
- getComponentID(Molecule) -
Method in class chemaxon.struc.RxnMolecule
- Gets the ID of a reaction component.
- getComponentID(MolAtom) -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction component ID of an atom.
- getComponentID(MolBond) -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction component ID of a bond.
- getComponentIndex() -
Method in class chemaxon.marvin.space.CellOrComponentId
- Returns the internal index of the component or -1 if this is a cell id.
- getComponentIndex(long) -
Method in class chemaxon.struc.RxnMolecule
- Gets the reactant, product or agent index from the ID.
- getComponentIterator() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the iterator of the
GraphicComponents of the cell.
- getComponentIterator() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the Iterator of its visualizers.
- getComponentPartId() -
Method in class chemaxon.marvin.space.ComponentElement
- In case of complex components the
componentPartId identifies
a part of the component.
- getComponents() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns its visualizers.
- getComponentType(long) -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction component type from the ID.
- getComposition() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the elemental analysis, the relative percent composition of a pure
chemical substance by element (w/w%).
- getConditions() -
Method in class chemaxon.jchem.db.Exporter
- Returns the SQL WHERE statement, if specified.
- getConfig() -
Method in class chemaxon.sss.screen.StrucFPConfig
- Creates a configuration string according to the internal values.
- getConfiguration() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the current configuration elements
- getConformer(int) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns a conformer.
- getConformerCount() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the number of different conformers.
- getConformers() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns all conformers in a Molecule[] array.
- getConnectedObject(int) -
Method in class chemaxon.struc.MDocument
- Gets an object from the document or from the chemical structure of the document.
- getConnectedObjectCount() -
Method in class chemaxon.struc.MDocument
- Gets the number of objects in this document and in the chemical structure of this document.
- getConnection() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property connection.
- getConnection() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
connection.
- getConnectionHandler() -
Method in class chemaxon.descriptors.MDDBWriter
- Gets the ConnectionHandler object used to reach the database.
- getConnectionHandler() -
Method in class chemaxon.jchem.db.Exporter
- Getter for property connectionHandler.
- getConnectionHandler() -
Method in class chemaxon.jchem.db.Importer
- Getter for property connectionHandler.
- getConnectionHandler() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property connectionHandler.
- getConnections() -
Method in class chemaxon.jchem.db.Importer
- Deprecated. since 2.2 replaced by
Importer.getFieldConnections().
- getConnectivity() -
Method in class chemaxon.struc.Sgroup
- Gets S-group connectivity.
- getContext() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- Returns the evaluation context
- getContext() -
Method in class chemaxon.struc.sgroup.DataSgroup
-
- getContextFunctionNames() -
Method in class chemaxon.jep.ChemContext
- Returns context element accessor function names.
- getContextFunctionNames() -
Method in class chemaxon.jep.context.AtomContext
- Returns {"mol", "fingerprint", "atom"}.
- getContextFunctionNames() -
Method in class chemaxon.jep.context.MolContext
- Returns {"mol", "fingerprint"}.
- getContextFunctionNames() -
Method in class chemaxon.jep.context.ReactionContext
- Returns {"reactant", "product", "ratom", "patom"}.
- getContextFunctionNames() -
Method in class chemaxon.jep.context.SearchContext
- Returns {"mol", "target", "query", "fingerprint", "tfingerprint", "qfingerprint",
"m", "hit", "h", "hm", "hitmap"}.
- getContextId() -
Method in class chemaxon.struc.sgroup.DataSgroup
-
- getControl() -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Returns the control of this monitor.
- getControllableObject(String) -
Method in class chemaxon.marvin.space.GraphicCell
- Returns a component if there is any which allows itself to be controlled.
- getControllableObject(String) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns a selected component from the active cell what can be controlled
by the given tye controller.
- getControlLayout() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the controlLayout
- getControlPanel() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Initializes and returns control panel (south section)
- getCoordinateBondStyle() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the "coordinative" bond line style when both atoms are single.
- getCoordinateBondStyle() -
Method in class chemaxon.marvin.MolPrinter
- Gets the coordinate bond line style when both atoms are single.
- getCoordinateBondStyleAtMulticenter() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the "coordinative" bond line style when one of the atoms is multicenter.
- getCoordinateBondStyleAtMulticenter() -
Method in class chemaxon.marvin.MolPrinter
- Gets the coordinate bond line style.
- getCoordinates(float[]) -
Method in class chemaxon.marvin.space.ComponentElement
- Returns the world coordinates of the
ComponentElement.
- getCoordinates(float[]) -
Method in class chemaxon.marvin.space.GraphicComponent
- Gets the coordinates of the previously picked but not yet processed part
if there is any in the given preallocated array.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.GraphicComponent
- Gets the coordinates of the given ComponentElement in the given preallocated array.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Sets the coordinates of the given ComponentElement in the given array.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Sets the coordinates of the given element in the given preallocated array.
- getCoordinates(float[]) -
Method in class chemaxon.marvin.space.monitor.AngleMonitor
- Returns the centroid of the selected elements.
- getCoordinates(float[]) -
Method in class chemaxon.marvin.space.monitor.DihedralMonitor
- Returns the centroid of the second and third selected elements.
- getCoordinates(float[]) -
Method in class chemaxon.marvin.space.monitor.Label
- Returns the coordinates of the selected item as a GeomCalc vector.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.monitor.Label
- Returns the coordinates of the selected item as a GeomCalc vector.
- getCoordinates(float[]) -
Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
- Returns the centroid of the selected elements.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
- Returns the centroid of the selected elements.
- getCoordinates(float[]) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Returns the coordinates of the selected item.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Returns the coordinates of the selected item.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.PharmacophoreArrow
- Gets the position of the component.
- getCoordinates(ComponentElement, float[]) -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Gets the position of the pharmacophore point.
- getCoordinatesOfAligned() -
Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getCoordinatesOfReference() -
Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getCopyAsFormat() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the selected format from the Copy As dialog.
- getCopyAsTransferableNames() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns the format's names that are available in the current environment
as transfer types for the Copy As dialog.
- getCorrectionLibraryIds() -
Static method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the id's of available pKa correction libraries.
- getCount() -
Method in class chemaxon.marvin.plugin.PluginFactory
- Returns the number of plugin records.
- getCounter() -
Method in class chemaxon.descriptors.GenerateMD
- Gets the number of molecules processed since
init() was
called.
- getCovalentRadius(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Covalent radius of the element in Angstroms.
- getCovalentRadius(int, int) -
Static method in class chemaxon.struc.PeriodicSystem
- Covalent radius of the element in specific bond type in Angstroms.
- getCrossingAtoms(MolBond[]) -
Method in class chemaxon.struc.Sgroup
- Gets the atoms that have crossing bonds.
- getCrossingAtoms(MolBond[]) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the atoms that have crossing bonds.
- getCrossingBonds(MolBond[], DPoint3, DPoint3) -
Static method in class chemaxon.marvin.util.MoleculeUtil
- Searches for the bonds, that crosses a segment.
- getCSSR() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the Complete Set of Smallest Ring atom indexes array.
- getCtab() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the connection table.
- getCtab() -
Method in class chemaxon.struc.RgMolecule
- Gets the connection table of the root structure.
- getCtab() -
Method in class chemaxon.struc.RxnMolecule
- Gets the connection table for the graph union.
- getCTAtom1() -
Method in class chemaxon.struc.MolBond
- Gets the first atom for cis/trans stereo calculation.
- getCTAtom4() -
Method in class chemaxon.struc.MolBond
- Gets the fourth atom for cis/trans stereo calculation.
- getCurrent() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getCurrent() -
Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getCurrent() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
- Deprecated.
- getCurrentCheckerName() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getCurrentCheckerName() -
Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getCurrentCheckerName() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
- Deprecated.
- getCurrentDefaultFontMetrics() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the current default FontMetrics.
- getCurrentEvaluatorFunction() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Gets the index of the current the evaluator function
- getCurrentForeground() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the current color.
- getCurrentHeight() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the current height of the text.
- getCurrentId() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property currentId.
- getCurrentLevelLength() -
Method in class chemaxon.metabolizer.Metabolizer
- Rerturns currentLevelLength
- getCurrentMetricIndex() -
Method in class chemaxon.descriptors.MDParameters
-
- getCurrentScriptCount(int) -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the number of subscripts or superscripts on the last normal
character.
- getCurrentSubLevel() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the current subscript/superscript level.
- getCurrentTextAttributes(int) -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the common attributes of the selected text or attributes for the
next character to be typed.
- getCurrentWidth() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the current width of the text.
- getCursorColumn() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the cursor's column number.
- getCursorPos() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the cursor position.
- getCursorRow() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the cursor's row number.
- getCusromToolBar(JTextPane, String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Returns a custom toolbar for textPane instance
NOTE: textPane have to be created with this factory
- getCustomFuzzyIncrements(int, int) -
Method in class chemaxon.descriptors.PFParameters
- Gets fuzzy increments for the fuzzy smoothing with a user-defined
custom distribution (fuzzy smoothing vector).
- getCutBond(int, int) -
Method in class chemaxon.fragmenter.Fragmenter
- Return the cut-reaction index if
i - j is a cut-bond,
-1 otherwise.
- getCyclomaticNumber() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the smallest number of graph edges which must be removed such
that no circuit remains.
- getDarkestMolId() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the id of that molecule which had the minimum number of non-zero
cells among all descriptors generated since the initialization of the
generator object.
- getData() -
Method in class chemaxon.descriptors.MDParameters
- Gets the byte array which is used for conversions between internal and
external data formats.
- getData(Molecule, int) -
Static method in class chemaxon.fragmenter.Fragmenter
- Returns fragment data from atom alias.
- getData() -
Method in class chemaxon.sss.search.MarkushFeature
- Returns the feature data.
- getData() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the data value to be set.
- getData() -
Method in class chemaxon.util.UploadThread
- Returns the saved data in bytes.
- getDataFromClipboard(DataFlavor) -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Returns the Molecule from the
Transferable object.
- getDataFromClipboardOLE() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getDataLine(int) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets a line of data.
- getDataLineCount() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the number of data lines.
- getDataToClipboard(DataFlavor) -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Returns the clipboard representation of the given
Molecule.
- getDebug() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the debugging level.
- getDecForm() -
Method in class chemaxon.descriptors.MDParameters
- Gets the formatter object that is capable of formatting fractions with
given precision.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.BCUT
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.CustomDescriptor
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.ECFP
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.ScalarDescriptor
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDissimilarityMetricThresholds() -
Method in class chemaxon.descriptors.ShapeDescriptor
- Gets the default dissimilarity threshold values for all dissimilarity
metrics defined.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.BCUTParameters
- Gets the default XML configuration string.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.CDParameters
- Gets the XML configuration string.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.CFParameters
- Gets the default XML configuration string.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.ECFPParameters
- Get the default XML configuration string.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.MDParameters
- Gets the default XML configuration string.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.PFParameters
- Gets the default XML configuration string.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.RFParameters
- Get the default XML configuration string.
- getDefaultDocumentFrame() -
Method in class chemaxon.descriptors.ShapeParameters
- Get the default XML configuration string.
- getDefaultFileName() -
Method in class chemaxon.util.UploadThread
- Returns the original name of saved file.
- getDefaultFont() -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the default font.
- getDefaultHelpText() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the default help text
- getDefaultIcon() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the default icon of the element
- getDefaultMetricIndex() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets the index of the default metric.
- getDefaultMetricIndex() -
Method in class chemaxon.descriptors.ECFP
- Gets the index of the default metric.
- getDefaultMetricIndex() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the index of the default metric.
- getDefaultMetricIndex() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the index of the default metric.
- getDefaultMyTemplatesValue() -
Static method in class chemaxon.marvin.common.UserSettings
- Deprecated. since 5.4 use
TemplateHandler.DEFAULT_MY_TEMPLATES_VALUE instead.
- getDefaultOutputTransferFormatIds() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. since 5.3 not needed anymore won't be supported after 5.4
- getDefaultProperty(String) -
Method in class chemaxon.marvin.common.UserSettings
- Gets the value of the given key in the default configuration or null if
the key does not exist.
- getDefaultSaveFormat() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the default molecule format in the "Save As" dialog.
- getDefaultScale() -
Static method in class chemaxon.marvin.beans.MSketchPane
- Returns the default scale factor which is equivalent
to 100% magnification.
- getDefaultServiceDescriptorEditorProvider() -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the default
ServiceDescriptorEditorProvider instance
- getDefaultServiceDescriptorReader() -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the default
ServiceDescriptorReader instance
- getDefaultServiceDescriptorWriter() -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the default
ServiceDescriptorWriter instance
- getDefaultServiceDialogProvider() -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the default
ServiceDialogProvider instance
- getDefaultSize() -
Method in class chemaxon.marvin.view.swing.TableSupport
- Gets the default size of an MViewPane containing the generated table.
- getDefaultStandardizerConfiguration() -
Static method in class chemaxon.descriptors.ECFPParameters
- Gets the default configuration of the standardizer.
- getDefaultStandardizerConfiguration() -
Static method in class chemaxon.descriptors.MDParameters
- Gets the default configuration of the standardizer.
- getDefaultStandardizerConfiguration() -
Static method in class chemaxon.descriptors.PFParameters
- Gets the default configuration of the standardizer.
- getDefaultStandardizerConfiguration() -
Static method in class chemaxon.descriptors.ShapeParameters
- Gets the default configuration of the standardizer.
- getDefaultThreshold(int) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets a metric dependent default threshold value.
- getDefaultThreshold(int) -
Method in class chemaxon.descriptors.ECFP
- Gets a metric dependent default threshold value.
- getDefaultThreshold(int) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets a metric dependent default threshold value.
- getDefaultThreshold(int) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets a metric dependent default threshold value.
- getDefaultThreshold(int) -
Method in class chemaxon.descriptors.ScalarDescriptor
- Gets a metric dependent default threshold value.
- getDefaultThreshold(int) -
Method in class chemaxon.descriptors.ShapeDescriptor
- Gets a metric dependent default threshold value.
- getDefaultTransferFormatId() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getDelimiter() -
Method in class chemaxon.jchem.db.Exporter
- Gets the field delimiter character between columns
for JTF format output.
- getDensityCounts() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the array of bit density.
- getDescent(Graphics, FontMetrics) -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the descent of this portion.
- getDescription() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getDescription() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getDescription() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getDescription() -
Method in interface chemaxon.checkers.StructureChecker
- Deprecated. This method isn't needed anymore and will be removed in 6.0
- getDescription() -
Method in class chemaxon.fixers.AbstractStructureFixer
-
- getDescription() -
Method in interface chemaxon.fixers.StructureFixer
-
- getDescription() -
Method in class chemaxon.formats.MFileFormat
- Gets the format description.
- getDescription(String, String) -
Static method in class chemaxon.marvin.common.UserSettings
- Gets the human readable description of a property.
- getDescription() -
Method in class chemaxon.marvin.space.ComponentElement
- Returns the brief description of the
ComponentElement,
for example type of the atom.
- getDescription() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returs the short description of the component or of the previously picked
but not yet processed part if there is any or the description of the whole component.
- getDescription(ComponentElement) -
Method in class chemaxon.marvin.space.GraphicComponent
- Returs the short description of the given part of the component.
- getDescription(ComponentElement) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the short description of the given element.
- getDescription(ComponentElement) -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getDescription(ComponentElement) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returs the short description of the given part of the component.
- getDescription() -
Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
- Returns the measurement as a description.
- getDescription(ComponentElement) -
Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
- Returns the measurement as a description.
- getDescription() -
Method in class chemaxon.marvin.space.PharmacophoreArrow
- Returns a descriptive text.
- getDescription() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Returns textual description.
- getDescription() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Gets the description.
- getDescriptor() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getDescriptor() -
Method in interface chemaxon.checkers.StructureChecker
- Returns a
StructureCheckerDescriptor instance which represents the user interface
related informations of the checker
- getDescriptor(int) -
Method in class chemaxon.descriptors.MDSet
- Gets a specified component of the
MDSet.
- getDescriptor() -
Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
- Returns the
ServiceDescriptor represented by editor state or null
if the editor is in not valid state
- getDescriptorConfig() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the screening configuration string used for descriptor dissimilarity search
- getDescriptorLongName(String) -
Static method in class chemaxon.descriptors.DescriptorGenerator
- Returns the long name for the given molecular descriptor type.
- getDescriptorName() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the name of descriptor used for descriptor similarity search
- getDescriptorTypeName(String) -
Static method in class chemaxon.descriptors.MDParameters
- Takes the descriptor type name from the root element of the XML configuration.
- getDescriptorTypes() -
Static method in class chemaxon.descriptors.DescriptorGenerator
- Returns the list of the built-in molecular descripor types.
- getDescriptorURI() -
Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
- Gets the URI of the JSON RPC descriptor file
- getDescrType() -
Method in class chemaxon.descriptors.CDParameters
- Gets the type of the descriptor.
- getDesiredLength(int, int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the ideal bond length in Angstroms.
- getDesiredLength(MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the ideal bond length in Angstroms.
- getDiagnosticMessage(int) -
Method in class chemaxon.marvin.modules.AutoMapper
- Returns a short text message that discribes the outcome of the last search.
- getDialog(Component, ServiceDescriptor) -
Method in interface chemaxon.marvin.services.ServiceDialogProvider
- Returns dialog with argument editor and result view
- getDiameter() -
Method in class chemaxon.descriptors.ECFPFeature
- Gets the diameter of the represented substructure.
- getDiameter() -
Method in class chemaxon.descriptors.ECFPParameters
- Gets the preset diameter parameter.
- getDihedral(int, int, int, int) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the dihedral of 4 atoms.
- getDihedral(int[]) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the dihedral of 4 atoms.
- getDim() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the dimension.
- getDimensions() -
Method in class chemaxon.clustering.Common
- Gets the number of dimensions.
- getDirectory() -
Method in class chemaxon.marvin.beans.MarvinPane
- Sets the working directory.
- getDisabledGroupTypes() -
Method in class chemaxon.marvin.beans.MSketchPane
-
- getDisabledIcon() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the disabled icon of the element (or null if not set)
- getDisplay(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets a display object, loads it if needed.
- getDisplay() -
Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getDisplayedChars() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the number of characters to be displayed(1...999 or 0 for all)
- getDisplayedLines() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the number of lines to be displayed (0: show all)
- getDisplayMolecule() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the molecule object to be used for GUI display.
- getDisplayMolecule() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the molecule object to be used for GUI display.
- getDisplayMolecule() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the molecule object to be used for GUI display.
- getDisplayQuality() -
Method in class chemaxon.marvin.MolPrinter
- Gets the display quality.
- getDispopts() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets display options.
- getDispopts() -
Method in class chemaxon.marvin.MolPrinter
- Returns the actual display options.
- getDispoptsExt() -
Method in class chemaxon.marvin.MolPrinter
- Returns the actual extended display options.
- getDispQuality() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the display quality.
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.BCUT
- Calculates the dissimilarity ratio between two
BCUT
objects using the current default metric.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.BCUT
- Calculates the dissimilarity between two
BCUT
objects using the specified metric, apart from that it is the same as
getDissimilarity( final MolecularDescriptor other ).
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the dissimilarity between two chemical fingerprints using
the default distance measure.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the dissimilarity between two chemical fingerprints using
the specified distance metric.
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.CustomDescriptor
- Calculates the dissimilarity between two pharmacophore fingerprints using
the default distance measure.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.CustomDescriptor
- Calculates the dissimilarity between two descriptors using
the specified parametrized dissimilarity metric.
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.ECFP
- Calculates the dissimilarity ratio between two
ECFP
objects using the current default metric.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.ECFP
- Calculates the dissimilarity between two
ECFP
objects using the specified metric, apart from that it is the same as
getDissimilarity(final MolecularDescriptor other).
- getDissimilarity(MDSet) -
Method in class chemaxon.descriptors.MDSet
- Calculates the dissimilarity between two
MDSet objects.
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Calculates the dissimilarity ratio between two
MolecularDescriptor
objects using the default metric.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Calculates the dissimilarity between two
MolecularDescriptor
objects using the specified metric, apart from that it is the same as
getDissimilarity( final MolecularDescriptor other ).
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the dissimilarity between two pharmacophore fingerprints using
the default distance measure.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the dissimilarity between two pharmacophore fingerprints using
the specified parametrized distance metric.
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Calculates the dissimilarity between two reaction fingerprints using
the default distance measure.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Calculates the dissimilarity between two reaction fingerprints using
the specified distance metric.
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.ScalarDescriptor
- Calculates the dissimilarity between two scalar descriptor using the
default metrics
In the present implementation it is always the absolute difference
between them.
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.ScalarDescriptor
- Calculates the dissimilarity between two scalar descriptor using the
specified metric.
- getDissimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.ShapeDescriptor
-
- getDissimilarity(MolecularDescriptor, int) -
Method in class chemaxon.descriptors.ShapeDescriptor
-
- getDissimilarity(T) -
Method in class chemaxon.descriptors.SimilarityCalculator
- Gets the dissimilarity value according to previously defined metric and its parameters.
- getDissimilarity(int) -
Method in class chemaxon.jchem.db.JChemSearch
- Indexed getter for property dissimilarity.
- getDissimilarity() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for dissimilarity results.
- getDissimilarityCoeff(int, int, int) -
Method in class chemaxon.descriptors.MDSimilarity
- Retrieves query dissimilarity coefficients (one at a time) of the last
compareQueries() or compare() method called.
- getDissimilarityCoeffs(int, int) -
Method in class chemaxon.descriptors.MDSimilarity
- Retrieves query dissimilarity coefficients with all metrics and one descriptor of
the last
compareQueries() or compare() method
called.
- getDissimilarityCoeffs(int) -
Method in class chemaxon.descriptors.MDSimilarity
- Retrieves query dissimilarity coefficients with all metrics and one query of
the last
compareQueries() or compare() method
called.
- getDissimilarityMetric() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the property dissimilarity metric property.
- getDissimilarityMetricIndex(String) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the internal index of the given metric.
- getDissimilarityMetricParameters() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the parameters of the dissimilarity metric.
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.BCUT
- Gets the dissimilarity metric names introduced for this class of
MolecularDescriptor.
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets the dissimilarity metric names
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.CustomDescriptor
- Gets the dissimilarity metric names.
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.ECFP
- Gets the dissimilarity metric names introduced for this class of
MolecularDescriptor.
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the dissimilarity metric names in an array.
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the dissimilarity metric names.
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the dissimilarity metric names
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.ScalarDescriptor
- Gets the dissimilarity metric names
- getDissimilarityMetrics() -
Method in class chemaxon.descriptors.ShapeDescriptor
-
- getDissimilarityMetrics(ConnectionHandler, String) -
Static method in class chemaxon.jchem.db.JChemSearch
- Returns the available dissimilarity metrics for the given table.
- getDissimilarityMetricsParamDefault() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the dissimilarity metric parameter names -> no parameters.
- getDissimilarityMetricsParamHelp() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the dissimilarity metric parameter names -> no parameters.
- getDissimilarityMetricsParamNames() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the dissimilarity metric parameter names -> no parameters.
- getDissimilarityMetricsParamNum() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the dissimilarity metric parameter number -> no parameters.
- getDissimilarityMetricsParamRanges() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the dissimilarity metric parameter ranges -> no parameters.
- getDissimilarityThreshold() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the dissimilarity threshold.
- getDistance(int, int) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the distance of 2 atoms.
- getDistance(int[]) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the distance of 2 atoms.
- getDistanceCount(int, int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Counts the given value in a row of the distance matrix.
- getDistanceDegree(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the distance degree of an atom, which is the sum of the
corresponding row values in the distance matrix.
- getDoc(int, String) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the specified document.
- getDoc(int, String, MProgressMonitor) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the specified document.
- getDocLabel(int, MDocument) -
Method in class chemaxon.marvin.io.MDocSource
- Returns the display label for the given document and document index.
- getDocLabel(int, MDocument) -
Method in class chemaxon.marvin.view.MDocStorage
- Returns the display label for the given document and document index.
- getDocSource() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the document source.
- getDocSourcePosition() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the current position in the input.
- getDocStorage() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the sparse dynamic document storage.
- getDocStorage() -
Method in class chemaxon.marvin.view.swing.TableSupport
- Gets the sparse dynamic document storage.
- getDocument() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the document.
- getDocument(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the nth document.
- getDocument(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns encapsulating document, creates it if needed.
- getDocument() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the document object.
- getDocumentForChild(MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the parent document for a child molecule graph.
- getDocumentForChild(MoleculeGraph) -
Method in class chemaxon.struc.RgMolecule
- Gets the parent document for a child graph.
- getDocuments() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the array of documents.
- getDominantTautomerDistribution(int) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the distribution of the dominant tautomer.
- getDonorAtomCount() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the overall donor atom count (without multiplicity) in the molecule.
- getDonorCount(int) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the atomic donor count corresponding to the specified atom index.
- getDonorCount() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the overall donor count (with multiplicity) in the molecule.
- getDotDir() -
Static method in class chemaxon.util.DotfileUtil
- Gets the directory of the configuration files.
- getDotDirName() -
Static method in class chemaxon.util.DotfileUtil
- Gets the subdirectory name of the configuration files.
- getDotDisconnectedFormula() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the dot-disconnected molecular formula of a multifragment
molecule.
- getDotDisconnectedIsotopeFormula() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the dot-disconnected isotope formula of a multifragment
molecule.
- getDotDisconnectedIsotopeFormula(boolean) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the dot-disconnected isotope formula of a multifragment
molecule.
- getDotFile(String) -
Static method in class chemaxon.util.DotfileUtil
- Gets a configuration file with the specified relative path.
- getDotFileWithEnsuredPath(String) -
Static method in class chemaxon.util.DotfileUtil
-
- getDoubleArray() -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Gets the integer value.
- getDoubleBondStereoMatchingMode() -
Method in class chemaxon.sss.search.SearchOptions
- Get the double bond stereo matching mode.
- getDoublePrecision() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the precision.
- getDownWedge() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the wedge bond display convention.
- getDownWedge() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the wedge bond display convention.
- getDownWedge() -
Method in class chemaxon.marvin.MolPrinter
- Gets the down wedge orientation.
- getDraggedObject() -
Method in class chemaxon.struc.MDocument
- Gets the dragged object
- getDrawProperties() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the set draw properties of the component.
- getDrawProperty(String) -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the value of a draw property.
- getDrawProperty(String) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the draw property of the scene or null if the property is not defined.
- getDrawProperty(String) -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getDrawType() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the drawing type of the molecular surface.
- getDrawType() -
Method in class chemaxon.marvin.space.PharmacophoreArrow
- Returns the name of the drawing type.
- getDrawType() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Returns the name of the drawing type.
- getDrawType() -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the actual drawing type.
- getDreidingEnergy() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the energy of the conformer in kcal/mol.
- getDriver() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
driver.
- getDuplicateIDs() -
Method in class chemaxon.jchem.db.Importer
- Returns the IDs (cd_id column in database table) of duplicate structures.
- getDuplicates() -
Method in class chemaxon.jchem.db.Importer
- Returns the number of molecules that were not imported, because
they are duplicates.
- getDx() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the x shift.
- getDy() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the y shift.
- getEccentricity(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the eccentricity of an atom, which is the greatest value in
the corresponding row of the distance matrix.
- getEdge(int) -
Method in class chemaxon.struc.MolAtom
- Deprecated. As of Marvin 5.3, replaced by
MolAtom.getBond(int).
- getEdge(int) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.getBond(int).
- getEdgeArray() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.getBondArray().
- getEdgeCount() -
Method in class chemaxon.struc.MolAtom
- Deprecated. As of Marvin 5.3, replaced by
MolAtom.getBondCount().
- getEdgeCount() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.getBondCount().
- getEdgeTo(MolAtom) -
Method in class chemaxon.struc.MolAtom
- Deprecated. As of Marvin 5.3, replaced by
MolAtom.getBondTo(MolAtom).
- getEdgeVector() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
Arrays.asList(getAtomArray()).
- getEditable() -
Method in class chemaxon.marvin.beans.MViewEditor
- Returns the mode that determines if the structure is editable.
- getEditable() -
Method in class chemaxon.marvin.beans.MViewPane
- Returns the mode that determines if the structure is editable.
- getEditor() -
Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
- Returns the editor component for the
ServiceDescriptor
- getEditor(Class<T>) -
Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider
- Returns a
ServiceDescriptorEditor instance for specified ServiceDescriptor class
- getEditorClassName() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getEditorClassName() -
Method in interface chemaxon.checkers.StructureChecker
- Deprecated. This method isn't needed anymore and will be removed in 6.0
- getEditorComponent(ConfigElement) -
Method in interface chemaxon.alchemist.configbuilder.ConfigElementEditor
- Sets an initial
value for the editor.
- getEditorComponent() -
Method in class chemaxon.marvin.beans.MViewEditor
- Returns the editor component.
- getEditorValue() -
Method in interface chemaxon.alchemist.configbuilder.ConfigElementEditor
- Returns the
ConfigElement contained in the editor
- getEigenVector() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Deprecated. Use
HuckelAnalysisPlugin.getHMOEigenVector()
- getElapsedTime() -
Method in class chemaxon.clustering.Common
- Gets the elapsed time.
- getElectronDensity(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the electron density of an atom
calculated with HMO,
Double.NaN for no value.
- getElectronProp() -
Method in class chemaxon.struc.MolAtom
- Returns the number of lone pairs on this atom.
- getElectrophilicEnergy(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the electrophilic energy (localization energy L+) of an atom,
Double.NaN for no value.
- getElectrophilicOrder(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Deprecated. Use
HuckelAnalysisPlugin.getHMOElectrophilicOrder(int)
- getElementCount() -
Static method in class chemaxon.struc.PeriodicSystem
- Number of elements in the periodic system
- getElementIndex() -
Method in class chemaxon.marvin.space.ComponentElement
- Returns the internal index of the
ComponentElement
in the GraphicComponent.
- getElementPropertyChangeSupport() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the elementPropertyChangeSupport
- getElementType() -
Method in class chemaxon.marvin.space.ComponentElement
- Returns the type of the
ComponentElement.
- getEmptyStructures() -
Method in class chemaxon.jchem.db.Importer
- Returns the number of molecules that were not imported, because
they are empty strucures.
- getEmptyStructuresAllowed() -
Method in class chemaxon.jchem.db.Importer
- Gets whether empty structures are allowed.
- getEnantiomer(MoleculeGraph) -
Static method in class chemaxon.calculations.stereo.Stereochemistry
- Get the enantiomer pair of the given molecule
- getEncapsulatedReader() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Gets the encapsulated record reader if it exists.
- getEncapsulatedReader() -
Method in interface chemaxon.marvin.io.MRecordReader
- Gets the encapsulated record reader if it exists.
- getEnclosingCube() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the cube that encloses the atoms of molecule graph.
- getEncoding() -
Method in class chemaxon.marvin.io.MolExportModule
- Gets the output encoding.
- getEncoding() -
Method in class chemaxon.marvin.io.MRecord
- Gets the encoding.
- getEncoding() -
Method in class chemaxon.marvin.io.PositionedInputStream
- Gets the encoding.
- getEncodingFromOptions(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the encoding that was explicitly given as an import option.
- getEndDx() -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the x shift at the end.
- getEndLineCount() -
Method in class chemaxon.marvin.io.MRecord
- Gets the line number at the ending point.
- getEndPos() -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the position of the last character + 1.
- getEndPosition() -
Method in class chemaxon.marvin.io.MRecord
- Gets the end position in the input file.
- getEndPosition() -
Method in class chemaxon.struc.MDocument
- Gets the end position of this document in the input file.
- getEndPosition() -
Method in class chemaxon.struc.Molecule
- Gets the end position of this molecule in the input file.
- getEnergy() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the energy of the lowest energy conformer in kcal/mol.
- getEnergy(int) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the energy of the i-th conformer in kcal/mol.
- getEnumCodeNeeded() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Tests whether unique Markush enumeration code
should be generated
- getEol() -
Method in class chemaxon.jchem.db.Exporter
- Gets the End Of Line character(s).
- getError() -
Method in class chemaxon.util.ErrorHandler
- Getter for property error.
- getError() -
Method in class chemaxon.util.MolAligner
- Get the error for the best alignment
- getError() -
Method in class chemaxon.util.UploadThread
- For retrieving stored exceptions.
- getErrorCause() -
Method in class chemaxon.jchem.db.Importer
- Retrieves Throwable caught in
Importer.run() method.
- getErrorCode() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getErrorCode() -
Method in class chemaxon.checkers.ExternalStructureChecker
-
- getErrorCode() -
Method in interface chemaxon.checkers.result.ExternalStructureCheckerResult
- This function returns a
String which identifies the problems thus this
must be unique for each class that implements this interface
- getErrorCode() -
Method in interface chemaxon.checkers.StructureChecker
- Returns the
String represented error code of the checker (this error code
should be used for external implementation support instead of StructureChecker.getErrorType())
- getErrorComponent() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns a component with the appropriate error message.
- getErrorDescription(int) -
Method in class chemaxon.checkers.AbstractStructureChecker
- Generate the error description depends on erroCount
- getErrorLevel() -
Method in exception chemaxon.marvin.plugin.PluginException
- Returns the error level.
- getErrorMessage() -
Method in class chemaxon.jchem.db.Importer
- If error occures this function returns the error message.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the calculation error information message if
ChargePlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the calculation error information message if
HBDAPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the calculation error information message if
HuckelAnalysisPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Returns the calculation error information message if
IonChargePlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the calculation error information message if
IsoelectricPointPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the calculation error information message if
logDPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the calculation error information message if
logPPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the calculation error information message if
MSAPlugin.run()
returned false (calculation error).
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the calculation error information message if
OrbitalElectronegativityPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the calculation error information message if
pKaPlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the calculation error information message if
PolarizabilityPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the calculation error information message if
RefractivityPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the calculation error information message
or the empty string if there is no error.
- getErrorMessage() -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the calculation error information message if
TPSAPlugin.run()
returned false (calculation error): hydrogen valence error.
- getErrorMessage() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the calculation error information message if
CalculatorPlugin.run()
returned false (calculation error).
- getErrorMessage() -
Method in class chemaxon.util.ErrorHandler
- Getter for property errorMessage.
- getErrorType() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getErrorType() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getErrorType() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getErrorType() -
Method in interface chemaxon.checkers.StructureChecker
-
- getErrorTypeDefaultFixerMap() -
Method in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
-
- getErrorTypeDefaultFixerMap() -
Method in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
-
- getEstimatedTotalCharacters() -
Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
- Return an estimation of the total number of characters in the document.
- getEuclidean(BCUT) -
Method in class chemaxon.descriptors.BCUT
- Calculates the Euclidean distance.
- getEuclidean(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the Euclidean distance.
- getEuclidean(CustomDescriptor) -
Method in class chemaxon.descriptors.CustomDescriptor
- Calculates the Euclidean distance.
- getEuclidean(ECFP) -
Method in class chemaxon.descriptors.ECFP
- Calculates the Euclidean distance.
- getEuclidean(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the Euclidean distance.
- getEuler() -
Method in class chemaxon.struc.CTransform3D
- Gets the Euler angles from the rotation transformation.
- getEvaluatorFunctionIndex(String) -
Method in class chemaxon.descriptors.MDHitEvaluator
- Gets the index of the evaluator function from its name
- getEvaluatorFunctionName(int) -
Method in class chemaxon.descriptors.MDHitEvaluator
- Gets the name of the evaluator function from its index
- getEventHandler() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the event handler of the scene.
- getEventHandler() -
Method in class chemaxon.marvin.space.MSpaceEasy
- Returns the actual event handler of MarvinSpace.
- getExactMass() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the weight of the MS molecule ion using the mass of the most
frequent natural isotope for element atoms.
- getExactMass() -
Method in class chemaxon.struc.MoleculeGraph
- Calculates the molecular exact weight of the molecule.
- getExactSpecialAtomMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get the identifiers of those special atoms
that should match exactly during structure comparison.
- getException() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property exception.
- getException() -
Method in exception chemaxon.marvin.plugin.PluginException
- Returns the wrapped exception.
- getException() -
Method in class chemaxon.util.ErrorHandler
- Getter for property exception.
- getExhaustiveModeLimit() -
Method in class chemaxon.sss.search.SearchOptions
- Upon reaching this number of steps, the search switches to
exhaustive mode from fast mode.
- getExplicitH() -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. since 5.4 returns false. will be unsupported in 5.5
- getExplicitHcount() -
Method in class chemaxon.struc.MolAtom
- Gets number of hydrogen connections.
- getExplicitHcount() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the total number of explicit hydrogens attached to the molecule.
- getExplicitHcount(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the number of explicit hydrogen atom neighbors of the given atom.
- getExplicitLonePairCount(int) -
Method in class chemaxon.struc.MoleculeGraph
-
- getExporter() -
Method in class chemaxon.metabolizer.MetabolizerTemporaryFileStorage
-
- getExporter() -
Method in class chemaxon.metabolizer.MetabolizerTemporaryMemoryStorage
-
- getExporter() -
Method in interface chemaxon.metabolizer.MetabolizerTemporaryStorage
- Returns MetabolizerExporter instance for metabolites
- getExpression() -
Method in class chemaxon.marvin.services.DynamicArgument
- Returns the expression used for evaluations
- getExpTimeString() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns text for displaying the expected remaining time.
- getExtensions() -
Method in class chemaxon.formats.MFileFormat
- Gets the extension list.
- getExternalConnections(MolAtom) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the number of bonds of a specified atom where the neighbor doesn't belong to the S-group.
- getExtraLabel() -
Method in class chemaxon.struc.MolAtom
- Gets the label string (also called atom value):
"result" or "result1|result2".
- getExtraLabelColor() -
Method in class chemaxon.struc.MolAtom
- Gets the extra label color(s):
lower 32 bits and upper 32 bits as
(alpha<<24 + red<<16 + green<<8 + blue).
- getExtraLabelColor(int) -
Method in class chemaxon.struc.MolAtom
- Gets the extra label color:
(alpha<<24 + red<<16 + green<<8 + blue).
- getExtraLabelColor(long, int) -
Static method in class chemaxon.struc.MolAtom
- Gets extra label color from composed color value.
- getExtraLabelSetColorMode(int) -
Method in class chemaxon.struc.MDocument
- Gets the coloring mode of extra label set sequences.
- getExtraLabelSetFont(int) -
Method in class chemaxon.struc.MDocument
-
- getExtraLabelSetRGBs(int) -
Method in class chemaxon.struc.MDocument
-
- getExtraLabelSetSeq() -
Method in class chemaxon.struc.MolAtom
-
- getExtraLabelSetSize() -
Method in class chemaxon.struc.MDocument
-
- getFamily() -
Method in class chemaxon.struc.graphics.MFont
- Gets the font family name.
- getFarClip() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the z coordinate of the farther clipping plane
which is computed considering all components.
- getFavoritesComboBox() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates and returns the favorites combo instance
- getFeatureCount() -
Method in class chemaxon.descriptors.ECFP
- Deprecated. As of JChem 5.4.1, replaced by
ECFP.getIdentiferCount().
- getFeatureCount() -
Method in class chemaxon.pharmacophore.PMap
- Returns the number of features.
- getFeatureCount(int) -
Method in class chemaxon.pharmacophore.PMap
- Returns the number of features corresponding to the given atom index.
- getFeatureCoverageTable() -
Method in class chemaxon.sss.search.MarkushTagger
- Returns the feature coverage table.
- getFeatures(int) -
Method in class chemaxon.pharmacophore.PMap
- Returns the feature indices corresponding to the given atom index.
- getFeaturesFromBitPosition(int) -
Method in class chemaxon.descriptors.ECFPFeatureLookup
- Returns the substructural features represented by the given bit position.
- getFeaturesFromIdentifier(int) -
Method in class chemaxon.descriptors.ECFPFeatureLookup
- Returns the substructural features represented by the given integer identifier.
- getFeatureTable() -
Method in class chemaxon.sss.search.MarkushTagger
- Returns the Markush feature table of the Markush structure.
- getFID() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Not used. Returns
null.
- getFieldAccessor() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the field accessor.
- getFieldConnections() -
Method in class chemaxon.jchem.db.Importer
- Returns the specified table field - file field pairs.
- getFieldFont(String) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the font of a named field in a table.
- getFieldFontSize() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the field font size.
- getFieldList() -
Method in class chemaxon.jchem.db.Exporter
- Returns the specified list of fields.
- getFieldName() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the data field name.
- getFieldNames() -
Method in class chemaxon.jchem.db.Importer
- Returns field names in an SDfile.
- getFieldNames(InputStream, int) -
Static method in class chemaxon.jchem.db.Importer
- Returns field names in an SDfile.
- getFieldNames(ConnectionHandler, String, ArrayList) -
Static method in class chemaxon.util.DatabaseTools
- Returns field names in a table.
- getFields(int, Molecule, String[], MProp[]) -
Method in class chemaxon.marvin.io.MFieldAccessor
- Extracts properties.
- getFieldsShown() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Are SDfile fields shown in table?
- getFieldType() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the field type.
- getFieldTypes(ConnectionHandler, String) -
Static method in class chemaxon.util.DatabaseTools
- Returns field types in a table.
- getFile() -
Method in class chemaxon.formats.MolImporter
- Gets the file object for the input.
- getFile() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the current molecule file.
- getFile() -
Method in class chemaxon.util.UploadThread
- Returns the file object.
- getFileContent() -
Method in class chemaxon.util.UploadThread
- Returns the file content, if the selected file haven't been saved on
the server side.
- getFileExtensionLC(File) -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the file extension in lower case.
- getFileExtensionLC(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the file extension in lower case.
- getFileName() -
Method in class chemaxon.formats.MolImporter
- Gets the name of the input file
- getFileName() -
Method in class chemaxon.util.UploadThread
- Returns the name of saved file.
- getFilePointer() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Get the file pointer.
- getFilePointer() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the current position in the input file.
- getFilePointer() -
Method in interface chemaxon.marvin.io.MRecordReader
- Gets the current position in the input file.
- getFilePointer() -
Method in class chemaxon.marvin.io.PositionedInputStream
- Get the file pointer.
- getFileSize() -
Method in class chemaxon.util.UploadThread
- Returns the size of saved file.
- getFilter() -
Method in class chemaxon.sss.search.MolSearch
- Returns the filtering expression.
- getFilterQuery() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the filter query property.
- getFinalCause() -
Method in exception chemaxon.formats.MolFormatException
- Gets the final cause of the exception.
- getFingerprint() -
Method in class chemaxon.jep.context.MolContext
- Returns the input molecule fingerprint.
- getFingerprint(Object) -
Method in class chemaxon.jep.context.MolContext
- Returns the input molecule fingerprint if argument is the input molecule,
null otherwise.
- getFingerprint(Molecule) -
Method in interface chemaxon.jep.FingerprintGenerator
- Returns the fingerprint of the structure.
- getFingerprintInBytes(int, int, int) -
Method in class chemaxon.util.MolHandler
- Deprecated. since JChem 3.1 the usage of
MolHandler.generateFingerprintInBytes(int, int, int)
is recommended
- getFingerprintInInts(int, int, int) -
Method in class chemaxon.util.MolHandler
- Deprecated. since JChem 3.1 the usage of
MolHandler.generateFingerprintInInts(int, int, int)
is recommended
- getFingerprintParams(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Return the fingerprint parameters of a table.
- getFirstHitTime() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the first hit's retrieving time (measured from start of screening).
- getFixedLocation(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MMidPoint
- Gets the fixed location in the polyline.
- getFixers(StructureCheckerResult) -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getFixers(StructureCheckerResult) -
Method in interface chemaxon.checkers.runner.CheckerRunner
- Returns all the
StructureFixer instances which associated with the
StructureCheckerErrorType of the result
- getFixers(StructureCheckerResult) -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
- Deprecated.
- getFlags() -
Method in class chemaxon.formats.MFileFormat
- Gets the format descriptor flags.
- getFlags() -
Method in class chemaxon.marvin.io.MRecord
- Gets the record descriptor flags.
- getFlags() -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the flags.
- getFlags() -
Method in class chemaxon.struc.MolAtom
- Gets flags.
- getFlags() -
Method in class chemaxon.struc.MolBond
- Gets bond type (4 bits), stereo (2+2+1 bits), topology (2 bits),
bond set (5 bits) and reacting center (7 bits) information.
- getFlags() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the dimension and chiral flags.
- getFlags() -
Method in class chemaxon.struc.RgMolecule
- Gets the dimension and chiral flags.
- getFlexibleRingRotatableBondCount() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getFlexibleRingSize() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getFloat(int) -
Method in class chemaxon.descriptors.CustomDescriptor
-
- getFocus() -
Method in class chemaxon.struc.MDocument
- Gets the focused object
- getFogFactor() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the fog factor.
- getFontFamily() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the font family name.
- getFontMetrics(Graphics, MFont) -
Method in class chemaxon.struc.graphics.MTextDocument.Section
- Gets and updates the font metrics of a document section.
- getFontScale() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the font scaling factor.
- getFooterAsString() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Gets the footer of the file as a string.
- getFooterAsString() -
Method in interface chemaxon.marvin.io.MRecordReader
- Gets the footer of the file as a string.
- getForefather() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the first parent.
- getForeground() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the foreground color.
- getForegroundColor() -
Method in class chemaxon.marvin.space.monitor.Label
- Returns the foreground color of the label.
- getFormalCharge() -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the formal charge of the molecule.
- getFormalCharge(int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the formal charge of a specified atom.
- getFormalCharge() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the (total) formal charge of the molecule.
- getFormat(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the file format descriptor for the specified codename.
- getFormat() -
Method in class chemaxon.formats.MolExporter
- Gets the output file format.
- getFormat() -
Method in class chemaxon.formats.MolImporter
- Get the file format.
- getFormat() -
Method in class chemaxon.formats.MolInputStream
- Get the molecule file format.
- getFormat() -
Method in class chemaxon.jchem.db.Exporter
- Gets the format of the export.
- getFormat() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the default molecule file format.
- getFormat() -
Method in class chemaxon.marvin.io.MolExportModule
- Returns the output format.
- getFormat() -
Method in class chemaxon.marvin.io.MRecord
-
- getFormat() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the file format.
- getFormula() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the molecular formula which is a string listing all atom types
an their occurence in the molecule.
- getFormula() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the molecular formula.
- getFormula() -
Method in class chemaxon.struc.RgMolecule
- Gets the molecular formula in Hill order.
- getFormula() -
Method in class chemaxon.struc.RxnMolecule
- Gets the molecular formula in Hill order.
- getFormulaSearchQuery() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the query set for formula search.
- getFormulaSearchType() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Gets the type set for formula search.
- getFovY() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the field of view.
- getFpSize() -
Method in class chemaxon.clustering.Common
- Gets chemical hashed fingerprint size.
- getFragCount() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. since 5.6, replaced by
MoleculeGraph.getFragCount(int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
- getFragCount(int) -
Method in class chemaxon.struc.MoleculeGraph
- Returns the number of fragments for the given fragmentation type.
- getFragIds() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. since 5.6, replaced by
MoleculeGraph.getFragIds(int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.getFragIds(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
- getFragIds(int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets an array containing the fragment id for each atom for the given
fragmentation type.
- getFragmentCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the number of fragments (disconnected parts) of the molecule.
- getFreeLegalAttachAtoms() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the unused legal attachment points.
- getFrequencyCounts() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the absolute frequence count array for all descriptors generated.
- getFunctionalGroupDisplayMolTable() -
Method in class chemaxon.jep.Evaluator
- Returns a hashtable containing |functional group name| -> |displayable molecule representation|.
- getFunctionData() -
Method in class chemaxon.jep.Evaluator
- Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects.
- getFunctionData(boolean) -
Method in class chemaxon.jep.Evaluator
- Returns information about Chemical Terms functions wrapped in chemaxon.jep.CTFunctionData objects.
- getFunctionParameterData() -
Method in class chemaxon.jep.Evaluator
- Deprecated. use
Evaluator.getFunctionData()
- getFusedAliphaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of fused aliphatic rings (SSSR smallest set of
smallest aliphatic rings) in the molecule.
- getFusedAliphaticRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of fused aliphatic rings in the molecule (rings
s).
- getFusedAliphaticRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic
rings) in the molecule.
- getFusedAliphaticRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies fused aliphatic rings (SSSR smallest set of smallest aliphatic
rings) in the molecule having the given size (number of atoms).
- getFusedAromaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of fused aromatic rings (SSSR smallest set of
smallest aromatic rings) in the molecule.
- getFusedAromaticRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of fused aromatic rings in the molecule (rings
s).
- getFusedAromaticRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies fused aromatic rings (SSSR smallest set of smallest aromatic
rings) in the molecule.
- getFusedAromaticRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies fused aromatic rings (SSSR smallest set of smallest aromatic
rings) in the molecule having the given size (number of atoms).
- getFusedRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of fused rings (SSSR smallest set of smallest rings)
in the molecule.
- getFuzzyExponents() -
Method in class chemaxon.descriptors.PFParameters
- Gets the precalculated fuzzy exponent used in the Fuzzy Bipolar
Autocorrelogram (FBPA) metric.
- getFuzzyLowerBound() -
Method in class chemaxon.descriptors.PFParameters
-
- getFuzzySmoothingFactor() -
Method in class chemaxon.descriptors.PFParameters
- Gets the fuzzy smoothing factor used in the construction of fuzzy
fingerprints.
- getGaussianFuzzyIncrements() -
Method in class chemaxon.descriptors.PFParameters
- Gets fuzzy increments for the fuzzy smoothing with a normal distribution.
- getGenNameFontSize() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the IUPAC name font size.
- getGL() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the OpenGL interface.
- getGLAutoDrawable() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the GLAutoDrawable object.
- getGLCanvas() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the GL canvas.
- getGLCapabilities() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the GLCapabilities of the GLCanvas
including information about hardware acceleration, buffers, color bits, etc.
- getGLInfo(boolean) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the OpenGL Renderer, Version, and Vendor
and Extensions in VERBOSE_LEVEL_DEVEL mode.
- getGlobalGUIProperties() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the Global GUI properties.
- getGlobalProperties() -
Method in class chemaxon.formats.MolImporter
- Gets the global properties in a container that was retrieved from
the input stream, earlier.
- getGlobalProperties() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the global properties.
- getGrabbedLines() -
Method in class chemaxon.marvin.io.PositionedInputStream
- Gets the grabbed lines.
- getGrabbedMoleculeString() -
Method in class chemaxon.formats.MolImporter
- Gets the last grabbed molecule string.
- getGraphicComponent() -
Method in class chemaxon.marvin.space.GraphicComponent
-
- getGraphicComponent(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the
GraphicComponent having the given index in the active cell.
- getGraphicComponent(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the
GraphicComponent of the given cell.
- getGraphicComponent(UOID) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the
GraphicComponent with the given id.
- getGraphicComponent() -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- getGraphicComponentCount() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the total number of
GraphicComponents in the cells.
- getGraphicScene() -
Method in class chemaxon.marvin.space.MSpaceEasy
- Returns the
GraphicScene of MarvinSpace to be able to explicitly
set more advanced features.
- getGraphUnion() -
Method in class chemaxon.struc.MoleculeGraph
- Gets a molecule graph containing all the atoms and bonds.
- getGraphUnion() -
Method in class chemaxon.struc.RgMolecule
- Gets a graph containing all the atoms and bonds.
- getGraphUnion() -
Method in class chemaxon.struc.RxnMolecule
- Gets a graph containing all the atoms and bonds.
- getGraphUnionAsSelection() -
Method in class chemaxon.struc.Molecule
- Gets a selection molecule containing all the atoms and bonds.
- getGrinv(int[]) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the graph invariants.
- getGrinv(int[], boolean) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. Please use getGrinv(int[], int) instead.
- getGrinv(int[], int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the graph invariants (canonical labels).
- getGrinv() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the graph invariants array.
- getGrinvCC() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the graph invariant change count.
- getGrinvCC() -
Method in class chemaxon.struc.MProp
- Gets the graph invariant change count at the moment of creation.
- getGrinvOptions() -
Method in class chemaxon.struc.MoleculeGraph
- Gets graph invariant calculation options passed to the module.
- getGroup(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets the menu group for a plugin.
- getGroupHit() -
Method in class chemaxon.sss.search.Decomposition
- Returns the group hit corresponding to the R-group decomposition.
- getGroupHit() -
Method in class chemaxon.sss.search.SearchHit
- Returns the group hit view.
- getGroupMnemonic(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets the group mnemonic for a plugin.
- getGroups() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the group names this element is a member of
- getGUIPropertyContainer() -
Method in class chemaxon.struc.MDocument
-
- getHaltOnError() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the current error handling behaviour option.
- getHararyIndex() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the Harary index which is the half-sum of the off-diagonal
elements of the reciprocal molecular distance matrix of the molecule.
- getHashCode(Molecule) -
Method in class chemaxon.sss.screen.HashCode
- Gets hash code with default recursion level.
- getHashCode(Molecule, int) -
Method in class chemaxon.sss.screen.HashCode
- Gets the hash code.
- getHashCode(Molecule, int[]) -
Method in class chemaxon.sss.screen.HashCode
- Gets hash code with default recursion level.
- getHashCode(Molecule, int[], int) -
Method in class chemaxon.sss.screen.HashCode
- Gets the hash code.
- getHcount(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the total number of hydrogens of an atom.
- getHCountMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get the interpretation of H count in the query.
- getHeadCrossingBonds() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Gets the head crossing bonds.
- getHeader() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the table header.
- getHeader() -
Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
- Returns the table header.
- getHeader() -
Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
- Returns the table header.
- getHeaderAsString() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Gets the header of the file as a string.
- getHeaderAsString() -
Method in interface chemaxon.marvin.io.MRecordReader
- Gets the header of the file as a string.
- getHeaderNewLineCount() -
Method in class chemaxon.marvin.io.MRecord
- Gets the number of new lines in the molecule header part.
- getHeavyAtomCount() -
Method in class chemaxon.util.MolHandler
- Retrieves the number of non-hydrogen atoms in the Molecule
stored in the MolHandler object.
- getHeight() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the height of the cell.
- getHelpPanelLabel() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the help panel label
- getHelpText() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the help text of the element
- getHelpText() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getHelpText() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getHelpText() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getHelpText() -
Method in interface chemaxon.checkers.StructureChecker
- Deprecated. This method isn't needed anymore and will be removed in 6.0
- getHelpText() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- Returns the help text displayed on empty component
- getHelpTextArea() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the text area for the help
- getHeteroaliphaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of aliphatic heterocyclic rings in the molecule
(aliphatic rings containing at least a non-carbon atom).
- getHeteroaliphaticRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of aliphatic heterocyclic rings in the molecule
(aliphatic rings containing at least a non-carbon atom) having a given
size (number of atoms).
- getHeteroaliphaticRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies heteroaliphatic rings in the molecule (aliphatic rings
containing at least a non-carbon atom).
- getHeteroaliphaticRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies heteroaliphatic rings in the molecule (aliphatic rings
containing at least a non-carbon atom) having a given size (number of atoms).
- getHeteroaromaticRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the heteroaromatic ring count.
- getHeteroaromaticRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of aromatic heterocyclic rings in the molecule
(aromatic rings containing at least a non-carbon atom) having a given size
(number of atoms).
- getHeteroaromaticRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies heteroaromatic rings in the molecule (aromatic rings containing
at least a non-carbon atom).
- getHeteroaromaticRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies heteroaromatic rings in the molecule (aromatic rings containing
at least a non-carbon atom) having a given size (number of atoms).
- getHeteroRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the hetero ring count.
- getHeteroRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of heterocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- getHeteroRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies heterocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- getHeteroRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Indentifies hetero rings in the molecule having a given size (number
of atoms).
- getHighestEigenvalue(int) -
Method in class chemaxon.descriptors.BCUT
- Gets the specified highest eigenvalue.
- getHighestEigenvaluesCount() -
Method in class chemaxon.descriptors.BCUTParameters
- Gets the number of highest eigenvalues calculated.
- getHistogramSimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.ShapeDescriptor
-
- getHit(Molecule) -
Method in class chemaxon.util.HitDisplayTool
- Processes the next target structure.
- getHitHomologyColor() -
Method in class chemaxon.util.HitColoringAndAlignmentOptions
- Get the color used for highlighting user defined homologies in a
substructure hit
- getHitIndexes() -
Method in class chemaxon.util.HitDisplayTool
- Returns the hit indexes for the last target.
- getHitIndexType() -
Method in class chemaxon.sss.search.MolSearchOptions
- Returns the representation on which the hit indexes are given in
case of Markush search.
- getHitOrdering() -
Method in class chemaxon.sss.search.SearchOptions
- Returns the hit ordering type.
- getHits() -
Method in class chemaxon.naming.DocumentExtractor
- Returns the hits found in the documents processed so far.
- getHits(Molecule, byte[], int) -
Method in class chemaxon.util.HitDisplayTool
- Processes the next target structure.
- getHits(Molecule, Molecule, int) -
Method in class chemaxon.util.HitDisplayTool
- Processes the next target structure.
- getHits(int) -
Method in class chemaxon.util.HitDisplayTool
- Processes the next target structure.
- getHitsAsHitDisplayTool(int[], HitColoringAndAlignmentOptions, ArrayList, ArrayList, List<Molecule>, List<byte[]>) -
Method in class chemaxon.jchem.db.JChemSearch
- Gets a HitDisplayTool object from which the results can be retrieved.
- getHitsAsMarkush() -
Method in class chemaxon.sss.search.RgDecompResults
- Returns a single RgMolecule that consists of the scaffold
and all the possible ligands as rgroup-definitions.
- getHitsAsMolecules(int[], HitColoringAndAlignmentOptions, ArrayList, ArrayList) -
Method in class chemaxon.jchem.db.JChemSearch
- Returns hits ready for display.
- getHitsAsRgDecomp(int[], int) -
Method in class chemaxon.jchem.db.JChemSearch
- Returns hits as result of r-group decomposition according to the
original query.
- getHitsAsRgDecomp() -
Method in class chemaxon.sss.search.RgDecompResults
- Returns All ligands of all targets.
- getHitsAsTable() -
Method in class chemaxon.sss.search.RgDecompResults
- Returns the table elements in Molecule[][] format.
- getHitsFound() -
Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
-
- getHMOChargeDensity(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the total charge density of an atom
calculated with HMO,
Double.NaN for no value.
- getHMOEigenVector() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the eigenvector.
- getHMOElectronDensity(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the electron density of an atom
calculated with HMO,
Double.NaN for no value.
- getHMOElectrophilicEnergy(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the electrophilic energy (localization energy L+) of an atom,
Double.NaN for no value.
- getHMOElectrophilicOrder(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the electrophilic order of an atom,
-1 for no value.
- getHMOHuckelOrbitalCoefficients() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the huckel orbital coefficients.
- getHMONucleophilicEnergy(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the nucleophilic energy (localization energy L-) of an atom,
Double.NaN for no value.
- getHMONucleophilicOrder(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the nucleophilic order of an atom,
-1 for no value.
- getHMORealEigenValue() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the real part of the eigenvalue.
- getHMOTotalPiEnergy() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the total pi energy of the input molecule.
- getHomologyBroadTranslation() -
Method in class chemaxon.sss.search.SearchOptions
- Get target-side homology matching option.
- getHomologyNarrowTranslation() -
Method in class chemaxon.sss.search.SearchOptions
- Get query-side homology matching option, which homology atoms can match specific atoms.
- getHorizontalAlignment() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the horizontal alignment.
- getHPolarizability(int) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the sum of the implicit H atom polarizability values
around the given heavy atom.
- getHResult(int) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns the sum result of the H neighbours of the given atom.
- getHTMLColorString(Color) -
Static method in class chemaxon.util.HTMLTools
- Returns the HTML string representation of a Color
- getHuckelOrbitalCoefficients() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Deprecated. Use
HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients()
- getHybridizationMatch() -
Method in class chemaxon.sss.search.MCES
- Gets the matching mode for atom hybridization.
- getHybridizationState() -
Method in class chemaxon.struc.MolAtom
- Gets the hybridization state.
- getHybridizationState(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the hybridization state of an atom.
- getHyperWienerIndex() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the hyper Wiener index of the molecule.
- getIcon() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the icon of the element, or the warning icon if element is at invalid state
- getIcon() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getIcon() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getIcon() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getIcon() -
Method in interface chemaxon.checkers.StructureChecker
- Deprecated. This method isn't needed anymore and will be removed in 6.0
- getIcon(int) -
Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo
- Returns a MarvinSketch icon in 16x16 or 32x32 size.
- getIcon(int) -
Method in class chemaxon.marvin.beans.MViewPaneBeanInfo
- Returns a MarvinView icon in 16x16 or 32x32 size.
- getIcon() -
Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- getIcon() -
Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
-
- getId() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the id of the element
- getId() -
Method in class chemaxon.descriptors.MDSet
- Gets the identifier of the
MDSet.
- getId(String) -
Static method in class chemaxon.marvin.services.json.JsonServiceDescriptor
- Gets an ID for a method name, to make sure the client can identify the
answer for the request.
- getId() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the cell id as a
UOID.
- getId() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the id of the component.
- getId() -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- getID(String) -
Method in class chemaxon.pharmacophore.PMapper
- Returns the ID corresponding to the given symbol.
- getID() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the reaction ID.
- getIDBackgroundRGBA(int) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the background color's RGBA value in a record.
- getIdentiferCount() -
Method in class chemaxon.descriptors.ECFP
- Gets the number of integer identifers generated for the fingerprint.
- getIdentifier() -
Method in class chemaxon.descriptors.ECFPFeature
- Gets the generated integer identifier for this ECFP feature.
- getIdentifier(MolAtom, int) -
Method in class chemaxon.descriptors.ECFPFeatureLookup
- Returns the corresponding integer identifier for the given atom neighborhood.
- getIDForegroundRGBA(int) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the foreground color's RGBA value in a record.
- getIdGeneration() -
Method in class chemaxon.clustering.Common
- Indicates whether id-s will be generated or taken from input data.
- getIDList() -
Method in class chemaxon.jchem.db.Exporter
- Returns the list of allowed cd_id values.
- getIgnoreRotatableBonds() -
Method in class chemaxon.descriptors.PFParameters
-
- getImage(double) -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the canvas contents as an image using a scale factor.
- getImage(Dimension) -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the canvas contents as an image scaled to fit in the specified
rectangle.
- getImageMolecule() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the molecule to be used for legend image.
- getImageSize(String) -
Method in class chemaxon.struc.Molecule
- Deprecated. since 5.5.0 please use MolPrinter with the desired display
options set, and call
MolPrinter.getBoundingRectangle(chemaxon.struc.MoleculeGraph[])
, to get the bounding rectangle for a given scale.
And call MolPrinter.maxScale(java.awt.Dimension) or
MolPrinter.maxScale(java.awt.Rectangle) to get the
maximum scale to fit the molecule to the given rectangle.
- getImageToClipboardTask(Image) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getImplicitH() -
Method in class chemaxon.marvin.beans.MarvinPane
- Query the display method of implicit hydrogens.
- getImplicitH() -
Method in class chemaxon.marvin.MolPrinter
- Returns the display method of implicit hydrogens.
- getImplicitHcount() -
Method in class chemaxon.struc.MolAtom
- Gets the number of implicit hydrogens attached.
- getImplicitHcount() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the total number of implicit hydrogens attached to the molecule.
- getImplicitHcount(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the number of implicit Hydrogens of an atom.
- getImplicitHcount() -
Method in interface chemaxon.struc.Smolecule
- Gets the total number of implicit Hydrogens.
- getImplicitHCount() -
Method in class chemaxon.util.MolHandler
- Counts the number of implicir hydrogens on the molecule
- getImplicitHMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get option for matching implicit and explicit hydrogens
- getImplicitizeFlag() -
Method in class chemaxon.checkers.result.ExplicitHydrogenResult
- Returns the flag which can used to identify which hydrogens should be implicitize.
- getImportedIDs() -
Method in class chemaxon.jchem.db.Importer
- Returns the IDs (cd_id column in database table) of imported structures.
- getImportedNumber() -
Method in class chemaxon.jchem.db.Importer
- Returns the number of imported molecules.
- getImporter() -
Method in class chemaxon.metabolizer.MetabolizerTemporaryFileStorage
-
- getImporter() -
Method in class chemaxon.metabolizer.MetabolizerTemporaryMemoryStorage
-
- getImporter() -
Method in interface chemaxon.metabolizer.MetabolizerTemporaryStorage
- Returns MetabolizerImporter instance for substrates
- getIncludedIds() -
Method in class chemaxon.sss.search.RgDecompResults
- Returns indexes of those targets that are matched by query.
- getIndex() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- Returns the index
- getIndex() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the internal index of the cell.
- getIndex(String) -
Method in class chemaxon.pharmacophore.PSymbols
- Gets the index associated of the specified symbol.
- getInnerPointRef(int, CTransform3D) -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- getInput() -
Method in class chemaxon.jchem.db.Importer
- Gets the source object.
- getInputCount() -
Method in class chemaxon.formats.MolConverter.Builder
- Gets the number of input files/streams.
- getInputCount() -
Method in class chemaxon.formats.MolConverter.Options
- Deprecated.
- getInputFormat() -
Method in class chemaxon.marvin.io.MRecord
- Gets the input format.
- getInputFormat() -
Method in class chemaxon.struc.MDocument
- Gets the input file format.
- getInputFormat() -
Method in class chemaxon.struc.Molecule
- Gets the input file format.
- getInputMolDim() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the input molecule dimension.
- getInputMolecule() -
Method in class chemaxon.reaction.ConcurrentStandardizerProcessor
- Returns the input molecule (the molecule before standardization).
- getInputPriority() -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- Priority of the
MTransferable object when importing from
clipboard.
- getInputStream(String) -
Static method in class chemaxon.marvin.space.MSpaceEasy
- Creates an
InputStream from the given String.
- getInputStreamFromClipboard() -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Gets an InputStream from the clipboard data if the format is supported by
this MTransferable
- getInputStructureCount() -
Method in class chemaxon.clustering.LibraryMCS
- Retrieves the total number of input structures clustered.
- getInsertedDissimilars() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Returns lists of dissimilars which have dissimilarity values lower than the
similars.
- getInstance(int, String, int, String, String, String) -
Static method in class chemaxon.util.ConnectionHandler
- Creates a ConnectionHandler using the appropriate driver and url determined
by given database type, host, port and name.
- getInt(int) -
Method in class chemaxon.descriptors.CustomDescriptor
-
- getIntArray() -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Gets the integer value.
- getInternalMetricIndex() -
Method in class chemaxon.descriptors.MDParameters
- Gets the MolecularDescriptor specific metric index of the current
parametrized metric.
- getInternalSize() -
Method in class chemaxon.descriptors.MDParameters
- Gets the required memory size to store the descriptor according to the
specified parameters.
- getInternalVersionId() -
Static method in class chemaxon.jchem.version.VersionInfo
- Retrieves the internal version number of JChem.
- getIntProperty(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Searches for the property with the specified key in the
JChemProperties table.
- getInverseName() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Gets the inverse option name.
- getInvisibleSets() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the visibility of the specified atom sets.
- getIonizerErrorMessage() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Returns the calculation error information message
or the empty string if there is no error.
- getIonizerErrorMessage() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the calculation error information message
or the empty string if there is no error.
- getIsotope(int, int) -
Static method in class chemaxon.struc.PeriodicSystem
- Retrieves an isotope of the element
- getIsotopeComposition() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the molecular composition (w/w%).
- getIsotopeComposition(boolean) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the molecular composition (w/w%).
- getIsotopeCount() -
Static method in class chemaxon.struc.PeriodicSystem
- Number of isotopes in the periodic system
- getIsotopeCount(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Number of isotopes of the element
- getIsotopeFormula() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the molecular formula (isotopes are separated).
- getIsotopeFormula(boolean) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the molecular formula (isotopes are separated).
- getIsotopeMatch() -
Method in class chemaxon.sss.search.MCES
- Gets the matching mode for isotopes.
- getIsotopeMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get option for matching isotopes
- getItsArrow() -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction arrow of this reaction.
- getJTFFields(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets fields delimited with {space} {tab} {;} {:} or {,}.
- getKeepCounts() -
Method in class chemaxon.descriptors.ECFPParameters
- Gets the counts (multiplicity) parameter.
- getKeepLargestComponent() -
Method in class chemaxon.sss.search.MCES
- Gets which components of the found MCES should be kept.
- getKey() -
Method in class chemaxon.marvin.plugin.gui.OptionsPane
- Returns the plugin key.
- getKey(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets the menu key for a plugin.
- getKey(int) -
Method in class chemaxon.struc.MPropertyContainer
- Gets a property key.
- getKey(int) -
Method in class chemaxon.struc.prop.MHashProp
- Gets a key.
- getKeys(int, Molecule) -
Method in class chemaxon.marvin.io.MFieldAccessor
- Gets the keys in a record.
- getKeys() -
Method in class chemaxon.struc.MPropertyContainer
- Returns the property keys.
- getKnownExtension(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Returns the file extension if it is a known extension.
- getL(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets a label.
- getL(int, int) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets a text label in a record.
- getLabel(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getLabel(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getLabelCenter() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Gets the index of the character in the label the bonds should point to.
- getLabelInformation(String, boolean) -
Method in class chemaxon.marvin.space.GraphicComponent
- Labels will be created associated to this GraphicComponent if the component
supports the given labeltype, and returns arbitrary numbers of ComponentElements
with correct coordinates and description to create a label.
- getLabelInformation(String) -
Method in class chemaxon.marvin.space.GraphicComponent
-
- getLabelInformation(String) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Collects the label information of the visualizers.
- getLabelInformation(String) -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getLabelInformation(String, boolean) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Labels will be created associated to this MoleculeComponent if the labeltype
is "atom", "extraatomlabel" or "molecule".
- getLabelInformation(String) -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- getLabels() -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. use isAtomSymbolsVisible() instead
- getLabels(double[]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns formatted array.
- getLargestRing() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the atoms of the largest ring (number of atoms) in the molecule.
- getLargestRingSize() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the largest ring size.
- getLargestRingSizeOfAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the size of largest ring containing the specified atom.
- getLargestRingSystem() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the atoms of the largest ring system (number of rings) in the
molecule.
- getLargestRingSystemSize() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the size of the largest ring system (number of rings) in the molecule.
- getLastID() -
Method in class chemaxon.descriptors.MDDBReader
- Gets the cd_id that belongs to the last processed descriptor from
the structure table
- getLastProcessedLineNum() -
Method in class chemaxon.formats.recognizer.Recognizer
- Gets the number of the last processed line.
- getlastStopCause() -
Method in class chemaxon.marvin.modules.AutoMapper
- Returns the code of the last termination status.
- getLeft() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the x coordinate of the left edge of the active cell.
- getLeftList() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- initializes left list (source list)
- getLeftListFilter() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the filter combo for the left list
- getLeftName() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Gets the string that will be shown at the left side of the molecule.
- getLegalAttachAtoms() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the legal attachment points.
- getLength() -
Method in class chemaxon.descriptors.MDParameters
- Returns the number of cells forming the descriptor.
- getLength() -
Method in class chemaxon.struc.MolBond
- Gets the actual length of the bond.
- getLevelCount() -
Method in class chemaxon.clustering.LibraryMCS
- Retrieves the total number of levels in the hierarchy.
- getLevelCount() -
Method in class chemaxon.formats.recognizer.RecognizerList
- Gets the number of levels.
- getLevelCount() -
Method in class chemaxon.metabolizer.Metabolizer
- Returns levelCount
- getLevelCounter() -
Method in class chemaxon.metabolizer.Metabolizer
- Return current level's ordinal number
- getLibrarySizeString() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the string representation of the Markush library size.
- getLicenseExceptionMessage() -
Static method in class chemaxon.license.LicenseManager
- Returns the common message used at license problems.
- getLicenseExceptionPanel(String) -
Static method in class chemaxon.license.LicenseManager
- Returns the common swing component used to indicate missing license.
- getLicenseExceptionPanel(LicenseException) -
Static method in class chemaxon.license.LicenseManager
- Returns the common swing component used to indicate missing license.
- getLicenseName() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the name of required license, or
null
- getLicenseSupport() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the license support
- getLigand(int) -
Method in class chemaxon.struc.MolAtom
- Gets the i-th ligand of this atom.
- getLigandIds() -
Method in class chemaxon.sss.search.Decomposition
- Returns the target ligand IDs.
- getLigandIndex(MolAtom) -
Method in class chemaxon.struc.MolAtom
- Returns the index of the specified ligand in this atom.
- getLigandOrder(MolAtom) -
Method in class chemaxon.struc.MolAtom
- Gets the order of a specified ligand.
- getLigandOrderVisibility() -
Method in class chemaxon.marvin.MolPrinter
- Gets the ligand order visibility setting.
- getLigands() -
Method in class chemaxon.sss.search.Decomposition
- Returns the R-ligand array.
- getLigands() -
Method in class chemaxon.struc.MolAtom
- Returns the atoms connected to this atom by a bond.
- getLigandsNumber() -
Method in class chemaxon.sss.search.RgDecompResults
- Returns the number of ligands in one target structure.
- getLigandTableHeader(int, int) -
Method in class chemaxon.sss.search.RGroupDecomposition
- Returns ligand table header.
- getLigandTableHeader(int, int, String) -
Method in class chemaxon.sss.search.RGroupDecomposition
- Returns ligand table header.
- getLimitedStructureCount() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the number of structures to be generated.
- getLine(int) -
Method in class chemaxon.struc.graphics.MTextBox
- Gets a line.
- getLineColor() -
Method in class chemaxon.struc.MObject
- Gets the line color of the object.
- getLineCount() -
Method in class chemaxon.formats.MolImporter
- Gets the current line number.
- getLineCount() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Get the current line number.
- getLineCount() -
Method in class chemaxon.marvin.io.MolImportModule
- Returns the line count in the molecule input stream.
- getLineCount() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the current line number in the input file.
- getLineCount() -
Method in interface chemaxon.marvin.io.MRecordReader
- Get the current line number.
- getLineCount() -
Method in class chemaxon.marvin.io.PositionedInputStream
- Gets the current line number.
- getLineCount() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the number of lines.
- getLineNumber() -
Method in class chemaxon.marvin.io.MRecordReader.Position
- Gets the line number.
- getLineNumberInFile() -
Method in exception chemaxon.formats.MolFormatException
- Gets the line number relative to the first line of the file.
- getLineNumberInRecord() -
Method in exception chemaxon.formats.MolFormatException
- Gets the line number relative to the first line of the record.
- getLineNumberMap() -
Method in class chemaxon.marvin.io.MRecord
- Gets the line number to original line number mapping.
- getLineOnScreen(int) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Returns the i-th row of the data sgroup label, as displayed on the screen
(with tag, query operator, units etc.)
- getLinesToCheck() -
Method in class chemaxon.jchem.db.Importer
- Gets the number of lines to check for file format.
- getLinkNodeOuterAtom(int) -
Method in class chemaxon.struc.MolAtom
- Gets the index of one of the link node's outer neighbor atoms.
- getList() -
Method in class chemaxon.struc.MolAtom
- Gets the atom list.
- getList() -
Method in class chemaxon.struc.prop.MListProp
- Gets the array.
- getListeners() -
Method in class chemaxon.marvin.view.MDocStorage
-
- getLoadSaveLocation() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the load/save filechooser working directory selection method names,
based on the preferences dialog.
- getLoadWorkingDir() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the filechooser's default working directory, if it is set, and the
filechooser working directory selection method is saveCustomLocation.
- getLocalMenuName() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getLocalMenuName() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getLocalMenuName() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getLocalMenuName() -
Method in interface chemaxon.checkers.StructureChecker
- Deprecated. This method isn't needed anymore and will be removed in 6.0
- getLocalParity(int) -
Method in class chemaxon.struc.MoleculeGraph
- Computes the local parity of an atom of the Molecule instance
based on both the coordinates of the neighboring atoms
and the stereo information of the bonds to those.
- getLocalParity(int) -
Method in class chemaxon.struc.RgMolecule
- Computes the local parity of an atom of the RgMolecule instance
based on both the coordinates of the neighboring atoms
and the stereo information of the bonds to those.
- getLocalParity(int) -
Method in class chemaxon.struc.RxnMolecule
- Computes the local parity of an atom of the RxnMolecule instance
based on both the coordinates of the neighboring atoms
and the stereo information of the bonds to those.
- getLocation(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Gets the location.
- getLocation(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Gets the location.
- getLocation(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MMidPoint
- Gets the location.
- getLocation(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MMidPoint.Sticky
- Gets the location.
- getLocation(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
- Gets the location.
- getLocation() -
Method in class chemaxon.struc.MolAtom
- Gets the coordinates.
- getLocation(DPoint3) -
Method in class chemaxon.struc.MolAtom
- Gets the coordinates.
- getLocation() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the origin of the molecule.
- getLocation(DPoint3, CTransform3D) -
Method in class chemaxon.struc.MPoint
- Gets the point's location.
- getLocation(CTransform3D) -
Method in class chemaxon.struc.MPoint
- Gets the point's location.
- getLocation() -
Method in class chemaxon.struc.MPoint
- Gets the point's location.
- getLock() -
Method in class chemaxon.struc.MolAtom
- Get lock object for synchronization.
- getLock() -
Method in class chemaxon.struc.MolBond
- Gets lock object for synchronization.
- getLock() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the lock object for synchronization.
- getLog() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns the Logger of the Clipboard handler subsystem.
- getlogD() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the logD value for the pH specified in
logDPlugin.setpH(double).
- getlogDpI() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the logD value at pI.
- getlogDs() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the logD array.
- getLoggingLevel() -
Static method in class chemaxon.sss.search.MarkushTagger
- Returns the logging level.
- getLogicalValue(Object) -
Static method in class chemaxon.jep.ChemJEP
- Returns the logical correspondent of the specified result object:
ChemJEP.TRUE, ChemJEP.FALSE or ChemJEP.UNDECIDED.
- getLoginName() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
loginName.
- getlogPMicro() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the micro logP value.
- getlogPNonionic() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the logP value for the non-ionic form.
- getLogPTrainingIds() -
Static method in class chemaxon.marvin.calculations.logDPlugin
- Returns the id's of available logP trainings.
- getlogPTrue() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the most typical logP among logD at pI, micro logP and nonionic logP.
- getLonePairCount() -
Method in class chemaxon.struc.MolAtom
- Returns the automatically calculated lone pair count of this atom.
- getLonePairCount(int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the number of lone pairs.
- getLonePairCount(int) -
Method in class chemaxon.struc.RgMolecule
- Gets the number of lone pairs.
- getLonePairsVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Tests whether lone pairs are visible.
- getLowerBound(Object) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the lower bound estimate of the dissimilarity from the given
fingerprint.
- getLowerBound(Object) -
Method in class chemaxon.descriptors.MDSet
- Gives a lower bound estimation for the value of
getDissimilarity( final Object o ).
- getLowerBound(MolecularDescriptor) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Calculates an estimate for the minimum value of the distance
using the default distance metric.
- getLowerBound(MolecularDescriptor) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the lower bound estimate of the dissimilarity from the given
fingerprint.
- getLowerBound(MolecularDescriptor) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Calculates the lower bound estimate of the dissimilarity from the given
fingerprint.
- getLowerBound(MolecularDescriptor) -
Method in class chemaxon.descriptors.ScalarDescriptor
- Calculates the lower bound estimate of the dissimilarity from the given
descriptor.
- getLowestEigenvalue(int) -
Method in class chemaxon.descriptors.BCUT
- Gets the specified lowest eigenvalue.
- getLowestEigenvaluesCount() -
Method in class chemaxon.descriptors.BCUTParameters
- Gets the number of lowest eigenvalues calculated.
- getLowestEnergyConformer() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the calculated lowest energy conformer.
- getLowestEnergyConformer() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the lowest energy conformer of the molecule.
- getM(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the nth molecule in memory.
- getM(int, String) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the nth molecule in a text format.
- getMacroMolecule() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the
MacroMolecule this component visualizes.
- getMacroMoleculeComponent() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getMacroMoleculeComponent() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the macromolecule visualizer if this
MoleculeComponent visualizes
a ligand in a complex.
- getMacropKaValues(int, double[], int[]) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Calculates the least acidic pKa values in ascending order
or the biggest basic pKa values in descending order.
- getMacropKaValues(int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Calculates the acidic pKa values in ascending order or the basic pKa values in descending order.
- getMacroSpeciesCharge(int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the formal charges of a given macrospecies.
- getMag() -
Method in class chemaxon.marvin.beans.MSketchPane
- Deprecated. As of Marvin 2.8.1, replaced by getScale()
- getMainDoc(int) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the document at the specified position.
- getMainDoc(int, MProgressMonitor) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the document at the specified position.
- getMainLayout() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the mainLayout
- getMainMolecule(int, Molecule) -
Method in class chemaxon.marvin.io.MFieldAccessor
- Gets the main molecule object in a record.
- getMainMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Deprecated. Use
CalculatorPlugin.createModifiedInputMolecule(Molecule) instead
- getMainMoleculeGraph() -
Method in class chemaxon.struc.MDocument
- Gets the main molecule graph.
- getMainMolFieldness() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Tests whether the main molecule is a field.
- getMajorMicrospecies() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the major microspecies at the pH set in
MajorMicrospeciesPlugin.setpH(double).
- getMap() -
Method in class chemaxon.struc.prop.MHashProp
- Gets the map.
- getMap(MoleculeGraph) -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Gets a map containing MolAtom objects as keys and DPoint3 arrays as
values.
- getMapCount() -
Method in class chemaxon.marvin.modules.AutoMapper
- Get number of solution maps found.
- getMarkush() -
Method in class chemaxon.sss.search.MarkushTagger
- Returns the Markush structure.
- getMarkushArom() -
Method in class chemaxon.sss.search.MolSearchOptions
- Gets the Markush aromatic search behavior.
- getMarkushData() -
Method in class chemaxon.jchem.db.UpdateHandler.RowData
-
- getMarkushScreeningType(MarkushScreeningType) -
Method in class chemaxon.sss.search.JChemSearchOptions
- Internal use only!
- getMarkushViewer() -
Method in class chemaxon.alchemist.markushview.CompactMarkushViewer
- Gets the
MarkushViewerComponent.
- getMass() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Calculates the molecular weight of the molecule.
- getMass() -
Method in class chemaxon.struc.MolAtom
- Gets the atomic weight.
- getMass() -
Method in class chemaxon.struc.MoleculeGraph
- Calculates the molecular weight of the molecule.
- getMass(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Atomic weight of the element based on the natural abundance of its
isotopes
- getMass(int, int) -
Static method in class chemaxon.struc.PeriodicSystem
- Atomic weight of an isotope
- getMass() -
Method in class chemaxon.struc.RgMolecule
- Calculates the molecular weight of the molecule.
- getMass() -
Method in class chemaxon.struc.RxnMolecule
- Calculates the molecular weight of the molecule.
- getMassno() -
Method in class chemaxon.struc.MolAtom
- Gets the mass number.
- getMassno(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the mass number of an atom.
- getMassPrecision(int) -
Static method in class chemaxon.struc.PeriodicSystem
- The precision of an elemental mass is the number of measured digits after
the decimal separator.
- getMassPrecision(int, int) -
Static method in class chemaxon.struc.PeriodicSystem
- The precision of an isotopic mass is the number of measured digits after
the decimal separator.
- getMatchCount() -
Method in class chemaxon.sss.search.Search
- The number of times the query molecule appears in the target molecule.
- getMatchCountHighLimit() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- getMatchCounthitLimit() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- getMatchCountLowLimit() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- getMatchCountOptions() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the match count options.
- getMatchCountRelation() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- getMatchedQueryAtoms() -
Method in class chemaxon.sss.search.MCES
- Gets the query atoms that are part of the found MCES.
- getMatchedQueryBonds() -
Method in class chemaxon.sss.search.MCES
- Gets the query bonds that are part of the found MCES.
- getMatchedTargetAtoms() -
Method in class chemaxon.sss.search.MCES
- Gets the target atoms that are part of the found MCES.
- getMatchedTargetBonds() -
Method in class chemaxon.sss.search.MCES
- Gets the target bonds that are part of the found MCES.
- getMatchingQuery() -
Method in class chemaxon.sss.search.MolSearch
- Returns the most specific enumeration of the query which produced the hit
vector of the last findNext(), findFirst() or findAll() result.
- getMatchingQuery() -
Method in class chemaxon.sss.search.Search
- Returns the query which produced the hit vector of the last findNext(),
findFirst() or findAll() result.
- getMatchingTarget() -
Method in class chemaxon.sss.search.MolSearch
- Returns the most specific enumeration of the target which produced the
hit vector of the last findNext(), findFirst() or findAll() result.
- getMaxAttachmentPointOrder(int) -
Method in class chemaxon.struc.RgMolecule
- Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID.
- getMaxCols() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Get maximum value of columns in the table.
- getMaxDimCached() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the maximum molecule dimension.
- getMaxDist() -
Method in class chemaxon.descriptors.PFParameters
- Gets the miximum distance of pharmacophore points that is considered.
- getMaxDist() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getMaximalProjectionArea() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the maximal projection area in Angstrom^2.
- getMaximalProjectionRadius() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the radius of the circle surrounding the maximal projection in Angstrom.
- getMaximum() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the maximum value -- the higher end of the progress value.
- getMaximumBitRatio() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the maximum percentage of non-zero cells in descriptors generated.
- getMaximumMappedValue() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the maximum value of the mapped property on this surface.
- getMaximumValue() -
Method in class chemaxon.marvin.space.SurfaceColoring
- Returns the greatest property value of the surface vertices.
- getMaxRepetitions() -
Method in class chemaxon.struc.MolAtom
- Gets the maximum number of repetitions for a link atom.
- getMaxResultCount() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the maximum result count.
- getMaxRgroupAttachmentPointOrder() -
Method in class chemaxon.struc.MoleculeGraph
- Returns the maximal attachment point order of R-group attachment point atoms in
this molecule graph.
- getMaxRows() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Get maximum value of rows in the table
- getMaxSimilar() -
Method in class chemaxon.clustering.Compare
- Gets the maximum allowed number of similar objects for a compound.
- getMaxSize() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Get the maximum number of molecules displayed in the table.
- getMaxTime() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the maximum time option.
- getMaxX() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the maximum x coordinate of the box.
- getMaxY() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the maximum y coordinate of the box.
- getMaxZ() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- getMaxZ() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the maximum z coordinate of the box.
- getMDComment(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Gets the value of the Comment property of the MolecularDescriptor
specified by its name from the property table of the JChem database.
- getMDConfig(String, String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Retrieves the value of the specified MolecularDescriptor configuration
- getMDConfigs(String, String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Retrieves the names of stored configurations associated with a certain
Molecular Descriptor.
- getMDConfigs(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Retrieves the names of stored configurations associated with a certain
Molecular Descriptor
- getMDNames() -
Method in class chemaxon.descriptors.GenerateMD
- Gets the names of all descriptor types stored in the database that are
associated with the current structure table.
- getMDNames() -
Method in class chemaxon.descriptors.MDDBWriter
- Gets the names of the Molecular Descriptors in database
- getMDParameters(int) -
Method in class chemaxon.descriptors.MDDBWriter
- Gets the actual parameter settings of the specified component.
- getMDParameters(int) -
Method in class chemaxon.descriptors.MDFileWriter
- Gets the actual parameter settings of the specified component.
- getMDParameters(int) -
Method in class chemaxon.descriptors.MDWriter
- Gets the actual parameter settings of the specified component.
- getMDSet() -
Method in class chemaxon.descriptors.MDDBReader
- Gets the molecular descriptor set.
- getMDSet() -
Method in class chemaxon.descriptors.MDFileWriter
- Gets the last molecular descriptor set generated and put into the output
file.
- getMDSet() -
Method in class chemaxon.descriptors.MDReader
- Gets the molecular descriptor set.
- getMDSettings(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Gets the value of the Settings property of the MolecularDescriptor
specified by its name from the property table of the JChem database.
- getMDTableName(String, String) -
Static method in class chemaxon.jchem.db.MDTableHandler
- Generates table name for storing Molecular Descriptors
- getMDTableProperty(String, String, String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Gets MD table property from the
JChemProperties table.
- getMDTables() -
Method in class chemaxon.jchem.db.MDTableHandler
- Retrieves the names of Molecular Descriptor tables assigned to the
structure table and
stored in the JChem database.
- getMDType(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Gets the Type property of the MolecularDescriptor specified by its name.
- getMDUpdateOnInsert(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Gets the value of the UpdateOnInsert property of the MolecularDescriptor
specified by its name from the property table of the JChem database.
- getMediumReactionTanimoto(ReactionFingerprint) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Returns the tanimoto distance of the reaction centers and their neighbouring atoms
and bonds.
- getMenu(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets the menu string for a plugin.
- getMergedst() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the merge distance.
- getMetabolicPathwayTolerance() -
Method in class chemaxon.metabolizer.Metabolizer
-
- getMetricIndex(String) -
Method in class chemaxon.descriptors.MDParameters
- Gets the index of the given parametrized metric.
- getMetricIndex(int) -
Method in class chemaxon.descriptors.MDSetParameters
- Gets the index of the metric used by a component to calculate the
dissimilarity coefficient.
- getMetricIndex(String) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the index of the given parameterized metric.
- getMetricName() -
Method in class chemaxon.descriptors.MDParameters
- Gets the user defined symbolic name of the current parametrized metric.
- getMetricName(int) -
Method in class chemaxon.descriptors.MDParameters
- Gets the user defined symbolic name of the specified parametrized metric.
- getMetricName() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the name of the current parameterized metric.
- getMetricName(int) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the name of a metric specified parameterized metric by its index.
- getMicrospecies(int) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the microspecies molecule.
- getMicrospeciesCount() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the number of microspecies.
- getMidPointLocation(int, CTransform3D) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the middle point of the arc.
- getMIMEType() -
Method in class chemaxon.formats.MFileFormat
- Gets the MIME type.
- getMinCommonRatio() -
Method in class chemaxon.clustering.JarvisPatrick
- Gets the minimum ratio of common neighbors of two compounds.
- getMinComponentSize() -
Method in class chemaxon.sss.search.MCES
- Gets the minimum required size of the components of MCES.
- getMinDist() -
Method in class chemaxon.descriptors.PFParameters
- Gets the minimum distance of pharmacophore points that is considered.
- getMinDist() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getMinimalProjectionArea() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the minimal projection area in Angstrom^2.
- getMinimalProjectionRadius() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the radius of the circle surrounding the minimal projection in Angstrom.
- getMinimum() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the minimum value -- the lower end of the progress value.
- getMinimumBitRatio() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the minimum percentage of non-zero cells in descriptors generated.
- getMinimumHeight() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the minimum height of the text.
- getMinimumMappedValue() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the minimum value of the mapped property on this surface.
- getMinimumValue() -
Method in class chemaxon.marvin.space.SurfaceColoring
- Returns the lowest property value of the surface vertices.
- getMinRepetitions() -
Method in class chemaxon.struc.MolAtom
- Gets the minimum number of repetitions for a link node.
- getMinX() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the minimum x coordinate of the box.
- getMinY() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the minimum y coordinate of the box.
- getMinZ() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- getMinZ() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the minimum z coordinate of the box.
- getMirroredArrowFlags(int) -
Method in class chemaxon.struc.graphics.MPolyline
- Mirror transformation for arrow heads.
- getMMFF94Energy() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the MMFF94 energy of the structure in kcal/mol.
- getMMFF94OptimizedStrucutre() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the MMFF94 optimized structure.
- getMnemonic(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets the menu mnemonic for a plugin.
- getMode() -
Method in class chemaxon.clustering.Ward
- Gets the clustering mode.
- getMode() -
Method in enum chemaxon.marvin.alignment.AlignmentAccuracyMode
-
- getMode() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- getMol() -
Method in class chemaxon.marvin.beans.MSketchPane
- Returns the clone of the current molecule being on the canvas.
- getMol(String) -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the molecule in a text format.
- getMolbg() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the molecule background color.
- getMolBytes() -
Method in class chemaxon.marvin.io.MRecord
- Gets the molecule bytes, with preprended header and appended footer
if appropriate.
- getMolCenter(int, String) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets a molecule center.
- getMolConstant(String) -
Method in class chemaxon.pharmacophore.PMapper
- Returns the molecule constant corresponding to the given ID.
- getMolCrd() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getMolecularDescriptors(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Retrieves the names of MolecularDescriptors assigned to the structure
table and stored in the JChem database.
- getMolecularDescriptors() -
Method in class chemaxon.jchem.db.MDTableHandler
- Retrieves the names of MolecularDescriptors assigned to the structure
table and stored in the JChem database.
- getMolecule() -
Method in class chemaxon.calculations.stereo.Stereochemistry
- Retrieves the input molecule
- getMolecule() -
Method in class chemaxon.calculations.TopologyAnalyser
- Retrieves the input molecule
- getMolecule() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getMolecule() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getMolecule() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- Returns the molecule
- getMolecule() -
Method in class chemaxon.checkers.runner.SketchCheckerRunner
-
- getMolecule() -
Method in class chemaxon.descriptors.MDDBReader
- Gets the molecule that belongs to the last processed descriptor from
the structure table
- getMolecule() -
Method in class chemaxon.descriptors.MDFileReader
- Gets the current molecular structure as read from the input file (that
is before any transformation were applied).
- getMolecule() -
Method in class chemaxon.descriptors.MDReader
- Gets the current molecular structure as read from the input file (that
is before any transformation were applied).
- getMolecule() -
Method in class chemaxon.fragmenter.CutBondReviser
- Returns the input molecule.
- getMolecule() -
Method in class chemaxon.jchem.db.UpdateHandler
- Returns the Molecule that was used during insert or update.
- getMolecule() -
Method in class chemaxon.jep.context.MolContext
- Returns the input molecule.
- getMolecule() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the
Molecule representation of the MacroMolecule.
- getMolecule() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the
Molecule of the MoleculeComponent.
- getMolecule() -
Method in class chemaxon.struc.prop.MMoleculeProp
- Gets the molecule.
- getMolecule() -
Method in class chemaxon.util.MolHandler
- Retrieves the Molecule from the MolHandler object.
- getMoleculeCount() -
Method in class chemaxon.descriptors.MDGenerator
- Gets the number of molecules processed (that is, the number of
descriptors generated) since the initialization of the object.
- getMoleculeCount() -
Method in class chemaxon.metabolizer.MetabolizerFileImporter
-
- getMoleculeCount() -
Method in interface chemaxon.metabolizer.MetabolizerImporter
- Returns the count of substrates
- getMoleculeCount() -
Method in class chemaxon.metabolizer.MetabolizerMemoryImporter
-
- getMoleculeGraph() -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Gets the stored molecule graph.
- getMoleculeIterator() -
Method in class chemaxon.marvin.io.MDocSource
- Gets a molecule iterator for this document source.
- getMoleculeIterator(MolImporter) -
Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
- Gets a molecule iterator from the importer.
- getMoleculeIterators(MolImporter[]) -
Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
- Gets molecule iterators from the importers in an array.
- getMoleculeMovie() -
Method in class chemaxon.struc.MDocument
- Gets the molecule movie.
- getMoleculeOrig() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getMolecules() -
Method in class chemaxon.sss.screen.StrucFPConfig
- Gets the Molecule objects for the keys
- getMoleculeString() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the last molecule as a string.
- getMoleculeToClipboardTask(Molecule, Properties, String) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getMoleculeWithAlignedCoordinates(int) -
Method in class chemaxon.marvin.alignment.Alignment
- After the alignment result molecule can be obtained.
- getMolfileExtensions() -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the array of known molecule file extensions.
- getMolfileFormats() -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the array of known molecule file formats.
- getMolfileVersion() -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Gets the molfile version.
- getMolfileVersion() -
Method in class chemaxon.marvin.io.formats.mdl.MolImport
- Gets the molfile version.
- getMolID() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getMolImportModule() -
Method in class chemaxon.formats.MolImporter
-
- getMolImportModule() -
Method in class chemaxon.marvin.io.MRecordImporter
-
- getMolIndex() -
Method in exception chemaxon.marvin.io.MolExportException
- Returns the molecule index.
- getMolInputStream() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Gets the molecule input stream.
- getMolInputStream() -
Method in interface chemaxon.marvin.io.MRecordReader
- Gets the molecule input stream.
- getMolInputStream(String) -
Static method in class chemaxon.marvin.space.MSpaceEasy
- Creates a
MolInputStream from the given String to
be able to manually add molecules to the event handler.
- getMolNameFontSize() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the molecule name font size.
- getMolObject(int) -
Method in class chemaxon.struc.graphics.MEFlow
- Gets the electron source or sink.
- getMolPainter(int, String) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets a molecule painter.
- getMolPanel() -
Method in class chemaxon.marvin.beans.MarvinPane
- Returns the underlying panel.
- getMolPolarizability() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the molecular polarizability value.
- getMolString() -
Method in class chemaxon.marvin.io.MRecord
- Gets the molecule string, with preprended header and appended footer
if appropriate.
- getMolStrings() -
Method in class chemaxon.sss.screen.StrucFPConfig
- Gets the original strings for the keys
- getMonitorColor() -
Method in class chemaxon.marvin.space.monitor.DihedralMonitor
- Returns the color of the control if it exists.
- getMonitorColor() -
Method in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
- getMostFrequentNaturalIsotope(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Returns the mass number of the most frequent natural isotope of the
element
- getMostLikelyMolFormat(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the most likey molecule file format from the file name extension.
- getMostSimplifiedMolecule() -
Method in class chemaxon.struc.Molecule
- Gets the simplified molecule object even if there is a parent document
with other objects.
- getMostSimplifiedMolecule() -
Method in class chemaxon.struc.RgMolecule
- Gets the simplified molecule object even if there is a parent document
with other objects.
- getMProp() -
Method in class chemaxon.struc.MDocument
- Gets the document as a property.
- getMrvWithSettings() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the molecule in the sketcher with its current settings in
MRV format.
- getMsAcceptorCounts() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the average acceptor counts over the microspecies distribution
for different pH-s.
- getMsCount() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the number of microspecies.
- getMsDistribution(int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the microspecies distribution array.
- getMsDistributions() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the microspecies distribution arrays for all microspecies:
the i-th element is the disrtibution array of the i-th microspecies.
- getMsDonorCounts() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the average donor counts over the microspecies distribution
for different pH-s.
- getMSketchPane() -
Method in class chemaxon.marvin.beans.MSketch
-
- getMSLogic() -
Method in class chemaxon.struc.RxnMolecule
- Gets the hash that stores arrow - reaction mapping.
- getMsMolecule(int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the microspecies molecule.
- getMultiplier() -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Gets the multiplier.
- getMViewPane() -
Method in class chemaxon.marvin.beans.MView
-
- getMViewParam() -
Method in class chemaxon.marvin.beans.MViewParams
- Generates the parameter string that can be set to MViewPane.
- getMyTemplatesKey() -
Static method in class chemaxon.marvin.common.UserSettings
- Deprecated. since 5.4 use
TemplateHandler.MYTEMPLATES_KEY
instead.
- getMyTemplatesValue(Properties) -
Static method in class chemaxon.marvin.common.UserSettings
- Deprecated. since 5.4 no replacements
- getMyTemplatesValue() -
Method in class chemaxon.marvin.common.UserSettings
- Deprecated. since 5.4
- getName() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the name of the element
- getName() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- getName() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getName() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getName() -
Method in interface chemaxon.checkers.StructureChecker
- Deprecated. This method isn't needed anymore and will be removed in 6.0
- getName() -
Method in class chemaxon.descriptors.BCUT
- Gets the name of the
BCUT descriptor object.
- getName() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets the name of the ChemicalFingerprint object.
- getName() -
Method in class chemaxon.descriptors.CustomDescriptor
- Gets the name of the
CustomDescriptor object.
- getName() -
Method in class chemaxon.descriptors.ECFP
- Gets the name of the
ECFP fingerprint object.
- getName() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the name of the descriptor.
- getName() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the name of the PharmacophoreFingerprint object.
- getName() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the nice name of the
ReactionFingerprint descriptor
object.
- getName() -
Method in class chemaxon.descriptors.ScalarDescriptor
- Gets the name of the ScalarDescriptor object.
- getName() -
Method in class chemaxon.descriptors.scalars.HAcc
- Gets the name of the HAcc descriptor object.
- getName() -
Method in class chemaxon.descriptors.scalars.HDon
- Gets the name of the HDon descriptor object.
- getName() -
Method in class chemaxon.descriptors.scalars.Heavy
- Gets the name of the HeavyAtomCount descriptor object.
- getName() -
Method in class chemaxon.descriptors.scalars.LogD
- Gets the name of the LogD descriptor object.
- getName() -
Method in class chemaxon.descriptors.scalars.LogP
- Gets the name of the LogP descriptor object.
- getName() -
Method in class chemaxon.descriptors.scalars.Mass
- Gets the name of the Mass descriptor object.
- getName() -
Method in class chemaxon.descriptors.scalars.TPSA
- Gets the name of the TPSA descriptor object.
- getName() -
Method in class chemaxon.descriptors.ShapeDescriptor
- Gets the name of the
ShapeDescriptor fingerprint object.
- getName() -
Method in class chemaxon.fixers.AbstractStructureFixer
-
- getName() -
Method in interface chemaxon.fixers.StructureFixer
-
- getName() -
Method in class chemaxon.formats.MFileFormat
- Gets the codename of the format.
- getName() -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- Gets the name of the represented
MTransferable.
- getName() -
Method in class chemaxon.marvin.services.ServiceArgument
- Returns the name of the argument
- getName() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the name of the component.
- getName() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getName() -
Method in class chemaxon.marvin.space.PharmacophoreArrow
-
- getName() -
Method in class chemaxon.marvin.space.PharmacophorePoint
-
- getName() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Gets the option name.
- getName() -
Method in interface chemaxon.struc.Incomplecule
- Gets the molecule name.
- getName() -
Method in class chemaxon.struc.Molecule
- Gets the molecule name.
- getName() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the molecule name.
- getName(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Name of the element
- getName() -
Method in class chemaxon.struc.RgMolecule
- Gets the name of the root molecule.
- getNameFieldInDB() -
Method in class chemaxon.jchem.db.Importer
-
- getNames() -
Method in class chemaxon.formats.MFileFormat
- Gets all the codename of the format.
- getNameSpace() -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- Returns the namespace
- getNaturalId() -
Method in class chemaxon.descriptors.MDSet
- Gets the natural identifier of the source
Molecule of the
MDSet.
- getNavmode() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the mouse drag action.
- getNDists() -
Method in class chemaxon.descriptors.PFParameters
- Gets the number of histograms bars, that is that number of
distance values disguished.
- getNearClip() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the z coordinate of the nearer clipping plane
which is computed considering all components.
- getNeededMetaboliteSmiles() -
Method in class chemaxon.metabolizer.Metabolizer
-
- getNeighbor(int, int) -
Method in interface chemaxon.struc.Smolecule
- Gets the index of a neighbor of an atom.
- getNeighborCount(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the number of neighbors of an atom.
- getNewToOld() -
Method in class chemaxon.reaction.Standardizer
- Returns the new -> old atom index mapping.
- getNext() -
Method in class chemaxon.util.concurrent.marvin.CompositeInputProducer
- Returns the next input object array (one input from each input producer).
- getNext() -
Method in class chemaxon.util.concurrent.marvin.MolInputProducer
- Returns the next input molecule.
- getNext() -
Method in class chemaxon.util.concurrent.marvin.ReusableInputProducer
- Returns the next input object.
- getNextAromatizedStructure() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the next enumerated structure.
- getNextDissimilarHit() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Retrieves ids of target hits found in a previous screen or evaluation
one by one.
- getNextHit() -
Method in class chemaxon.jchem.db.JChemSearch
- Used with run mode =
JChemSearch.RUN_MODE_ASYNCH_PROGRESSIVE.
- getNextHit() -
Method in class chemaxon.util.HitDisplayTool
- Gets the next hit.
- getNextSimilarHit() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Retrieves ids of known similar hits found in a previous screen or evaluation
one by one.
- getNextStructure() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the next enumerated structure, or
null if no more structures.
- getNextUpdateInfo() -
Method in class chemaxon.jchem.db.Updater
- Returns the update information for the next update step.
- getNode(int) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.getAtom(int).
- getNode1() -
Method in class chemaxon.struc.MolBond
- Deprecated. As of Marvin 5.3, replaced by
MolBond.getAtom1().
- getNode2() -
Method in class chemaxon.struc.MolBond
- Deprecated. As of Marvin 5.3, replaced by
MolBond.getAtom2().
- getNodeCount() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getNodeCount() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.getAtomCount().
- getNodes() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getNodeVector() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
Arrays.asList(getAtomArray()).
- getNonAromrings() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. please use getAromaticAndAliphaticRings instead.
- getNonAromrings(int) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. please use getAromaticAndAliphaticRings instead.
- getNonHitBondEndpoints(Molecule, Molecule, int[]) -
Static method in class chemaxon.util.MolHandler
- Returns the bonds of the target molecule that should not be colored
in hit highlighting.
- getNonHitBonds(Molecule, Molecule, int[]) -
Static method in class chemaxon.util.HitDisplayUtil
- Returns the bonds of the target molecule that should not be colored
in hit highlighting.
- getNonHitBonds(Molecule, Molecule, int[]) -
Static method in class chemaxon.util.MolHandler
- Returns the bonds of the target molecule that should not be colored
in hit highlighting.
- getNonQueryImplicitHcount() -
Method in class chemaxon.struc.MolAtom
- Gets the number of implicit hydrogens attached.
- getNormal(int) -
Method in class chemaxon.marvin.space.SurfaceComponent
- Warning: for internal use only.
- getNormalViewSplit() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the normalViewSplit
- getNote() -
Method in class chemaxon.jchem.db.Importer
- Returns the note of the progresswriter.
- getNote() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the additional note that is displayed along with the
progress message.
- getNotSpec() -
Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- getNrOfQueries() -
Method in class chemaxon.descriptors.MDSimilarity
- Gets the number of queries that have already been added.
- getNrOfUsedMetrics(int) -
Method in class chemaxon.descriptors.MDSimilarity
- Return the number of metrics used with the given molecular descriptor
in similarity calculations.
- getNucleophilicEnergy(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the nucleophilic energy (localization energy L-) of an atom,
Double.NaN for no value.
- getNucleophilicOrder(int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Deprecated. Use
HuckelAnalysisPlugin.getHMONucleophilicOrder(int)
- getNumberFormat() -
Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
-
- getNumberOfDissimilarHits() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Returns the number of hits from the set of target molecules, found in a
previous evaluation or screen.
- getNumberOfDissimilars() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Returns the number of target molecules (read by dissimilarReader
previously).
- getNumberOfFeatures() -
Method in class chemaxon.descriptors.PFParameters
- The number of pharmacophore features (aka types, properties) used in the
fingerprints.
- getNumberOfFeatures() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getNumberOfIntegersNeeded() -
Method in class chemaxon.sss.screen.StrucFPConfig
- Indicates the number of 32 bit units needed to store the fingerprint.
- getNumberOfKeys() -
Method in class chemaxon.sss.screen.StrucFPConfig
- Indicates the number of structural keys.
- getNumberOfMetrics() -
Method in class chemaxon.descriptors.MDParameters
- Gets the total number of parametrized metrics available in the present
configuration.
- getNumberOfMetrics() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the number of parameterized metrics available for the particular
descriptor.
- getNumberOfMetrics() -
Method in class chemaxon.descriptors.SDParameters
- Gets the total number of parametrized metrics available in the present
configuration.
- getNumberOfSimilarHits() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Returns the number of hits from the known similar molecules, found in a
previous evaluation or screen.
- getNumberOfSimilars() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Returns the number of known similar molecules (read by similarReader
previously).
- getNumberOfWeights(int) -
Method in class chemaxon.descriptors.BCUTParameters
- Gets the number of weight factors used by the specified metric.
- getNumberOfWeights(int) -
Method in class chemaxon.descriptors.CDParameters
- Gets the number of weight factors used by the specified metric.
- getNumberOfWeights(int) -
Method in class chemaxon.descriptors.CFParameters
- Gets the number of weight factors used by the specified metric.
- getNumberOfWeights(int) -
Method in class chemaxon.descriptors.ECFPParameters
- Gets the number of weight factors used by the specified metric.
- getNumberOfWeights() -
Method in class chemaxon.descriptors.MDParameters
- Gets the number of weights the current parametrized metric takes.
- getNumberOfWeights(int) -
Method in class chemaxon.descriptors.MDParameters
- Gets the number of weight factors used by the specified metric.
- getNumberOfWeights(String) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the number of weight factors used by the specified metric.
- getNumberOfWeights(int) -
Method in class chemaxon.descriptors.PFParameters
- Gets the number of weight factors used by the specified metric.
- getNumberOfWeights(int) -
Method in class chemaxon.descriptors.RFParameters
- Gets the number of weight factors used by the specified metric.
- getNumElectrons() -
Method in class chemaxon.struc.graphics.MEFlow
- Gets the number of electrons the arrow represents.
- getObject(int) -
Method in class chemaxon.struc.MDocument
- Gets an object from the document.
- getObject(String) -
Method in class chemaxon.struc.MPropertyContainer
- Gets a property object.
- getObjectAtPointer() -
Method in class chemaxon.marvin.beans.MSketchPane
- Get the object at the mouse pointer.
- getObjectContainingSelection() -
Method in class chemaxon.struc.MDocument
- Gets the object that contains the selection.
- getObjectCount() -
Method in class chemaxon.struc.MDocument
- Gets the number of objects in this document.
- getObjectCount() -
Method in class chemaxon.struc.Molecule
-
- getObjectCount() -
Method in class chemaxon.struc.RgMolecule
-
- getObjectCount() -
Method in class chemaxon.struc.RxnMolecule
-
- getObjectFromClipboard() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns the current content of the clipboard if the data can be imported
in any of data formats supported by MolImporter.
- getObjectFromClipboard(boolean) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getObjectFromTransferable(Transferable) -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns the content of Transferable if the data can be imported in any of
data formats supported by MolImporter.
- getObjectFromTransferable(Transferable, boolean) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getObjectsMiddle(DPoint3) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Calculates the middle point of the coordinates of objects this sgroup is
associated to.
- getOffset() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the offset in the document source.
- getOldToNew() -
Method in class chemaxon.reaction.Standardizer
- Returns the old -> new atom index mapping.
- getOLEToClipboardTask(Molecule, Properties) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getOpenFileAction() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the
Action associated with open file event, or null if no Action
- getOperatorToolBar(JTextPane) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Returns the operator toolbar for textPane instance
NOTE: textPane have to be created with this factory
- getOption(String) -
Method in class chemaxon.sss.search.JChemSearchOptions
- Returns search option value in string format.
- getOption(String) -
Method in class chemaxon.sss.search.MolSearchOptions
- Returns search option value in string format.
- getOption(String) -
Method in class chemaxon.sss.search.SearchOptions
- Returns option value in string format.
- getOptionDescriptors(String, String, List<OptionDescriptor>) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Gets the option descriptors.
- getOptionDescriptors(String) -
Method in class chemaxon.marvin.io.MolExportModule
- Gets an array of option descriptors for the specified format.
- getOptionDescriptors(String, String, List<OptionDescriptor>) -
Method in class chemaxon.marvin.io.MolExportModule
- Gets an array of option descriptors.
- getOptionDescriptors(ResourceBundle, String, String, List<OptionDescriptor>) -
Static method in class chemaxon.marvin.io.MolExportModule
- Gets an array of option descriptors.
- getOptionFlags() -
Method in class chemaxon.formats.MolImporter
- Deprecated. As of Marvin 5.2, use the "MOLMOVIE" and "NOMOLMOVIE" import
options instead. See
MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie().
- getOptionNames() -
Method in class chemaxon.sss.search.JChemSearchOptions
-
- getOptionNames() -
Method in class chemaxon.sss.search.MolSearchOptions
- Gets the names for all search options.
- getOptionNames() -
Method in class chemaxon.sss.search.SearchOptions
-
- getOptions() -
Method in class chemaxon.formats.MolImporter
- Gets the import options.
- getOptions() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Gets the import options.
- getOptions() -
Method in class chemaxon.marvin.io.MolExportModule
- Returns the output options.
- getOptions() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the options for the import module.
- getOptions() -
Method in interface chemaxon.marvin.io.MRecordReader
- Gets the import options.
- getOptionSign() -
Method in class chemaxon.marvin.io.MolExportModule
- Gets the sign of the options.
- getOptionsPane(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets the options pane for a plugin, loads it if needed.
- getOptionsPane() -
Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getOptionsToDeselect() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Gets the options that must be deselected if this option is selected.
- getOptionsToDisable() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Gets the options that must be switched off if this option is selected.
- getOptionsToEnable() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Gets the options that must be switched off if this option is selected.
- getOrder() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property order.
- getOrientation() -
Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- getOrientationType() -
Method in class chemaxon.marvin.alignment.Alignment
-
- getOrigQueryAtom(int) -
Method in class chemaxon.sss.search.MolComparator
- Converts search internal atom index (in the query) to the original
atom index in the query molecule.
- getOrigQueryAtom1(int) -
Method in class chemaxon.sss.search.MolComparator
- Returns the index of the first atom (atom index in the query molecule)
of the given query bond(search internal bond index in the query).
- getOrigQueryAtom2(int) -
Method in class chemaxon.sss.search.MolComparator
- Returns the index of the second atom (atom index in the query molecule)
of the given query bond(search internal bond index in the query).
- getOrigQueryBond(int) -
Method in class chemaxon.sss.search.MolComparator
- Returns bond index in the query molecule
for the given query bond (search internal bond index in the query).
- getOrigQueryNeighbour(int) -
Method in class chemaxon.sss.search.MolComparator
- For a search internal atom index (in the query), returns a neighbour
atom index (original atom index in the query molecule).
- getOrigTargetAtom(int) -
Method in class chemaxon.sss.search.MolComparator
- Converts search internal atom index (in the target) to the original
atom index in the target molecule.
- getOrigTargetAtom1(int) -
Method in class chemaxon.sss.search.MolComparator
- Returns the index of the first atom (atom index in the target molecule)
of the given target bond(search internal bond index in the target).
- getOrigTargetAtom2(int) -
Method in class chemaxon.sss.search.MolComparator
- Returns the index of the second atom (atom index in the target molecule)
of the given target bond(search internal bond index in the target).
- getOrigTargetBond(int) -
Method in class chemaxon.sss.search.MolComparator
- Returns bond index in the target molecule
for the given target bond (search internal bond index in the target).
- getOrigTargetNeighbour(int) -
Method in class chemaxon.sss.search.MolComparator
- For a search internal atom index (in the target), returns a neighbour
atom index (original atom index in the target molecule).
- getOtherAtom(MolAtom) -
Method in class chemaxon.struc.MolBond
- Gets the other end of the bond.
- getOtherCrossingBond(MolBond) -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Gets the other bond if a bond is a crossing bond in a ladder-type polimer
bracket.
- getOtherEnd() -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Gets the atom at the other end point.
- getOtherNode(MolAtom) -
Method in class chemaxon.struc.MolBond
- Deprecated. As of Marvin 5.3, replaced by
MolBond.getOtherAtom(MolAtom).
- getOutputFieldConversion() -
Method in class chemaxon.jchem.db.Exporter
- Get the DB field name / user defined name conversion rules.
- getOutputFieldNames() -
Method in class chemaxon.jchem.db.Exporter
- Get the names of the data fields in the output file.
- getOutputStream() -
Method in class chemaxon.jchem.db.Exporter
- Gets the OutputStream object to export to.
- getOutputTransferFormatIds() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getOwnerCount() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the current number of owners.
- getPageNumber() -
Method in class chemaxon.naming.DocumentExtractor.Hit
- For document formats that have a notion of page (for instance PDF),
this method returns the page the hit occurs on.
- getPageSettings() -
Method in class chemaxon.struc.MDocument
- Gets the page settings of multipage molecular document.
- getPalette() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the used built-in palette.
- getPaletteString() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the string identifier of the used built-in palette.
- getParameter(String) -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets a parameter.
- getParameter(String) -
Method in class chemaxon.util.UploadThread
- Returns the value of parameter posted by the HTML form.
- getParameterNames() -
Method in class chemaxon.util.UploadThread
- Returns the names of parameters posted by the HTML form.
- getParameterPanel() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns the parameter panel.
- getParameterPanel(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets the parameter panel for a plugin, loads it if needed.
- getParameterPanel() -
Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getParameters() -
Method in class chemaxon.descriptors.MDSet
- Gets the current parameter settings.
- getParameters() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the parameters associated with the object.
- getParameters(Properties) -
Method in class chemaxon.marvin.plugin.gui.OptionsPane
- Returns the parameters set by the user.
- getParameters(Properties) -
Method in class chemaxon.marvin.plugin.gui.ParameterPanel
- Returns the plugin parameters.
- getParameters(Properties) -
Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
- Returns the plugin parameters.
- getParametersClassName() -
Method in class chemaxon.descriptors.BCUT
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.CustomDescriptor
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.ECFP
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the name of the parameters class corresponding to the descriptor
(prefixed with the package name as getClass().getName() would return).
- getParametersClassName() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.ScalarDescriptor
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.scalars.HAcc
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.scalars.HDon
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.scalars.Heavy
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.scalars.LogD
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.scalars.LogP
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.scalars.Mass
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.scalars.TPSA
- Gets the name of the parameters class corresponding to the descriptor.
- getParametersClassName() -
Method in class chemaxon.descriptors.ShapeDescriptor
- Gets the name of the parameters class corresponding to the descriptor.
- getParams() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the parameter string.
- getParent() -
Method in class chemaxon.struc.MolAtom
- Return the molecule graph that contains this atom.
- getParent() -
Method in class chemaxon.struc.MolBond
- Gets the parent graph.
- getParent() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the parent graph that contains this substructure.
- getParentDocument() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the document or the document of the parent graph.
- getParentLine() -
Method in class chemaxon.struc.graphics.MMidPoint
- Gets the parent line.
- getParentMolecule() -
Method in class chemaxon.struc.Sgroup
- Gets the parent molecule.
- getParentRect() -
Method in class chemaxon.struc.graphics.MRectanglePoint
- Gets the parent rectangle.
- getParentSgroup() -
Method in class chemaxon.struc.Sgroup
- Gets the parent S-group.
- getParentSgroupGraph() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the parent exact sgroupgraph.
- getParity(int) -
Method in class chemaxon.struc.MoleculeGraph
- Computes the parity of an atom of the Molecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- getParity(int) -
Method in class chemaxon.struc.RgMolecule
- Computes the parity of an atom of the RgMolecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- getParity(int) -
Method in class chemaxon.struc.RxnMolecule
- Computes the parity of an atom of the RxnMolecule instance based on both
the coordinates of the neighboring atoms and the stereo information
of the bonds to those.
- getParity(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the parity of an atom.
- getParityType(int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets parity type.
- getParsed() -
Method in exception chemaxon.naming.NamePrefixException
-
- getPartialAtomCharge(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getPartialAtomCharge(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getPassword() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
password.
- getPath() -
Method in class chemaxon.formats.MolInputStream
- Gets the path or URL of the file.
- getPercent() -
Method in class chemaxon.util.UploadThread
- Returns the rate of saved data and whole data.
- getpH() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Returns the pH where the major microspecies should be taken.
- getpH() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the pH where the major microspecies should be taken.
- getpH() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the pH where the major microspecies should be taken.
- getPharmacophore() -
Method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- getpHs() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the pH array.
- getpHs() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the pH array.
- getpHs() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the pH array.
- getpHs() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the pH array.
- getpI() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the isoelectric point.
- getPiCharge(int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the pi charge of a specified atom.
- getPiece(String) -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the current molecule piece in the specified format.
- getPiOEN(int) -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the pi orbital electronegativity of a specified atom.
- getpKa(int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the most significant pKa value for the given atom index.
- getpKa(int, int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Deprecated. Use
pKaPlugin.getpKaValues(int, int)
- getpKaPrefixType() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the pKa prefix type.
- getpKaType(int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the pKa type:
pKaPlugin.ACIDIC, pKaPlugin.BASIC or 0
if there is no pKa value for the given atom.
- getpKaValues(int, int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the pKa values for the given atom index and pKa type.
- getPlaceholderText() -
Method in class chemaxon.marvin.services.DynamicArgument
- Returns the value placeholder text.
- getPlacementOrigin(DPoint3) -
Method in class chemaxon.struc.sgroup.DataSgroup
- If isAbsolutePlacement is false it calculates the middle point of the
coordinates of atoms this S-group is associated to.
- getPlainText() -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the document as plain text.
- getPlainText() -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the selected text as a plain text string.
- getPlattIndex() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the Platt index of the molecule which is equal to the total
sum of the edge degrees of a molecular graph.
- getPlugin() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns the plugin.
- getPlugin() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the calculator plugin object.
- getPlugin() -
Method in exception chemaxon.marvin.plugin.concurrent.PluginExecutionException
- Returns the plugin object.
- getPlugin(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets a plugin, loads it if needed.
- getPlugin() -
Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- getPluginIDs() -
Method in class chemaxon.jep.Evaluator
- Deprecated. use
Evaluator.getFunctionData()
- getPluginIndex(String) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets a plugin index from record key.
- getPluginList() -
Static method in class chemaxon.license.LicenseManager
- Returns the list of the plugin identifiers known by the license manager.
- getPluginParameters() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the plugin parameter table (this should be set in the plugin).
- getPluginResource(String) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the plugin JAR as resource URL,
given the JAR file path relatively to the "plugins" directory.
- getPMap(Molecule, PSymbols) -
Method in class chemaxon.descriptors.PFGenerator
- Gets pharmacophore map of the input molecule.
- getPMAPTagName() -
Method in class chemaxon.descriptors.PFGenerator
- Gets the name of the SDfile tag (Molecule property) which stores
the pharmacophore map data.
- getPoint(int) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Gets the point.
- getPoint(int) -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Gets a point of the object.
- getPoint(int) -
Method in class chemaxon.struc.graphics.MEFlow
- Gets a point of the line.
- getPoint(int) -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Gets the point.
- getPoint(int) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets a point of the line.
- getPoint(int) -
Method in class chemaxon.struc.MObject
- Gets a point of the object.
- getPoint(int) -
Method in class chemaxon.struc.MPoint
- Gets the point.
- getPointCount() -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Gets the number of points (atoms).
- getPointCount() -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the number of points.
- getPointCount() -
Method in class chemaxon.struc.MObject
- Gets the number of points.
- getPointCount() -
Method in class chemaxon.struc.MPoint
- Gets the number of points.
- getPointRef(int, CTransform3D) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets a reference to a point or midpoint in the polyline.
- getPointRef(int, CTransform3D) -
Method in class chemaxon.struc.graphics.MRectangle
- Gets an internal selectable point of the rectangle.
- getPointRef(int, CTransform3D) -
Method in class chemaxon.struc.graphics.MRoundedRectangle
- Gets an internal selectable point of the rectangle.
- getPointRef(int, CTransform3D) -
Method in class chemaxon.struc.MObject
- Gets a reference to a point of the object.
- getPointRef(int, CTransform3D) -
Method in class chemaxon.struc.MPoint
- Gets a point of the line.
- getPointRefCount() -
Method in class chemaxon.struc.graphics.MEFlow
- Gets the number of point references.
- getPointRefCount() -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the number of point references.
- getPointRefCount() -
Method in class chemaxon.struc.graphics.MRectangle
- Gets the number of internal selectable point references.
- getPointRefCount() -
Method in class chemaxon.struc.graphics.MRoundedRectangle
- Gets the number of internal selectable point references.
- getPointRefCount() -
Method in class chemaxon.struc.MObject
- Gets the number of point references.
- getPointRefCount() -
Method in class chemaxon.struc.MPoint
- Gets the number of point references.
- getPoints() -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the points.
- getPoints() -
Method in class chemaxon.struc.MoleculeGraph
- Gets an array containing the atom coordinates.
- getPoints(int) -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Gets the Hydrogen locations for an atom.
- getPolarizability(int) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the atom polarizability value.
- getPopupMenusEnabled() -
Method in class chemaxon.marvin.beans.MarvinPane
- Are popup menus enabled?
- getPortion(int, int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets a portion of the document.
- getPortion(int, int) -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets a portion of the text relative to this portion.
- getPortName() -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- Returns the port name
- getPos() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the data display DASP position (0...9).
- getPosition() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Gets the current position.
- getPosition() -
Method in exception chemaxon.marvin.io.MRecordParseException
- Gets the position of the error.
- getPosition() -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Returns the monitor's position.
- getPosition() -
Method in class chemaxon.struc.graphics.MTextDocument.Section
- Gets the position in the document.
- getPositionInPolyline() -
Method in class chemaxon.struc.graphics.MMidPoint
- Gets the position in the polyline.
- getPositionInRect() -
Method in class chemaxon.struc.graphics.MRectanglePoint
- Gets the position in the rectangle.
- getPositionsString() -
Method in class chemaxon.naming.DocumentExtractor.Hit
-
- getPossibleRotatableBondCount() -
Method in class chemaxon.marvin.alignment.AtropIsomerDetector
- Rotatable bond count before the atrop isomer calculation.
- getPreBreakingChars() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the breaking characters before that the text in the text
box can be broken if it doesn't fit into the text box.
- getPrecalculatedRowNumber(ConnectionHandler, String) -
Static method in class chemaxon.jchem.db.UpdateHandler
-
- getPredictedValue() -
Method in class chemaxon.marvin.calculations.PredictorPlugin
- Returns the predicted value.
- getPreferredIUPACName() -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns the preferred IUPAC name.
- getPreferredLabelDir(CTransform3D, int) -
Method in class chemaxon.struc.MolAtom
- Gets the preferred direction for an additional label.
- getPreferredSize() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the preferred size of the component.
- getPreferredTableType(Molecule) -
Static method in class chemaxon.jchem.db.UpdateHandler
- Returns the preferred table type for the given molecule object.
- getPreferredView() -
Method in class chemaxon.marvin.io.MolImportModule
- Specifies which view style is preferred (for instance in MarvinView) for this format.
- getPrefix() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- Returns the code assist invoke prefix
- getPresentationChooser() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the presentationChooser
- getPreviousNormalTextSectionIndex() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the index of the last `normal' text section before the
current subscript/superscript section.
- getPrimaryMolecule() -
Method in class chemaxon.struc.MDocument
- Gets the primary molecule object.
- getPrimaryMolecules() -
Method in class chemaxon.struc.MDocument
- Gets an array containing the primary molecule objects.
- getPrimitives() -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the primitives (for example triangles) of the surface.
- getPrincipalPolarizabilityComponents() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the principal components
a(xx), a(yy), a(zz)
of polarizability tensor
(for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
- getPrintableStats(ConnectionHandler, String) -
Method in class chemaxon.jchem.db.TableStatistics
- Get printable statistics for the JChem table specified.
- getPriority(String) -
Method in class chemaxon.formats.MFileFormat
- Gets the priority determining format recognition order.
- getPriority() -
Method in class chemaxon.formats.recognizer.Recognizer
- Deprecated. as of Marvin 5.1,
use
MFileFormat.getPriority(java.lang.String) instead
- getPriority() -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- Gets the priority of the
MTransferable object by exporting to
clipboard.
- getProbeRadius() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the probe radius the surface computing will use.
- getProduct(int) -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the i-th product.
- getProduct(int) -
Method in class chemaxon.struc.RxnMolecule
- Gets a product.
- getProductAtom(int) -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the i-th atom existing only on the product side.
- getProductAtomCount() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the number of atoms existing only on the product side.
- getProductCount() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the number of products.
- getProductCount() -
Method in class chemaxon.reaction.Reactor
- Returns the number of products.
- getProductCount() -
Method in class chemaxon.struc.RxnMolecule
- Gets the number of products.
- getProductList(boolean) -
Static method in class chemaxon.license.LicenseManager
- Returns the list of the product identifiers known by the license manager.
- getProductName() -
Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- getProductName() -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
- getProductName() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- getProductName() -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
-
- getProductName() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getProductName() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProductName() -
Method in class chemaxon.marvin.calculations.TPSAPlugin
-
- getProductName() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the product identifier of the plugin as given by
LicenseManager.
- getProducts() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the reaction products.
- getProducts() -
Method in class chemaxon.struc.RxnMolecule
- Gets all products in an array.
- getProductStandardizer() -
Method in class chemaxon.reaction.Reactor
- Deprecated. Will be removed. Use
Standardizer to standardize products.
- getProductTanimoto(ReactionFingerprint) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Returns the tanimoto distance of the product sides.
- getProfile() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the current profile
Note, that profile may be out of sync as various editors may
use the same profile to store custom properties.
- getProgessLength() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getProgessLength() -
Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getProgessLength() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
- Deprecated.
- getProgress() -
Method in class chemaxon.jchem.db.Importer
- Gets the status of the importing progress.
- getProgress() -
Method in class chemaxon.jchem.file.ProgressWriter
- Return the current value of the monitored progress.
- getProgress() -
Method in class chemaxon.reaction.ConcurrentReactorProcessor
- Estimates the progress.
- getProgress() -
Method in class chemaxon.reaction.ConcurrentStandardizerProcessor
- Estimates the progress.
- getProgress() -
Method in interface chemaxon.reaction.ReactantSetEnumeration
- Returns a number between 0 and 1 that indicates the status of the enumeration progress.
- getProgressBar() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getProgressMessage() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property progressMessage.
- getProgressMonitor(Component) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates a progress observer object to be used in
CalculatorPlugin.setProgressMonitor(chemaxon.common.util.MProgressMonitor).
- getProgressWriter() -
Method in class chemaxon.jchem.db.Importer
- Gets the ProgressWriter object used for monitoring.
- getPropArraySize() -
Method in class chemaxon.struc.MDocument.Prop
- Gets the array size.
- getPropArraySize() -
Method in class chemaxon.struc.MProp
- Gets the array size.
- getPropArraySize() -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Gets the array size.
- getPropArraySize() -
Method in class chemaxon.struc.prop.MHashProp
- Gets the array size.
- getPropArraySize() -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Gets the array size.
- getPropArraySize() -
Method in class chemaxon.struc.prop.MListProp
- Gets the array size.
- getPropertiesDescriptionChangedByOtherApp() -
Method in class chemaxon.marvin.common.UserSettings
- The method collects the changes in the config file, if its timestamp was
changed.
- getProperty(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Searches for the property with the specified key in the
JChemProperties table.
- getProperty(String) -
Method in class chemaxon.marvin.common.UserSettings
- Returns the value for the given key.
- getProperty(String) -
Method in class chemaxon.struc.MolAtom
- Returns the property value to which the specified property key is mapped
at this atom, or null if this atom has no mapping for this property key.
- getProperty(String) -
Method in class chemaxon.struc.Molecule
- Deprecated. as of Marvin 5.7 replaced by
MPropHandler.convertToString(MProp, String),
the following usage will give the same results:
String property = MPropHandler.convertToString(mol.properties(), key);
- getPropertyChangeSupport() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the propertyChangeSupport
- getPropertyChangeSupport() -
Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
- Returns the
PropertyChangeSupport associated with this editor
- getPropertyContainer() -
Method in class chemaxon.marvin.io.MRecord
- Gets the properties.
- getPropertyCount() -
Method in class chemaxon.struc.Molecule
- Gets the total number of RDfile/SDfile properties.
- getPropertyDescriptors(Class, Vector) -
Method in class chemaxon.marvin.beans.MarvinPaneBeanInfo
- Puts the descriptors of the common Marvin bean properties into the
specified Vector.
- getPropertyDescriptors() -
Method in class chemaxon.marvin.beans.MSketchPaneBeanInfo
- Returns the property descriptor array.
- getPropertyDescriptors() -
Method in class chemaxon.marvin.beans.MViewPaneBeanInfo
- Returns the property descriptor array.
- getPropertyKey(int) -
Method in class chemaxon.struc.Molecule
- Gets an RDfile/SDfile property key.
- getPropertyKeys() -
Method in class chemaxon.struc.Molecule
- Deprecated. as of Marvin 4.1, replaced by
properties().getKeys()
- getPropertyMap() -
Method in class chemaxon.marvin.common.UserSettings
- Shortcut to getPropertyMap(UserSettings.PROPERTY_TYPE_ALL)
- getPropertyMap(String) -
Method in class chemaxon.marvin.common.UserSettings
- Returns a map of properties from the given type.
- getPropertyObject(String) -
Method in class chemaxon.struc.Molecule
- Gets an RDfile/SDfile property object.
- getPropertyTable() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
propertyTable.
- getPropertyText(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns molecule properties is text form.
- getPropList() -
Method in class chemaxon.struc.MPropertyContainer
- Gets the list of basic properties.
- getPropType() -
Method in class chemaxon.struc.MDocument.Prop
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.MProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MBooleanProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MDoubleProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MHashProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MIntegerProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MListProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MMoleculeProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MObjectProp
- Gets the type name of the property.
- getPropType() -
Method in class chemaxon.struc.prop.MStringProp
- Gets the type name of the property.
- getPropValue() -
Method in class chemaxon.struc.MDocument.Prop
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.MProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MBooleanProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MDoubleProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MHashProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MIntegerProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MListProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MMoleculeProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MObjectProp
- Gets the property value as an object.
- getPropValue() -
Method in class chemaxon.struc.prop.MStringProp
- Gets the property value as an object.
- getPropXSDType() -
Method in class chemaxon.struc.MDocument.Prop
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.MProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MBooleanProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MCollectionProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MDoubleProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MIntegerProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MMoleculeProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MObjectProp
- Gets the XSD type name of the property.
- getPropXSDType() -
Method in class chemaxon.struc.prop.MStringProp
- Gets the XSD type name of the property.
- getPSymbols() -
Method in class chemaxon.descriptors.PFParameters
- Gets the pharmacophore type symbols used in the current configuration.
- getQProp(String) -
Method in class chemaxon.struc.MolAtom
- Gets a query property.
- getQPropAsInt(String) -
Method in class chemaxon.struc.MolAtom
- Gets a query property as an integer.
- getQPropAsInt(int, String) -
Method in interface chemaxon.struc.Smolecule
- Gets a query property as an integer.
- getQPropMinMax(String) -
Method in class chemaxon.struc.MolAtom
- Gets the minimum and maximum possible values of a query property.
- getQPropNames() -
Method in class chemaxon.struc.MolAtom
- Gets the names of query properties with non-null values.
- getQPropNameSet() -
Method in class chemaxon.struc.MolAtom
- Gets the names of query properties with non-null values, or null if no
query properties are set.
- getQuery(int) -
Method in class chemaxon.descriptors.MDSimilarity
- Gets a query.
- getQuery() -
Method in class chemaxon.jep.context.SearchContext
- Returns the query molecule.
- getQuery() -
Method in class chemaxon.sss.formula.FormulaSearch
- Gets the chemical formula query string used for seaching
- getQuery() -
Method in class chemaxon.sss.search.Decomposition
- Returns the R-grouped query used in the R-group decomposition.
- getQuery() -
Method in class chemaxon.sss.search.MarkushGenerator
- Returns the query.
- getQuery() -
Method in class chemaxon.sss.search.MolSearch
- Retrieves the query structure stored in the MolSearch object.
- getQuery() -
Method in class chemaxon.sss.search.RGroupDecomposition
- Retrieves the original query structure.
- getQuery() -
Method in class chemaxon.sss.search.Search
- Retrieves the query structure stored in the MolSearch object.
- getQueryAromaticity() -
Method in class chemaxon.struc.MolAtom
- Gets the aromatic/aliphatic query property.
- getQueryAsString() -
Method in class chemaxon.sss.search.Search
- For internal purposes only.
- getQueryCode() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the program code of the query option.
- getQueryFingerprint() -
Method in class chemaxon.jep.context.SearchContext
- Returns the query molecule fingerprint.
- getQueryFingerprint(Object) -
Method in class chemaxon.jep.context.SearchContext
- Returns the query molecule fingerprint if argument is the query molecule,
null otherwise.
- getQueryLabel() -
Method in class chemaxon.struc.MolAtom
- Gets the string representation of the query atom
- getQueryMode() -
Method in class chemaxon.formats.MolImporter
- Gets query mode.
- getQueryMode() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the query mode.
- getQueryMode() -
Method in class chemaxon.util.MolHandler
- Gets query mode.
- getQueryMolecule() -
Method in class chemaxon.sss.search.MCES
- Gets the query molecular structure.
- getQueryMoleculeErrorMessage(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- getQueryName(int) -
Method in class chemaxon.descriptors.MDSimilarityResultWriter
- Gets the name of the specified query.
- getQueryOp() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the data query operator.
- getQuerystr() -
Method in class chemaxon.struc.MolAtom
- Deprecated. As of release 5.7, replaced by
MolAtom.getQueryString()
- getQuerystr() -
Method in class chemaxon.struc.MolBond
- Gets the query properties.
- getQuerystr() -
Method in class chemaxon.struc.QueryBond
- Gets the query properties.
- getQueryString() -
Method in class chemaxon.struc.MolAtom
- Returns s the query string assigned to this atom.
- getQueryStructure() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property queryStructure.
- getQueryToPrint() -
Method in class chemaxon.sss.search.Search
- For internal purposes only.
- getQuotation() -
Method in class chemaxon.jchem.db.Exporter
- Gets the field enclosing character for JTF format output.
- getRadical() -
Method in class chemaxon.struc.MolAtom
- Gets the radical value.
- getRadical(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the radical value of an atom.
- getRadicalCount() -
Method in class chemaxon.struc.MolAtom
- Gets the number of free electrons.
- getRadicalMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get option for radical matching behaviour.
- getRadius() -
Method in class chemaxon.marvin.space.PharmacophoreArrow
- Returns the radius of the arrow.
- getRadius() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Returns the radius of the PharmacophorePoint in angstroms.
- getRainbowPalette() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns the color palette that is used when the coloring mode of the component
is rainbow coloring.
- getRandicIndex() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the Randic index or molecular connectivity index as the
harmonic sum of the geometric means of the node degrees for each edge.
- getRCSBLink(String) -
Static method in class chemaxon.marvin.space.MSpaceEasy
- Returns the URL of the RCSB database
- getRCSBLink(String, boolean) -
Static method in class chemaxon.marvin.space.MSpaceEasy
- Returns the URL of the RCSB database
- getReactant(int) -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the i-th reactant.
- getReactant(int) -
Method in class chemaxon.struc.RxnMolecule
- Gets a reactant.
- getReactantAtom(int) -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the i-th atom existing only on the reactant side.
- getReactantAtomCount() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the number of atoms existing only on the reactant side.
- getReactantCount() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the number of reactants.
- getReactantCount() -
Method in class chemaxon.reaction.Reactor
- Returns the number of reactants.
- getReactantCount() -
Method in class chemaxon.struc.RxnMolecule
- Gets the number of reactants.
- getReactants() -
Method in class chemaxon.reaction.ConcurrentReactorProcessor
- Returns the input reactants of the last processed reaction.
- getReactants() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the reaction reactants.
- getReactants() -
Method in class chemaxon.reaction.Reactor
- Returns the input reactants.
- getReactants() -
Method in class chemaxon.struc.RxnMolecule
- Gets all reactants in an array.
- getReactantTanimoto(ReactionFingerprint) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Returns the tanimoto distance of the reactant sides.
- getReaction() -
Method in class chemaxon.reaction.Reaction
- Deprecated. Returns the reaction as
RxnMolecule.
- getReaction() -
Method in class chemaxon.reaction.Reactor
- Returns the reaction.
- getReaction(MoleculeGraph) -
Static method in class chemaxon.struc.RxnMolecule
- Returns the reaction represented by the given molecule if exists,
otherwise null.
- getReactionArrow() -
Method in class chemaxon.struc.RxnMolecule
- Gets a two-element array containing the endpoints of the reaction arrow.
- getReactionArrow(boolean) -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction arrow of this reaction with the possibility to
generate an arrow if the arrow is not yet set.
- getReactionArrowList() -
Method in class chemaxon.struc.RxnMolecule
- Gets the list of the reaction arrows of this reaction.
- getReactionArrowType() -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction arrow type.
- getReactionArrowTypeName() -
Method in class chemaxon.struc.RxnMolecule
- Gets the reaction arrow type name.
- getReactionID() -
Method in class chemaxon.reaction.Reactor
- Returns the reaction ID.
- getReactionIDPropertyName() -
Method in class chemaxon.reaction.Reactor
- Returns the reaction ID property (RDF/MRV tag) name.
- getReactionProduct(int) -
Method in class chemaxon.reaction.Reactor
- Returns a reaction product.
- getReactionReactant(int) -
Method in class chemaxon.reaction.Reactor
- Returns a reaction reactant.
- getReactionSteps() -
Method in class chemaxon.struc.RxnMolecule
- Divides this reaction into simple step reactions if this is a multistep
reaction.
- getReactionStereo() -
Method in class chemaxon.struc.MolAtom
- Gets the reaction stereo property describing how the stereo configuration
of the atom changes during the reaction.
- getReactionSupport() -
Method in class chemaxon.marvin.beans.MSketchPane
- Is reaction drawing supported?
- getReactivity(String, String) -
Static method in class chemaxon.reaction.Reaction
- Deprecated. Returns reactivity combined with exclude condition.
- getReadGlobalGUIProperties() -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. since Marvin 5.1 when this and the
MarvinPane.getSaveGlobalGUIProperties() function
have been merged.
- getReadGUIPropertiesFromMRV() -
Method in class chemaxon.marvin.common.UserSettings
- Deprecated. As of release 5.1, replaced by
UserSettings.getSaveGUIPropertiesInMRV(). It will be removed in a future version of Marvin.
- getRealBondCount() -
Method in class chemaxon.struc.MolAtom
- Gets the number of bonds connected to "real" atoms.
- getRealEigenValue() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Deprecated. Use
HuckelAnalysisPlugin.getHMORealEigenValue()
- getRealRotatableBondCount() -
Method in class chemaxon.marvin.alignment.AtropIsomerDetector
- Rotatable bond count (atrop bonds excluded)
- getRecognizedFormat() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Gets the recognized file format.
- getRecognizedFormat() -
Method in interface chemaxon.marvin.io.MRecordReader
- Gets the recognized file format.
- getRecognizer(int, int) -
Method in class chemaxon.formats.recognizer.RecognizerList
- Gets an element of the recognizer list at the specified level.
- getRecordCount() -
Method in class chemaxon.formats.MolImporter
- Gets the current record number.
- getRecordCount() -
Method in class chemaxon.marvin.io.ArrayMDocSource
- Gets the current record number.
- getRecordCount() -
Method in class chemaxon.marvin.io.MDocSource
- Gets the current record number.
- getRecordCountMax() -
Method in class chemaxon.formats.MolImporter
- Gets the total number of records read.
- getRecordCountMax() -
Method in class chemaxon.marvin.io.ArrayMDocSource
- Gets the total number of records.
- getRecordCountMax() -
Method in class chemaxon.marvin.io.MDocSource
- Gets the total number of records.
- getRecordIDBackground(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the highlight color of a record.
- getRecordIDForeground(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the foreground color of a record.
- getRecordIndex() -
Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
- Gets the requested, unavailable record index.
- getRecordIndexMax() -
Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
- Gets the maximum available record index.
- getRecordIndexMin() -
Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
- Gets the minimum available record index.
- getRecordNumber() -
Method in class chemaxon.marvin.io.MRecordReader.Position
- Gets the record number.
- getRecordReader() -
Method in class chemaxon.marvin.io.MRecordImporter
- Gets the record reader.
- getReferenceAndRotatedFused() -
Method in class chemaxon.marvin.alignment.AlignRigidEasy
- before getRotatedMolecule the
AlignRigidEasy.align() method must be called
- getReferenceWithNewCoordinates() -
Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getReflogDs() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the reference logD array.
- getRefpHs() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the reference pH array.
- getRefractivity() -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the refractivity value.
- getRefractivityHIncrement(int) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the refractivity increment on the H atoms attached to a given atom.
- getRefractivityIncrement(int) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the refractivity increment for a given atom.
- getRegenerationTypeForTable(DatabaseProperties, String) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Get which kind of regeneration is needed for a structure table.
- getRegisteredCacheIDs() -
Method in class chemaxon.jchem.db.CacheRegistrationUtil
- For internal use only!
- getRelativeNegativity() -
Method in class chemaxon.struc.MolAtom
- Check negativity compared to the neighbors.
- getRemainingDays() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the "days" part of the remaining time.
- getRemainingHours() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the "hours" part of the remaining time.
- getRemainingMinutes() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the "minutes" part of the remaining time.
- getRemainingSeconds() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the "seconds" part of the remaining time.
- getRemark() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the calculation remark: if no results (no result types) then
returns remark, otherwise returns
null.
- getRemark() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns a warning message in case of arithmetical overflow
(the number of enumerated structures exceeds
Long.MAX_VALUE),
null otherwise.
- getRemark() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns a warning message if there are no resonants,
null otherwise.
- getRemark() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns a warning message if there are no tautomers,
null otherwise.
- getRemark() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the calculation remark:
if no results (no result types) then returns remark,
otherwise returns
null.
- getRemark() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the calculation remark.
- getRemark() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns the calculation remark.
- getRemark() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the calculation remark.
- getRememberPassword() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
rememberPassword.
- getRendering() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the rendering style.
- getRendering() -
Method in class chemaxon.marvin.MolPrinter
- Returns the rendering style of atoms and bonds.
- getRenderingQuality() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the actual rendering quality of the component.
- getRepeatingUnitAtom(int) -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Gets a paradigmatic repeating unit atom.
- getRepeatingUnitAtomCount() -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Gets the number of atoms in the pararadigmatic repeating unit.
- getRepeatingUnitAtoms() -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Gets the repeating unit atoms.
- getRepresentationClass() -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- Gets the name of the representation class of the
MTransferable.
- getRequestMethod() -
Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
- Gets the HTTP method of the request.
- getResidueAtomId() -
Method in class chemaxon.struc.MolAtom
- Gets the residue atom identifier.
- getResidueSeq() -
Method in class chemaxon.struc.MolAtom
- Gets the residue sequence number.
- getResidueType() -
Method in class chemaxon.struc.MolAtom
- Gets the residue type.
- getResidueTypeId(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getResidueTypeId(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getResolution() -
Method in class chemaxon.descriptors.PFParameters
- Gets the resolution of histograms.
- getResolution() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getResourceBundle(String) -
Static method in class chemaxon.marvin.beans.MarvinPane
- Utility method to get a resource bundle.
- getResult(int) -
Method in class chemaxon.jchem.db.JChemSearch
- Indexed getter for property results.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the result item for the specified type and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the result item for the specified key and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the atom count of a specific atom.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the result item for the specified key and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the distance, angle or dihedral of 2, 3 or 4 atoms if type is set
to "distance", "angle" or "diheral".
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the result item for the specified type and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Returns the result item for the specified type and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the result item for the specified key and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the result item for the specified pH.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the result item for the specified type and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the result item for the specified pH.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the microsepcies if pH is different from
Double.NaN, otherwise returns the input molecule itself.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the result item for the specified key and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the enumerated structures.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the result item for the specified type and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the result item for the specified key and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the result item for the specified type ("acidic" or "basic")
and the specified strongness index ("1" means the strongest value,
"2" means the second strongest value, etc.) given in the argument string.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the result item for the specified type and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the result item for the specified key and index.
- getResult() -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the result item for the specified key and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the shortest path between two atoms if type is set ot "shortestPath",
returns connectivity info if type is set to "connected".
- getResult(Object, int) -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the result item for the specified key and index.
- getResult(Object, int) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result item for the specified type and index.
- getResult(Object, String) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result item for the specified argument string.
- getResult(int) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result item for the specified type and index.
- getResult(String) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result item for the specified argument string.
- getResult(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the result string for the given molecule.
- getResult() -
Method in class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
- Returns the cached results.
- getResult() -
Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
- Returns the calculation result after the plugin has been
CalculatorPlugin.run().
- getResult() -
Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
- Returns the plugin object itself.
- getResult() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets the result of an MCS/MCES/SSS search.
- getResultantImplicitHCharge(int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the implicit H charge around a central atom
- getResultAsMolecule() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets the MCS/MCES as a structure represented by a
Molecules
object.
- getResultAsRGB(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultAsRGB(Object, int, Object) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue):
RED for acidic pKa, BLUE for basic pKa.
- getResultAsRGB(Object, int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result color as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultAsRGB(int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result color as int format (alpha<<24 + red<<16 + green<<8 + blue).
- getResultAsSmiles(boolean) -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets the MCS/MCES as structure represented as SMILES.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the specified result molecule in SMILES format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
- Get a calculation result (returned by
StructuralFrameworksPlugin.getResultMolecule() after a
StructuralFrameworksPlugin.run() call in the given format StructuralFrameworksPlugin.setFormat(String)
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the specified result in String format.
- getResultAsString(Object, int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result in String format.
- getResultAsString(int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result in String format for the first result type.
- getResultComponent() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns the result component for display.
- getResultCount() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property resultCount.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the number of result items for the given result type.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the number of result items for the given result type.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the number of result items:
1.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the number of result items for the given result type.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the number of result items for the given result key.
- getResultCount() -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the number of result items for the given result key.
- getResultCount(Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the number of result items for the given result key.
- getResultCount() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the number of result items for the first result type.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the calculation domain.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the calculation domain.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the calculation domain
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the calculation domain.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the calculation domain.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the calculation domain
CalculatorPlugin.MOLECULE
or CalculatorPlugin.MOLECULE in case of increments .
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the calculation domain.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the calculation domain.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the calculation domain.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the calculation domain
CalculatorPlugin.MOLECULE.
- getResultDomain(Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
- getResultDomain() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the calculation domain
CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
- getResultDomain() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the domain for the first result type.
- getResultList() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- getResultList() -
Method in interface chemaxon.checkers.runner.CheckerRunner
-
- getResultList() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
- Deprecated.
- getResultMessage() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the plugin calculation error message,
error or warning.
- getResultMessage() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the plugin calculation error message,
error or warning.
- getResultMolecule() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- getResultMolecule() -
Method in class chemaxon.marvin.alignment.AtropIsomerDetector
- The result molecule will be 3D and aromatized version of the input molecules.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the major microspecies for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
- Get result structure
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the result molecule for display.
- getResultMolecule() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result molecule for display.
- getResultMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the decorated result molecule for the given target molecule.
- getResultMolecules() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the result molecules, molecular results are set in the first
molecule, atomic results are set in subsequent molecules as atom labels.
- getResultMolecules() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the result molecules, molecular results are set in the first molecule,
atomic results are set in subsequent molecules as atom labels.
- getResultMolecules() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result molecule array for display.
- getResultMolecules(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the result molecules for the given target molecule.
- getResultQueryAtoms() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets query atoms that are part of the MCS/MCES.
- getResultQueryBonds() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets bonds of the query structure that are part of the MCS/MCES found.
- getResults() -
Method in class chemaxon.jchem.db.JChemSearch
- Returns an
int array containing the
cd_id values of found compounds.
- getResults(Object) -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns result items for the given result type.
- getResultsAsRGB(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsRGB(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsRGB(Object, int, Object) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsRGB(Object, int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsRGB(int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result color(s) as int format
(alpha<<24 + red<<16 + green<<8 + blue).
- getResultsAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the specified result in GUI-specific String format:
A for acceptor, D for donor.
- getResultsAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the specified results in String format.
- getResultsAsString(Object, int, Object) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the specified result with possible subresults
(both pKa values instead of the most significant pKa) in String format.
- getResultsAsString(Object, int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result with possible subresults.
- getResultsAsString(int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the specified result with possible subresults.
- getResultSize() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets the size (number of atoms) of the MCS/MCES (and SSS) found.
- getResultSource() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the result as a document source object.
- getResultSource() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the result as a document source object.
- getResultSource() -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the result as a document source object.
- getResultSource() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the result as a document source object.
- getResultSource() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the result as a document source object.
- getResultSource() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the result as a document source object.
- getResultSource() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result as a document source object.
- getResultTable() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property resultTable.
- getResultTableMode() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property resultTableMode.
- getResultTargetAtoms() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets target atoms that are part of the MCS/MCES.
- getResultTargetBonds() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Gets bonds of the target structure that are part of the MCS/MCES found.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.AlignmentPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the result types (possible types: "sigma", "pi", "total").
- getResultTypes() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Returns the result types (possible type: "charge").
- getResultTypes() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the result types (possible types: "majority-ms").
- getResultTypes() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the result types (possible types: "sigma", "pi").
- getResultTypes() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the result types (possible types: pKa, acidic, basic, msdistr).
- getResultTypes() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns the result types (possible types: sigma, pi, total).
- getResultTypes() -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- getResultTypes() -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- getResultTypes() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the result types.
- getResultTypes() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the result types.
- getReturnTypes() -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- Returns the array of return types
- getRgroup() -
Method in class chemaxon.struc.MolAtom
- Gets the R-group ID.
- getRgroupAttachmentPointOrder() -
Method in class chemaxon.struc.MolAtom
- Gets the attachment point order of an R-group attachment point.
- getRgroupCount() -
Method in class chemaxon.struc.RgMolecule
- Gets the number of R-groups.
- getRGroupedQuery() -
Method in class chemaxon.sss.search.RGroupDecomposition
- Returns the R-grouped query.
- getRgroupId(int) -
Method in class chemaxon.struc.RgMolecule
- Gets the ID of an R-group.
- getRgroupId(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the R-group identifier of an atom.
- getRgroupIndex(long) -
Method in class chemaxon.struc.RgMolecule
- Gets the R-group index from the R-group member ID.
- getRgroupMember(int, int) -
Method in class chemaxon.struc.RgMolecule
- Gets an R-group member.
- getRgroupMemberCount(int) -
Method in class chemaxon.struc.RgMolecule
- Gets the number of R-group members.
- getRgroupMemberG(int, int) -
Method in class chemaxon.struc.RgMolecule
- Gets an R-group member.
- getRgroupMemberID(MolAtom) -
Method in class chemaxon.struc.RgMolecule
- Gets the unique indentifier of the R-group member that contains the
specified atom.
- getRgroupMemberIndex(long) -
Method in class chemaxon.struc.RgMolecule
- Gets the R-group member index from the R-group member ID.
- getRight() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the x coordinate of the right edge of the cell.
- getRightList() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- initializes right list (configuration)
- getRightName() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Set the string that will be shown at the right side of the molecule.
- getRingAtomCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the ring atom count.
- getRingBondCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the ring bond count.
- getRingCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the ring count.
- getRingCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of rings (SSSR smallest set of smallest rings) of a
given size in the molecule.
- getRingCountOfAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of rings (SSSR smallest set of smallest rings) an
atom is part of.
- getRingCountOfSize(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Deprecated. Use
TopologyAnalyserPlugin.getRingCount(int)
- getRingIndex(Molecule, MolBond) -
Static method in class chemaxon.checkers.BondAngleChecker
- This function returns the index of the ring which contains the
MolBond
instance represented by bond parameter
- getRings() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the rings in the molecule.
- getRings(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies rings in the molecule having a given size.
- getRingSystemCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the number of ring systems.
- getRingSystemCount(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the number of ring systems having a given size (number of
rings) in the molecule.
- getRingSystemCountOfSize(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Deprecated. Use
TopologyAnalyserPlugin.getRingSystemCount(int)
- getRingSystems() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the ring systems in the molecule.
- getRingSystems(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Indentifies the ring systems in the molecule having a given size (number
of rings).
- getRLigandEqualityCheck() -
Method in class chemaxon.sss.search.SearchOptions
- Returns
true if undefined R-atoms with the same R-group ID
should match the same structure.
- getRlogic(int) -
Method in class chemaxon.struc.RgMolecule
- Gets R-logic flags.
- getRlogicRange(int) -
Method in class chemaxon.struc.RgMolecule
- Gets R-logic occurence range.
- getRLogicVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Tells whether the R-logic is visible if exists
- getRmsd() -
Method in class chemaxon.marvin.alignment.Alignment
-
- getRmsd() -
Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
- getRoot() -
Method in class chemaxon.struc.RgMolecule
- Gets the root structure.
- getRootG() -
Method in class chemaxon.struc.RgMolecule
- Gets the root structure.
- getRootSgroups() -
Method in class chemaxon.struc.Molecule
- Gets root s-groups (groups that are not embedded into another s-group).
- getRotatableBondCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the rotatable bond count.
- getRotatedCoordinates() -
Method in class chemaxon.marvin.alignment.AlignRigidEasy
- before getRotatedCoordinates the
AlignRigidEasy.align() method must be called
- getRotatedMolecule() -
Method in class chemaxon.marvin.alignment.AlignRigidEasy
- before getRotatedMolecule the
AlignRigidEasy.align() method must be called
- getRotateMatrix() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the matrix of rotation.
- getRotationMatrix(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the rotation part of the transformation matrix.
- getRotBondCount() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getRow(int) -
Static method in class chemaxon.struc.MolAtom
- The row or or period of an element in the periodic system.
- getRow(int) -
Static method in class chemaxon.struc.PeriodicSystem
- The row or or period of an element in the periodic system.
- getRowCount() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the number of rows in the scene.
- getRowHeight() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the row height.
- getRunMode() -
Method in class chemaxon.jchem.db.JChemSearch
- Retruns the current run mode.
- getSaveFileAction() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the
Action associated with save file event, or null if no Action
- getSaveGlobalGUIProperties() -
Method in class chemaxon.marvin.beans.MarvinPane
- Checks whether we have to read GUI properties from a .MRV file
- getSaveGUIPropertiesInMRV() -
Method in class chemaxon.marvin.common.UserSettings
-
- getSaveLoadZoomFactorToMRV() -
Method in class chemaxon.marvin.common.UserSettings
- Tells if marvin save the zoom factor to mrv or not.
- getScaffold() -
Method in class chemaxon.sss.search.Decomposition
- Returns the scaffold in target.
- getScaffold() -
Method in class chemaxon.sss.search.RgDecompResults
- Returns scaffold of the query
(r-groups are added automatically if needed).
- getScaffoldOrientatedHit(Molecule, Molecule) -
Static method in class chemaxon.util.HitDisplayUtil
- Only for internal use!
- getScaffoldOrientatedHit(Molecule, Molecule, int[]) -
Static method in class chemaxon.util.HitDisplayUtil
- Returns an aligned (rotated) version of molToAlign that contains
scaffold - possibly in the same position or optimally close to it.
- getScale() -
Method in class chemaxon.marvin.beans.MSketchPane
- Returns the scale factor of the current magnification.
- getScale() -
Method in class chemaxon.marvin.MolPrinter
- Returns the scale factor in units of regular bond length.
- getScale() -
Method in class chemaxon.struc.CTransform3D
- Gets the scale factor.
- getScale() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the relative size of the font compared to the base font.
- getScaledAWTFont(Float) -
Method in class chemaxon.struc.graphics.MFont
- Gets an AWT font instance after scaling.
- getScaledTanimoto(CustomDescriptor) -
Method in class chemaxon.descriptors.CustomDescriptor
- Gets the Tanimoto dissimilarity coefficient.
- getScaledTanimoto(PharmacophoreFingerprint, PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the scaled Tanimoto metric (adapted to hystograms).
- getScaleFactor() -
Method in class chemaxon.descriptors.MDParameters
- Gets the scale factor used in the current parametrized scalable metrics.
- getScalingHypothesis() -
Method in class chemaxon.descriptors.MDParameters
- Gets the scaling hypothesis used in scaled metrics.
- getScreenedCount() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the number of total screened structures.
- getScreenedCountTotal() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the number of total screened structures.
- getScreenedCountUnique() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the number of unique screened structures.
- getScreenedResults() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the screened unique structures' ids.
- getScreeningConfigurationString(String, String, String) -
Method in class chemaxon.descriptors.MDParameters
- Returns parts of the parameter values in string.
- getScreeningTime() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the screening time.
- getScriptCount(int, int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the number of subscripts or superscripts on the last normal
character.
- getSearchMode() -
Method in class chemaxon.sss.search.MCES
- Gets the current search mode.
- getSearchOptions() -
Method in class chemaxon.jchem.db.JChemSearch
- Returns the SearchOptions object associated
with this Search object.
- getSearchOptions() -
Method in class chemaxon.sss.search.MarkushGenerator
- Returns the search options.
- getSearchOptions() -
Method in class chemaxon.sss.search.MarkushTagger
- Returns the search options.
- getSearchOptions() -
Method in class chemaxon.sss.search.Search
- Returns the SearchOptions object associated with this Search object.
- getSearchTime() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the total search time.
- getSearchType() -
Method in class chemaxon.sss.formula.FormulaSearch
- Gets the formula search type.
- getSearchType() -
Method in class chemaxon.sss.search.SearchOptions
- Returns the currently set global search operation mode.
- getSearchType(String) -
Static method in class chemaxon.sss.search.SearchOptions
- Decodes the string representation of the search type and returns
the predefined constant value defined in
SearchConstants.
- getSecondaryStructureType(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
- Gets the type of the secondary structure element which the current
atom belongs to.
- getSecondaryStructureType(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getSection(int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets a section of the document.
- getSectionCount() -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the number of sections in the document.
- getSectionIndexOfCharAt(int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the section index of a character.
- getSectionShiftY(int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the y shift of a section.
- getSelectedAtom(int) -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- getSelectedAtoms(int, String) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the selected atom indices.
- getSelectedElements() -
Method in class chemaxon.marvin.space.monitor.Monitor
- Returns the set of the monitored items.
- getSelectedFieldCount() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the number of selected fields.
- getSelectedFields() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Get selected fields array which are selected in Table Options dialog box
- getSelectedFieldTypes() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Get type array of selected field types.
- getSelectedIndex() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the index of the molecule that is selected by the user.
- getSelectedItem() -
Method in class chemaxon.marvin.space.monitor.Label
-
- getSelectedString() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the selected substring.
- getSelection() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets a clone of the selection.
- getSelectionEndColumn() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the selection's end column number.
- getSelectionEndPos() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the selection's end position.
- getSelectionEndRow() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the selection's end row number.
- getSelectionStartColumn() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the selection's start column number.
- getSelectionStartPos() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the selection's start position.
- getSelectionStartRow() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the selection's start row number.
- getSelectivityAsymmetryFactor() -
Method in class chemaxon.descriptors.MDHitEvaluator
- Returns the value of the asymmetry factor (weight) of the evaluator
funcion selectivity effectiveness.
- getSeparator(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Gets if a separator is required after the plugin menuitem in the Tools menu.
- getServiceDescriptorConfigurationAsStream() -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns an
InputStream with service configuration
- getServiceDescriptorConfigurationAsStream(UserSettings) -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns an
InputStream with service configuration
- getServiceDescriptorEditorProvider(String) -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the
ServiceDescriptorEditorProvider instance if available, or null
- getServiceDescriptorReader(String) -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the
ServiceDescriptorReader instance if available, or null
- getServiceDescriptorWriter(String) -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the
ServiceDescriptorWriter instance if available, or null
- getServiceDialogProvider(String) -
Static method in class chemaxon.marvin.services.ServiceDescriptorTools
- Returns the
ServiceDialogProvider instance if available, or null
- getServiceHandler() -
Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
-
- getServiceHandler() -
Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
- getServiceHandler() -
Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- getServiceHandler() -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
- getServiceHandler() -
Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
-
- getServicesConfigURL() -
Method in class chemaxon.marvin.common.UserSettings
- Returns the URL of configuration for Services in marvin sketch
- getSet() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the set of attributes used.
- getSetChiralFlag() -
Method in class chemaxon.jchem.db.Importer
- Gets whether chiral flag is set on import.
- getSetChiralFlag() -
Method in class chemaxon.jchem.db.UpdateHandler
- Getter for property setChiralFlag.
- getSetColor(int) -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 3.3, replaced by getAtomSetColor
- getSetSeq() -
Method in class chemaxon.struc.MolAtom
- Gets the atom set sequence number.
- getSetSeq() -
Method in class chemaxon.struc.MolBond
- Gets the bond set.
- getSgroup(int) -
Method in class chemaxon.struc.Molecule
- Gets an S-group.
- getSgroup() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Gets the S-group corresponding to this superatom.
- getSgroupArray() -
Method in class chemaxon.struc.Molecule
- Gets the array of S-groups.
- getSgroupCount() -
Method in class chemaxon.struc.Molecule
- Gets the number of S-groups.
- getSgroupGraph() -
Method in class chemaxon.struc.Sgroup
- Gets a COPY of the molecule graph.
- getSgroupGraph() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the molecule graph as a selection.
- getSgroupLigands() -
Method in class chemaxon.struc.Molecule
- Gets the S-group's ligands if the structure represents an S-group.
- getSgroups() -
Method in class chemaxon.checkers.result.SgroupCheckerResult
- Returns a
List which contains the affected groups of the problem
- getSgroupType(String) -
Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
- Gets the S-group type.
- getShapeSimilarity(MolecularDescriptor) -
Method in class chemaxon.descriptors.ShapeDescriptor
-
- getShapeTanimoto() -
Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- getShapeTanimoto() -
Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- getShapeTanimoto() -
Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- getShiftX() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the shifting value of the x direction.
- getShiftX(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns corrected shifting value of the given cell.
- getShiftY() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the shifting value of the y direction.
- getShiftY(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns corrected shifting value of the given cell.
- getShortestPath(int, int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the shortest topological path (number of bonds) between two
atoms.
- getShortName() -
Method in class chemaxon.descriptors.BCUT
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.CustomDescriptor
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.ECFP
- Gets the short name of the fingerprint.
- getShortName() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.ScalarDescriptor
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.scalars.HAcc
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.scalars.HDon
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.scalars.Heavy
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.scalars.LogD
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.scalars.LogP
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.scalars.Mass
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.scalars.TPSA
- Gets the short name of the descriptor.
- getShortName() -
Method in class chemaxon.descriptors.ShapeDescriptor
- Gets the short name of the fingerprint.
- getSigmaCharge(int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the sigma charge of a specified atom.
- getSigmaOEN(int) -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns the sigma orbital electronegativity of a specified atom.
- getSimilarity(T) -
Method in class chemaxon.descriptors.SimilarityCalculator
- Gets the similarity value according to previously defined metric and its parameters.
- getSimpleName() -
Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
-
- getSimpleName() -
Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
- getSimpleName() -
Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- getSimpleName() -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
- getSimpleName() -
Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
-
- getSimpleParamString() -
Method in enum chemaxon.descriptors.MetricsType
-
- getSimplifiedMolecule() -
Method in class chemaxon.struc.Molecule
- Gets the simplified molecule object.
- getSimpView() -
Method in class chemaxon.marvin.beans.MSketchPane
- Deprecated. as of Marvin 3.5, replaced by
MSketchPane.isBondDraggedAlong()
- getSingleHit() -
Method in class chemaxon.sss.search.SearchHit
- Returns the single hit view.
- getSingleMsDistribution(int) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the microspecies distribution
at the specified pH value set in
pKaPlugin.setpH(double).
- getSize() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the total number of entries.
- getSizeDouble() -
Method in class chemaxon.struc.graphics.MFont
- Gets the font size.
- getSketchAnyBond() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the default any bond drawing style in the sketcher.
- getSketchArrowHeadLength() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the current arrow head length.
- getSketchArrowHeadWidth() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the current arrow head width.
- getSketchArrowTailLength() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the current arrow tail length.
- getSketchArrowTailWidth() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the current arrow tail width.
- getSketchCarbonVisibility() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the default carbon displaying style in the sketcher.
- getSketchColorScheme() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the sketcher's default color scheme.
- getSketchImplicitH() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the display method of implicit hydrogens for the sketcher.
- getSketchLigandOrderVisibility() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the default ligand order displaying style in the sketcher.
- getSketchLoadWorkingDir() -
Method in class chemaxon.marvin.common.UserSettings
- Based on the preferences this funtion returns the proper working
directory for the MarvinSketch application's load filechooser.
- getSketchMode() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the sketching mode.
- getSketchMolbg2d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the sketcher's default 2D molecule background color.
- getSketchMolbg3d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the sketcher's default 3D molecule background color.
- getSketchRecentFileList() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the recent files' list at marvinsketch, the last item is the most
recent.
- getSketchRecentFileListSize() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the recent file list requested size, based on a preferences setting
- getSketchRendering2d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the rendering style for the 2D sketcher.
- getSketchRendering3d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the rendering style for the 3D sketcher.
- getSketchSaveWorkingDir() -
Method in class chemaxon.marvin.common.UserSettings
- Not implemented yet don't use it.
- getSkip() -
Method in class chemaxon.jchem.db.Importer
- Gets the number of molecules to skip from the beginning ogf file.
- getSkip(int) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the distance of the (visible) head or tail from the corresponding
line end point.
- getSkippedIds() -
Method in class chemaxon.sss.search.RgDecompResults
- Returns indexes of those targets that are not matched by query.
- getSkippedTargetIndexes() -
Method in class chemaxon.sss.search.MarkushGenerator
- Returns the target array indexes of targets that have been skipped in the
last
RgMolecule generation in MarkushGenerator.generate().
- getSmallestRing() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the smallest ring (number of stoms) in the molecule.
- getSmallestRingSize() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the smallest ring size.
- getSmallestRingSizeForIdx() -
Method in class chemaxon.struc.MoleculeGraph
- Get the smallest ring size in which the atom
(specified with it's index) can be located.
- getSmallestRingSizeOfAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the size of smallest ring containing the specified atom.
- getSmallestRingSystem() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Identifies the smallest ring system (number of rings) in the molecule.
- getSmallestRingSystemSize() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns the size of the smallest ring system (number of rings) in the molecule.
- getSmartsMode() -
Method in class chemaxon.sss.screen.StrucFPConfig
- Indicates if molecule strings should be interpreted as SMARTS.
- getSMILESFontSize() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the SMILES font size.
- getSmolecule() -
Method in class chemaxon.calculations.ElementalAnalyser
- Retrieves the input molecule
- getSmoleculeAtomProperty() -
Method in class chemaxon.marvin.space.AtomProperty
-
- getSortedMicrospecies(int) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the microspecies molecule,
sorted by descreasing distribution at the given pH.
- getSortedMsDistribution(int) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the microspecies distribution,
sorted by descreasing distribution at the given pH.
- getSortedSgroups() -
Method in class chemaxon.struc.Molecule
- Gets the sorted S-groups in parent-child order.
- getSortedValues(int, double[], int[]) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Deprecated. Use
pKaPlugin.getMacropKaValues(int,double[],int[]) instead
- getSource() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getSource() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getSpecResult(Molecule, String) -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns a specific plugin result corresponding to the given molecule
and argument string.
- getSSRType() -
Method in class chemaxon.sss.search.SearchOptions
- Gets the type of the set of smallest rings to use
Default value is SetOfSmallestRingsOption.SSSR
- getSSSR() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the Smallest Set of Smallest Ring atom indexes array.
- getSSSRBonds() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the Smallest Set of Smallest Ring bond indexes array.
- getSSSRBondSet() -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. please use getSSSRBondSetInLong() instead.
- getSSSRBondSetInLong() -
Method in class chemaxon.struc.MoleculeGraph
- Get SSSR bond bitsets in long array.
- getSSSRIdxesForAtoms() -
Method in class chemaxon.struc.MoleculeGraph
- Get the sssr ring indexes in which the atom
(specified with it's index) can be located.
- getStackTrace() -
Method in class chemaxon.util.ErrorHandler
- Getter for property stackTrace.
- getStandardizer() -
Method in class chemaxon.reaction.Reactor
- Deprecated. Will be removed. Use
Standardizer to standardize reactants.
- getStartAt() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Get the index number of the molecule that is the first to be displayed.
- getStartLineCount() -
Method in class chemaxon.marvin.io.MRecord
- Gets the line number at the starting point.
- getStartPos() -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the position of the first character.
- getStartPosition() -
Method in class chemaxon.marvin.io.MRecord
- Gets the start position in the input file.
- getStartPosition() -
Method in class chemaxon.struc.MDocument
- Gets the starting position of this document in the input file.
- getStartPosition() -
Method in class chemaxon.struc.Molecule
- Gets the starting position of this molecule in the input file.
- getStartTime() -
Method in class chemaxon.clustering.Common
- Gets start time.
- getStatistics(int) -
Method in class chemaxon.descriptors.GenerateMD
- Gets statistical data on descriptors generated.
- getStatStream() -
Method in class chemaxon.clustering.Common
- Gets the stream used to print statistics.
- getStatus() -
Method in class chemaxon.marvin.alignment.Alignment
-
- getStepCountLimit() -
Method in class chemaxon.sss.search.MCES
- Gets the maximum allowed number of elementary search steps.
- getSteps() -
Method in enum chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
-
- getStereo(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates absolute stereo configuration of the given atom.
- getStereo(int, int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates absolute stereo configuration of the given double bond.
- getStereo1(MolAtom) -
Method in class chemaxon.struc.MolBond
- Gets wedge bond type relative to the specified chiral atom.
- getStereo2(int, int, int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolAtom, int, int, MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond, MolAtom, MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond, MolAtom, MolAtom, boolean) -
Method in class chemaxon.struc.MoleculeGraph
- Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Gets cis/trans (Z/E) stereo information for the given bond.
- getStereo2(MolBond, MolAtom, int, int, MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereo2(MolBond, MolAtom, int, int, MolAtom, boolean) -
Method in class chemaxon.struc.MoleculeGraph
- Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
- getStereoCare() -
Method in class chemaxon.struc.MolAtom
- Reports double bond stereo care information on the connected bonds.
- getStereoDoubleBondCount() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the number of stereo double bonds.
- getStereoGroupNumber() -
Method in class chemaxon.struc.MolAtom
- Gets the stereochemical group number for AND and OR groups of the
enhanced stereo representation.
- getStereoGroupType() -
Method in class chemaxon.struc.MolAtom
- Gets the stereochemical group type for the enhanced stereo
representation.
- getStereoisomer(int) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns a stereoisomer.
- getStereoisomerCount() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the number of different stereoisomers.
- getStereoisomers() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns the stereoisomers in a Molecule[] array.
- getStereoModel() -
Method in class chemaxon.sss.search.SearchOptions
- Get the stereo model option.
- getStereoSearchType() -
Method in class chemaxon.sss.search.SearchOptions
- Get the stereo search type option.
- getStericEffectIndex(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates topological steric effect index (TSEI) of an atom from
covalent radii values and topological distances.
- getStericHindrance(int) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Calculates hindrance of an atom from covalent radii values and distances.
- getStickdst() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the sticking distance.
- getStickThickness() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the stick thickness.
- getStickThickness() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the stick diameter for ball and stick mode.
- getStickThickness() -
Method in class chemaxon.marvin.MolPrinter
- Gets the 3D stick's diameter.
- getStopCause() -
Method in class chemaxon.clustering.LibraryMCS
- Internal code of last termination condition.
- getStopCauseExplanation() -
Method in class chemaxon.clustering.LibraryMCS
- Deatailed explanation why last search terminated.
- getStoredParameters(Properties) -
Method in class chemaxon.marvin.plugin.gui.ParameterPanel
- Returns the stored parameters.
- getStoredParameters(Properties) -
Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
- Returns the stored parameters.
- getStrictReactionTanimoto(ReactionFingerprint) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Returns the tanimoto distance of the reaction centers, their immediate neighbour atoms
and bonds, and the neighbours' neighbouring atoms and bonds.
- getString() -
Method in class chemaxon.marvin.io.MRecord
- Gets the record text as string.
- getString() -
Method in class chemaxon.struc.graphics.MFont
- Gets the string representation.
- getString() -
Method in class chemaxon.struc.graphics.MTextDocument.Section
- Gets the text string.
- getString(String) -
Method in class chemaxon.struc.MPropertyContainer
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MPropertyContainer, String)
- getStringFromClipboard() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns the String data from the clipboard contents, if the clipboard
contains a Transferable that provides support to
DataFlavor.stringFlavor
- getStringFromClipboard() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getStringToClipboardTask(String) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getStructCount() -
Method in class chemaxon.jchem.db.Importer
- Returns the current count of structures which were examined by the import process.
- getStructurallogPIncrement() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the structural logP increment.
- getStructure(int) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns a structure.
- getStructure(int) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns a resonant structure.
- getStructure(int) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns a tautomer.
- getStructure(int, int) -
Method in class chemaxon.struc.RxnMolecule
- Deprecated. as of Marvin 4.1, replaced by
RxnMolecule.getComponent(int, int)
- getStructureCount() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the number of all enumerated structures,
-1 in case of arithmetical overflow
(if the number would exceed Long.MAX_VALUE).
- getStructureCount() -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns the number of different structures.
- getStructureCount() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns the number of different resonant structures.
- getStructureCount() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the number of different tautomers.
- getStructureCount(int) -
Method in class chemaxon.struc.RxnMolecule
- Deprecated. as of Marvin 4.1, replaced by
RxnMolecule.getComponentCount(int)
- getStructureID() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the structure ID used in Markush code (enumeration ID) generation.
- getStructureNameField() -
Method in class chemaxon.jchem.db.UpdateHandler
- Get the name of that column which stores the structure names.
- getStructures() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the enumerated structures.
- getStructures() -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Returns all structures.
- getStructures() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Returns resonant structures in
Molecule[] array.
- getStructures() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns tautomers in
Molecule[] array..
- getStructureTable() -
Method in class chemaxon.descriptors.MDDBWriter
- Gets the name of the structure table
- getStructureTable() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property structureTable.
- getStructureTableNames() -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns the names of structure tables registered in
the
JChemProperties table.
- getStructureTables(ConnectionHandler) -
Static method in class chemaxon.jchem.db.UpdateHandler
- Collects the names of all structures tables in the database (from the records
of the JChemProperties table).
- getStyle() -
Method in class chemaxon.struc.graphics.MFont
- Gets the font style.
- getSubGraphCount() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the number of all "submolecules".
- getSubGraphCount() -
Method in class chemaxon.struc.RgMolecule
- Gets the number of all "submolecules".
- getSubGraphCount() -
Method in class chemaxon.struc.RxnMolecule
- Gets the number of all "submolecules".
- getSubGraphs() -
Method in class chemaxon.struc.MoleculeGraph
- Gets all "submolecules".
- getSubGraphs(MoleculeGraph[], int) -
Method in class chemaxon.struc.MoleculeGraph
- Gets all "submolecules".
- getSubGraphs(MoleculeGraph[], int) -
Method in class chemaxon.struc.RgMolecule
- Gets all "submolecules".
- getSubGraphs(MoleculeGraph[], int) -
Method in class chemaxon.struc.RxnMolecule
- Gets all "submolecules".
- getSubLevel() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Gets the subscript/superscript level.
- getSubscript() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the subscript for non-superatom S-groups.
- getSubscript() -
Method in class chemaxon.struc.Sgroup
- Gets the subscript for non-superatom S-groups.
- getSubscript() -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Gets the subscript.
- getSubstrateCounter() -
Method in class chemaxon.metabolizer.Metabolizer
- Return currentSubstrate's ordinal number
- getSubstructure() -
Method in class chemaxon.descriptors.ECFPFeature
- Gets the corresponding substructure as a
Molecule object.
- getSubType() -
Method in class chemaxon.struc.Sgroup
- Gets polymer S-group subtype.
- getSuccess() -
Method in class chemaxon.util.UploadThread
- Indicates if the operation was successful.
- getSuperAtom() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets the superatom.
- getSuperscript() -
Method in class chemaxon.struc.Sgroup
- Gets the superscript for non-superatom S-groups.
- getSuperscript() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Gets the superscript for Sru S-groups.
- getSupportedDescriptors() -
Method in interface chemaxon.marvin.services.ServiceDescriptorEditorProvider
- Returns a set of supported
ServiceDescriptor classes.
- getSurface() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the surface.
- getSurfaceArea() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns the surface area, calculation type is previously
set in
MSAPlugin.setSurfaceAreaType(int).
- getSurfaceArea() -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns the surface area.
- getSurfacePrecision() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the grid resolution from which the surface is computed.
- getSurfaceSimplificationEnabled() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns true if Surface Simplification is enabled.
- getSurfaceSmoothnessFactor() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Surfaces can be smoothed by the following algorithm:
Paul Bourke: Surface Relaxation and Smoothing
http://astronomy.swin.edu.au/~pbourke/modelling/relax/
This algorithm has a smoothness factor.
- getSurfaceThreshold() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the isovalue/threshold of the surface.
- getSurfaceType(String) -
Static method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- getSurfaceType() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns the type of the surface.
- getSurfaceTypeString(int) -
Static method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- getSymbol(int) -
Method in class chemaxon.descriptors.PFParameters
- Gets the symbol associated with the specified Pharmacophore.
- getSymbol(int) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getSymbol(int) -
Method in class chemaxon.pharmacophore.PSymbols
- Gets the symbol at the given index.
- getSymbol() -
Method in class chemaxon.struc.MolAtom
- Gets the element symbol.
- getSymbol(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Symbol of the element
- getSymbol() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Gets the abbreviated group symbol.
- getSymbolCount() -
Method in class chemaxon.pharmacophore.PSymbols
- returns the number of symbols
- getSymbolIndex(String) -
Method in class chemaxon.descriptors.PFParameters
- Gets the index associated with the specified Pharmacophore symbol.
- getSymbols() -
Method in class chemaxon.pharmacophore.PMapper
- Returns the symbol storing object.
- getSymbolTable() -
Method in class chemaxon.jep.Evaluator
- Returns the symbol table of predefined constants (molecules, molecule sets
and other constants defined in the built-in and the user-defined jep.script).
- getSymmetricFBPA(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the symmetric FBPA convolution product based distasnce of
the fingerprint from an other (given as parameter).
- getSzegedIndex() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the Szeged index of the molecule.
- getT(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets a text field value in a GridBagView table.
- getT(int, int) -
Method in class chemaxon.marvin.view.MDocStorage
- Gets a text field in a record.
- getTableCellEditorComponent(JTable, Object, boolean, int, int) -
Method in class chemaxon.marvin.beans.MViewEditor
- Sets up the editor component.
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) -
Method in class chemaxon.marvin.beans.MolRenderer
- The implementation of this method sets up the rendering component to
display the passed-in molecule, and then returns the component.
- getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) -
Method in class chemaxon.marvin.beans.MViewRenderer
- The implementation of this method sets up the rendering component to
display the passed-in molecule, and then returns the component.
- getTableIntProperty(String, String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Gets an integer table property from the
JChemProperties table.
- getTableName() -
Method in class chemaxon.jchem.db.Exporter
- Gets the name of the table to export from.
- getTableName() -
Method in class chemaxon.jchem.db.Importer
- Gets the name of the table to import into.
- getTableOptions() -
Method in class chemaxon.marvin.view.swing.TableSupport
- Gets the table options component.
- getTableProperties(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Return all properties for a table.
- getTableProperty(String, String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Gets a table property from the
JChemProperties table.
- getTablesToRegenerate(ConnectionHandler, int) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Give back the tables that need a type of regeneration.
- getTableSupport() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets an object that helps to build and use a viewer table.
- getTableText(String, String[], double[][]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns table in string form.
- getTableType(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns the type of the specified table.
- getTabScale() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the magnification in the molecule cells.
- getTabScale(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the magnification for a molecule cell.
- getTag() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the tag character for footnote display (or space if blank).
- getTags() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the array of tags
- getTags() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the tags of this element
- getTailCrossingBonds() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Gets the tail crossing bonds.
- getTanimoto(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the Tanimoto metric.
- getTanimoto(CustomDescriptor) -
Method in class chemaxon.descriptors.CustomDescriptor
- Gets the Tanimoto dissimilarity coefficient.
- getTanimoto(ECFP) -
Method in class chemaxon.descriptors.ECFP
- Calculates the Tanimoto distance.
- getTanimoto(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the Tanimoto metric (adapted to hystograms)
- getTanimoto(byte[], byte[]) -
Static method in class chemaxon.sss.screen.Similarity
- Calculates the Tanimoto coefficient of the two bit strings.
- getTanimoto(byte[], byte[], int) -
Static method in class chemaxon.sss.screen.Similarity
- Calculates the Tanimoto coefficient of the two bit strings.
- getTanimoto(int[], int[], int) -
Static method in class chemaxon.sss.screen.Similarity
- Calculates the Tanimoto coefficient of the two bit strings.
- getTarget() -
Method in class chemaxon.jep.context.SearchContext
- Returns the target molecule.
- getTarget() -
Method in class chemaxon.sss.formula.FormulaSearch
- Gets the chemical formula of the target used to search in
- getTarget() -
Method in class chemaxon.sss.search.Decomposition
- Returns the target.
- getTarget() -
Method in class chemaxon.sss.search.MolSearch
- Retrieves the target molecule to search in.
- getTarget() -
Method in class chemaxon.sss.search.Search
- Retrieves the target molecule
- getTargetAsString() -
Method in class chemaxon.sss.search.Search
- For internal purposes only.
- getTargetFingerprint() -
Method in class chemaxon.jep.context.SearchContext
- Returns the target molecule fingerprint.
- getTargetMolecule() -
Method in class chemaxon.sss.search.MCES
- Gets the target molecular structure.
- getTargets() -
Method in class chemaxon.sss.search.MarkushGenerator
- Returns the targets.
- getTargetToPrint() -
Method in class chemaxon.sss.search.Search
- For internal purposes only.
- getTautomerSearch() -
Method in class chemaxon.sss.search.SearchOptions
- Indicates if tautomers of the query should be enumerated for search.
- getTCenter() -
Method in class chemaxon.struc.graphics.MRectangle
- Gets the transformed point.
- getTemporaryObject(String) -
Method in class chemaxon.struc.MolAtom
- Gets a temporary object.
- getTermCondition() -
Method in class chemaxon.metabolizer.Metabolizer
- Returns termination condition
- getTerminalBondDeletionStyle() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the terminal bon deletion style.
- getTerminationCause() -
Method in class chemaxon.sss.search.MCES
- Gets the termination cause of the last search.
- getText() -
Method in class chemaxon.jchem.file.ProgressWriter
- Returns the main text of the progress message.
- getText() -
Method in class chemaxon.marvin.space.monitor.Label
- Returns the explicit text of the label, or null if there is no explicit label set.
- getText() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the text stored.
- getTextAttributesAtCursor() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the common attributes of the text on the cursor.
- getTextDocument() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the text document.
- getThickness() -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the line thickness.
- getThreshold() -
Method in class chemaxon.clustering.Compare
- Gets the threshold value.
- getThreshold() -
Method in class chemaxon.clustering.NearestNeighbors
- Gets the threshold value.
- getThreshold(int, int) -
Method in class chemaxon.descriptors.MDHitEvaluator
- Returns threshold set by last screen (given by user as a parameter) of
evaluation (set by evaluation).
- getThreshold(int) -
Method in class chemaxon.descriptors.MDParameters
- Gets a metric dependent threshold value.
- getThreshold() -
Method in class chemaxon.descriptors.MDParameters
- Gets the threshold value being set for the current parametrized version.
- getThreshold(int) -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets a metric dependent default threshold value.
- getThreshold() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Gets threshold value of the current parameterized metric.
- getThrowable() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns the throwable object.
- getThrowable() -
Method in interface chemaxon.util.iterator.MoleculeIterator
- Deprecated. Not used.
MoleculeIterator.next() throws NoSuchElementException in case of error.
- getTimeLimit() -
Method in class chemaxon.sss.search.MCES
- Gets the maximum allowed search time.
- getTimeout() -
Method in class chemaxon.jchem.db.JChemSearch
- Gets the current timout setting.
- getTimeoutLimit() -
Method in class chemaxon.sss.search.SearchOptions
- Deprecated. since 5.6 use
SearchOptions.getTimeoutLimitMilliseconds() instead
- getTimeoutLimitMilliseconds() -
Method in class chemaxon.sss.search.SearchOptions
- The search timeouts reaching this amount of time.
- getTimestamp(Connection) -
Method in class chemaxon.jchem.db.CacheRegistrationUtil
-
- getTitle() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Returns the frame title.
- getTitle() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns the frame title.
- getTolerances(String) -
Static method in class chemaxon.reaction.Reaction
- Deprecated. Returns
double[] created from ";" separated list of
real numbers.
- getToolBar(JTextPane) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Returns the default toolbar for textPane instance
NOTE: textPane have to be created with this factory
- getToolbarConfigPath() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- Returns the toolbar configuration path
- getTooltip() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the tooltip of the element
- getTop() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the y coordinate of the top of the cell.
- getTopLeftIndex() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the index of the top left cell.
- getTopLevelClusterCount() -
Method in class chemaxon.clustering.LibraryMCS
- Gets the number of clusters on the highest level of the hierarchy.
- getTopLevelContainer() -
Method in class chemaxon.marvin.beans.MarvinPane
-
- getTOption() -
Method in class chemaxon.struc.graphics.MRectangle
- Gets the transformation options.
- getTotalCharge(int) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns the total charge of a specified atom.
- getTotalCharge() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the total (formal) charge of the molecule.
- getTotalCharge() -
Method in class chemaxon.struc.Sgroup
- Calculates the sum of the charge values on the atoms in this
S-group.
- getTotalClusterCount() -
Method in class chemaxon.clustering.LibraryMCS
- Gets the total number of clusters in the hierarchy.
- getTotalPiEnergy() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Deprecated. Use
HuckelAnalysisPlugin.getHMOTotalPiEnergy()
- getTPSA() -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Deprecated. as of Marvin 4.1, replaced by
TPSAPlugin.getSurfaceArea()
- getTraditionalName() -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns the traditional IUPAC name.
- getTrainingIds() -
Static method in class chemaxon.marvin.calculations.logPPlugin
- Returns the id's of available logP trainings.
- getTrainingIds() -
Static method in class chemaxon.marvin.calculations.PredictorPlugin
- Returns the id's of available predictions.
- getTransferableFor(Molecule, Properties) -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Creates a
MTransferable object to the given Molecule with
the given properties.
- getTransferableFor(Molecule, Properties, String) -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Creates a
MTransferable to the given Molecule with the
given properties in the given format.
- getTransferableFor(Molecule, Properties) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getTransferableFor(Molecule, Properties, String) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- getTransferData(DataFlavor) -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
-
- getTransferData(DataFlavor) -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Returns the result of the transfer operation.
- getTransferDataFlavors() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
-
- getTransferDataFlavors() -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Returns the DataFlavors supported by the actual implementation.
- getTransformationCenter() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the transformation center.
- getTransformationCenter() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the center of transformation of the active cell or null
if there is no active cell.
- getTversky(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the Tversky !!
- getTversky(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the Tversky !!
- getTverskyAlpha() -
Method in class chemaxon.descriptors.MDParameters
- Gets Tversky alpha value for the given parametrized metric.
- getTverskyBeta() -
Method in class chemaxon.descriptors.MDParameters
- Gets Tversky beta value for the given parametrized metric.
- getType() -
Method in class chemaxon.checkers.AromaticityErrorChecker
- Returns the type of the aromatization
- getType() -
Method in class chemaxon.descriptors.BCUTParameters
- Gets the type of the BCUT descriptor.
- getType() -
Method in class chemaxon.descriptors.SDParameters
-
- getType() -
Method in class chemaxon.marvin.services.ServiceArgument
- Returns the argument type
- getType(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getType(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getType() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Gets the option type.
- getType() -
Method in class chemaxon.sss.search.MarkushFeature
- Returns the feature type.
- getType() -
Method in class chemaxon.struc.graphics.MBracket
- Gets the bracket type.
- getType() -
Method in class chemaxon.struc.MolBond
- Gets the bond type.
- getType(MoleculeGraph) -
Method in class chemaxon.struc.RxnMolecule
- Checks whether the atoms in the selection are all in reactants, products or agents.
- getType() -
Method in class chemaxon.struc.Sgroup
- Gets S-group type.
- getTypeName() -
Method in interface chemaxon.descriptors.MDHypothesisGenerator
- Returns type of generated hypothesis.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Returns a string representation of the given type.
- getTypeString(Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns a string representation of the given type.
- getUndefinedRAtom() -
Method in class chemaxon.sss.search.SearchOptions
- Returns undefined R atom matching behaviour mode.
- getUndo() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets the maximum undo depth.
- getUnguessableFormat(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Gets the file format from the file name extension for formats that
are not guessable from the file content.
- getUnits() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the unit of this data field.
- getUnmatchedQueryAtoms() -
Method in class chemaxon.sss.search.MCES
- Gets the query atoms that are not part of the found MCES.
- getUnmatchedQueryBonds() -
Method in class chemaxon.sss.search.MCES
- Gets the query bonds that are not part of the found MCES.
- getUnmatchedTargetAtoms() -
Method in class chemaxon.sss.search.MCES
- Gets the target atoms that are not part of the found MCES.
- getUnmatchedTargetBonds() -
Method in class chemaxon.sss.search.MCES
- Gets the target bonds that are not part of the found MCES.
- getUrl() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
url.
- getUsableObject(UOID) -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns the component that the given UOID identifies.
- getUsableObject(UOID) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
- getUsableObjectId(MacroMoleculeComponent.MoleculeVisualizer) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
-
- getUserComparators() -
Method in class chemaxon.sss.search.SearchOptions
- Because of efficiency reasons one should check hasUserComparators()
before calling this method!
- getUserData(int) -
Method in class chemaxon.descriptors.MDSet
- Deprecated. since 2.3
- getUserData() -
Method in class chemaxon.descriptors.MDSet
- Deprecated. since 2.3
- getUserDataWeight(int) -
Method in class chemaxon.descriptors.MDSetParameters
- Gets the weight of a userData component.
- getUserSettings() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the user settings object.
- getUserTypes() -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the user defined result types.
- getVagueBondLevel() -
Method in class chemaxon.sss.search.SearchOptions
- Getter for vague bond level.
- getValence() -
Method in class chemaxon.struc.MolAtom
- Gets the valence.
- getValence(int) -
Method in interface chemaxon.struc.Smolecule
- Gets the valence.
- getValenceProp() -
Method in class chemaxon.struc.MolAtom
- Gets the valence property.
- getValencePropMinMax() -
Method in class chemaxon.struc.MolAtom
- Gets the minimum and maximum possible values of the valence property.
- getValidationResultLabel(JTextPane) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Returns a
JLabel instance, dinamically showing validation result of textPane
NOTE: will validate against Molecular Context.
- getValidationResultLabel(JTextPane, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Returns a
JLabel instance, dinamically showing validation result of textPane
NOTE: textPane have to be created with this factory
- getValidationResultLabelForReactionContext(JTextPane) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Returns a
JLabel instance, dinamically showing validation result of textPane
NOTE: will validate against Reaction Context.
- getValidSinkAtomPairsForMolecule(Molecule, MolAtom) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the atom pairs can be chosen as a sink for an electron flow
with a MolAtom as a source in the molecule.
- getValidSinkAtomPairsForMolecule(Molecule, MolBond) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the atom pairs can be chosen as a sink for an electron flow
with a MolBond as a source in the molecule.
- getValidSinkAtomsForMolecule(Molecule, MolAtom) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the atoms can be chosen as a sink for an electron flow
with a MolAtom as a source in the molecule.
- getValidSinkAtomsForMolecule(Molecule, MolBond) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the atoms can be chosen as a sink for an electron flow
with a MolBomd as a source in the molecule.
- getValidSinkBondsForMolecule(Molecule, MolAtom) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the bonds can be chosen as a sink for an electron flow
with a MolAtom as a source in the molecule.
- getValidSinkBondsForMolecule(Molecule, MolBond) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the bonds can be chosen as a sink for an electron flow
with a MolBond as a source in the molecule.
- getValidSourceAtomPairsForMolecule(Molecule) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the atom pairs can be chosen as incipient bonds as a source for an electron flow
in the molecule.
- getValidSourceAtomsForMolecule(Molecule) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the atoms can be chosen as a source for an electron flow
in the molecule.
- getValidSourceBondsForMolecule(Molecule) -
Static method in class chemaxon.struc.graphics.MEFlow
- Returns the bonds can be chosen as a source for an electron flow
in the molecule.
- getValue() -
Method in class chemaxon.marvin.services.ServiceArgument
- Returns the argument value
- getVanDerWaalsRadius(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Van der Waals radius of the element in Angstroms.
- getVDWSA() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns van der Waals surface area.
- getVerboseLevel() -
Method in class chemaxon.marvin.space.GraphicCell
- Gets the verbose level.
- getVerboseLevel() -
Method in class chemaxon.marvin.space.GraphicScene
- Gets the verbose level.
- getVertexCount() -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the number of allocated vertices in the SurfaceComponent.
- getVertexX(int) -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the x coordinate of the ith vertex.
- getVertexY(int) -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the y coordinate of the ith vertex.
- getVertexZ(int) -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns the z coordinate of the ith vertex.
- getVerticalAlignment() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets the vertical alignment.
- getViewAnyBond() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the default any bond drawing style in the viewer.
- getViewCarbonVisibility() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the default carbon displaying style in the viewer.
- getViewColorScheme() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the viewer's default color scheme.
- getViewExplicitH() -
Method in class chemaxon.marvin.common.UserSettings
- Deprecated. As of release 5.3, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
- getViewHandlerType() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Gets the view handler type.
- getViewImplicitH() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the display method of implicit hydrogens for the viewer.
- getViewLayout() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the table layout of the Viewer.
- getViewLigandOrderVisibility() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the default ligand order displaying style in the viewer.
- getViewLoadWorkingDir() -
Method in class chemaxon.marvin.common.UserSettings
- Based on the preferences this funtion returns the proper working
directory for the MarvinView application's load filechooser.
- getViewMolbg2d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the viewer's default molecule background color for 2D.
- getViewMolbg3d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the viewer's default molecule background color for 3D.
- getViewNavmode2d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the navigation mode for the 2D viewer.
- getViewNavmode3d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the navigation mode for the 3D viewer.
- getViewportHeight() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the phisical height of the viewport.
- getViewportWidth() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the phisical width of the viewport.
- getViewRecentFileList() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the recent files' list in MarvinView, the last item is the most
recent.
- getViewRecentFileListSize() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the recent file list requested size, based on a preferences setting
- getViewRendering2d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the rendering style for the 2D viewer.
- getViewRendering3d() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the rendering style for the 3D viewer.
- getViewSaveWorkingDir() -
Method in class chemaxon.marvin.common.UserSettings
- Not implemented yet, don't use it.
- getVisibleAtomCount() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- getVisibleAtomCount() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns the number of atoms currently visible.
- getVisibleButtonB(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the i-th button in the visible area of the viewer.
- getVisibleButtonC(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the i-th checkbox in the visible area of the viewer.
- getVisibleCellComponent(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the canvas of the specified cell in a GridBag layout based table.
- getVisibleCellCount() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the number of the visible cells in a GridBag layout based table.
- getVisibleCellIndex(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Determines the visible cell index of a cell
- getVisibleCoords(MolAtom) -
Method in class chemaxon.struc.Molecule
- Returns the coordinates of the given atom (contained in the molecule).
- getVisibleCoords(MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Returns the coordinates of the given atom (contained in the molecule).
- getVisiblePointRef(int, CTransform3D) -
Method in class chemaxon.struc.graphics.MBracket
- Gets an internal selectable point of the rectangle.that is visible when highlighting.
- getVisiblePointRefCount() -
Method in class chemaxon.struc.graphics.MBracket
- Gets the number of internal selectable point references that are visible when highlighting.
- getVolume() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- getVolume() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
-
- getVolumeScore() -
Method in class chemaxon.marvin.alignment.Alignment
-
- getVolumeTanimoto() -
Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.AlignmentPlugin
- Returns the calculation warning information message.
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Returns a warning message if there are no conformers,
null
otherwise.
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Returns a warning message if lowest energy conformer calculation was unsuccessful
or aborted by user,
null otherwise.
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns the calculation warning information message
if no H-bond donor/acceptor atoms found, returns
the empty string otherwise.
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns the calculation warning information message.
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns the calculation warning information message
if no isoelectric point exists, returns the empty string otherwise.
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the calculation warning information message.
- getWarningMessage() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns a warning message if there are no stereoisomers,
null
otherwise.
- getWarningMessage() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the calculation warning information message.
- getWebServiceName() -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- Returns the service name
- getWeight(int) -
Method in class chemaxon.descriptors.MDSetParameters
- Gets the weight of a component.
- getWeightedAsymmetricEuclidean(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the weighted asymmetric Euclidean distance.
- getWeightedAsymmetricEuclidean(CustomDescriptor) -
Method in class chemaxon.descriptors.CustomDescriptor
- Calculates the weighted asymmetric Euclidean distance.
- getWeightedAsymmetricEuclidean(ECFP) -
Method in class chemaxon.descriptors.ECFP
- Calculates the weighted asymmetric Euclidean distance.
- getWeightedAsymmetricEuclidean(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the weighted asymmetric Euclidean distance.
- getWeightedEuclidean(BCUT) -
Method in class chemaxon.descriptors.BCUT
- Calculates the weighted Euclidean distance.
- getWeightedEuclidean(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Calculates the weighted Euclidean distance.
- getWeightedEuclidean(CustomDescriptor) -
Method in class chemaxon.descriptors.CustomDescriptor
- Calculates the weighted Euclidean distance.
- getWeightedEuclidean(ECFP) -
Method in class chemaxon.descriptors.ECFP
- Calculates the weighted Euclidean distance.
- getWeightedEuclidean(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the weighted Euclidean distance.
- getWeights() -
Method in class chemaxon.clustering.Common
- Gets descriptor weights used for distance calculation.
- getWeights() -
Method in class chemaxon.descriptors.MDParameters
- Gets all weights for the given parametrized metric.
- getWeights() -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Gets the atom weights used in average location calculation.
- getWidth() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the width of the cell.
- getWienerIndex() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the Wiener index of the molecule, which is the average
topological atom distance (half of the sumof all atom distances) in the
molecule.
- getWienerPolarity() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Calculates the Wiener polarity number of the molecule, which is the
number of 3 bond length distances in the molecule.
- getWinScale() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the magnification in the zoom windows.
- getWireThickness() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the line thickness for wireframe mode.
- getWireThickness() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the bond thickness in wireframe mode.
- getWireThickness() -
Method in class chemaxon.marvin.MolPrinter
- Gets the line thickness for wireframe mode.
- getWord(ByteBuffer, int) -
Method in class chemaxon.marvin.io.PositionedInputStream
-
- getWordsRead() -
Method in class chemaxon.naming.DocumentExtractor.ProgressInfo
-
- getWorkOnBackGround() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns whether the subsystem works on the current thread or on a
background thread.
- getWrapperException(Exception) -
Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
- Returns a wrapper exception to be returned.
- getWrapperException(Exception) -
Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
- Returns a wrapper exception to be returned.
- getWsdlURI() -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- Returns the WSDL URI
- getX(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getX(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getX() -
Method in class chemaxon.struc.MolAtom
- Gets the X coordinate.
- getX() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the X coordinate.
- getXml(String) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Read the xml file that contains the regeneration information.
- getXState() -
Method in class chemaxon.struc.Sgroup
- Gets the expanded/contracted state.
- getY(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getY(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getY() -
Method in class chemaxon.struc.MolAtom
- Gets the Y coordinate.
- getY() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets the Y coordinate.
- getZ(int) -
Method in class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty
-
- getZ(int) -
Method in class chemaxon.marvin.space.AtomProperty.SmoleculeAtomProperty
-
- getZ() -
Method in class chemaxon.struc.MolAtom
- Gets the Z coordinate.
- getZCoordinateTo2DPart() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns a third, z coordinate in order to display 2D parts in proper order.
- getZCoordinateTo2DPart() -
Method in class chemaxon.marvin.space.monitor.Label
- Returns a third, z coordinate in order to display 2D parts in proper order.
- gFuzzyIncrements -
Variable in class chemaxon.descriptors.PFParameters
- Fuzzy smoothing values for gaussian smoothing.
- gl -
Variable in class chemaxon.marvin.space.GraphicComponent
- must be accessible in derived classes
- glColor() -
Method in class chemaxon.marvin.space.GraphicComponent
- Sets the default/constant color of the component for drawing.
- GLInfo -
Static variable in class chemaxon.marvin.space.GraphicScene
-
- GlobalLocationControl - Class in chemaxon.marvin.space.monitor
- This control is to change the location say translate a
GraphicComponent
in the global coordinate system. - GlobalLocationControl(Monitor) -
Constructor for class chemaxon.marvin.space.monitor.GlobalLocationControl
- Creates a new instance of GlobalLocationControl
- GlobalOrientationControl - Class in chemaxon.marvin.space.monitor
- This control is to change the orientation say rotate a
GraphicComponent
in the global coordinate system. - GlobalOrientationControl(Monitor) -
Constructor for class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Creates a new instance of GlobalOrientationControl
- gltext -
Variable in class chemaxon.marvin.space.monitor.Label
- This is to draw labels in the viewing plane.
- glu -
Variable in class chemaxon.marvin.space.GraphicComponent
-
- GRAPH_INVARIANTS -
Static variable in class chemaxon.marvin.view.ViewParameterConstants
- Identifier of parameter:
"grinv".
- GRAPH_INVARIANTS_VISIBLE -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"grinvVisible".
- GraphicCell - Class in chemaxon.marvin.space
GraphicCell is a rectangular part of the OpenGL canvas containing GraphicComponents.- GraphicCell() -
Constructor for class chemaxon.marvin.space.GraphicCell
- Creates a new instance of
GraphicCell.
- GraphicCell(GL, GLU) -
Constructor for class chemaxon.marvin.space.GraphicCell
- Creates a new instance of
GraphicCell.
- graphicCell -
Variable in class chemaxon.marvin.space.GraphicComponent
- which cell of the scene is this component displayed in
- GraphicComponent - Class in chemaxon.marvin.space
- GraphicComponents are the basic objects what MarvinSpace can visualize and handle.
- GraphicComponent() -
Constructor for class chemaxon.marvin.space.GraphicComponent
- Creates an empty object.
- GraphicScene - Class in chemaxon.marvin.space
GraphicScene is the main "entry point" to MarvinSpace.- GraphicScene() -
Constructor for class chemaxon.marvin.space.GraphicScene
- Creates a hardware accelerated and double buffered
GraphicScene.
- GraphicScene(int, int) -
Constructor for class chemaxon.marvin.space.GraphicScene
- Creates a hardware accelerated and double buffered GraphicScene.
- graphInvariant() -
Method in class chemaxon.calculations.stereo.Stereochemistry
-
- graphInvariant() -
Method in class chemaxon.calculations.TopologyAnalyser
-
- GRID_MAPPING -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Coloring by mapping values form a grid to the surface.
- GRINV_DONT_STORE -
Static variable in class chemaxon.struc.MoleculeGraph
- Graph invariant option to instruct that the graph invariant should not be
stored in MoleculeGraph.
- GRINV_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Show graph invariants flag.
- GRINV_NOHYDROGEN -
Static variable in class chemaxon.struc.MoleculeGraph
- Graph invariant option for ignoring explicit hydrogens.
- GRINV_OLDSTEREO -
Static variable in class chemaxon.struc.MoleculeGraph
- Graph invariant option for calculating graph invariants using the old
stereo method.
- GRINV_STEREO -
Static variable in class chemaxon.struc.MoleculeGraph
- Graph invariant option for calculating graph invariants using stereo
information.
- GRINV_USEMAPS -
Static variable in class chemaxon.struc.MoleculeGraph
- Graph invariant option for calculating graph invariants considering
atom maps also.
- GRINV_VALUE_OPTIONS -
Static variable in class chemaxon.struc.MoleculeGraph
- Unified mask of graph invariant options affecting grinv value.
- grinvCC -
Variable in class chemaxon.struc.MoleculeGraph
- Graph invariant change count.
- GROUP_QUERY -
Static variable in class chemaxon.reaction.Standardizer
- Deprecated. Not used.
- GROUP_SCHEME -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Group color scheme in display option flags.
- GROUP_SCHEME_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Group color scheme.
- GROUP_TARGET -
Static variable in class chemaxon.reaction.Standardizer
- Deprecated. Not used.
- GROUP_TYPE_ANY -
Static variable in class chemaxon.jchem.db.RegenerationConstants
-
- GROUPTYPE_ALTERNATING_COPOLYMER_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_ANYPOLYMER_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_BLOCK_COPOLYMER_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_COMPONENT_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_COPOLYMER_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_CROSSLINK_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_GENERIC_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_GRAFT_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MER_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MODIFICATION_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MONOMER_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_MULTIPLE_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_ORDERED_MIXTURE_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_RANDOM_COPOLYMER_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_RANGE_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_SRU_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_SUPERATOM_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- GROUPTYPE_UNORDERED_MIXTURE_GROUP -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
- guessMappingStyle(RxnMolecule) -
Method in class chemaxon.marvin.modules.AutoMapper
- Guesses mapping style of the input reaction.
- guessPeptideFormat(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Deprecated. as of Marvin 5.0,
PeptideRecognizer.guessPeptideFormat(String)
must be used instead
- guessPeptideFormat(String) -
Static method in class chemaxon.formats.recognizer.PeptideRecognizer
- Tries to distinguish between one letter and two letter peptides.
- GZIP -
Static variable in class chemaxon.formats.MFileFormat
- GZIPped file.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if filter is set.
true if element is in group
true if element has any groups
true if filter is set and
references the hit, not only the query/target structures.
JChemSearch.RUN_MODE_ASYNCH_PROGRESSIVE.
true if there are more structures.
true if all input producers have next input.
true if there are more molecules,
false if end has been reached.
true.
true if plugin has parameter panel,
false otherwise.
ComponentElement
in the active cell.
SmartsAtomQuerifier.hasSMARTSProps(MolAtom atom)
SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude)
true if element has the tag
true if element has any tags
MESH_TYPE or TRANSPARENT_TYPE.
DRAW_TYPE_WIRE or
DRAW_TYPE_BALL_AND_WIRE mode.
GraphicComponent.hasTransparentPart().
MESH_TYPE or TRANSPARENT_TYPE.
MolAtom.haveSimilarBonds(MolAtom).
HDon and HAcc scalar
descriptor classes.Ring.heteroaliphaticRingCount()
Ring.heteroaliphaticRingCount(int)
Ring.heteroaliphaticRings()
Ring.heteroaliphaticRings(int)
Ring.heteroaromaticRingCount()
Ring.heteroaromaticRingCount(int)
Ring.heteroaromaticRings()
Ring.heteroaromaticRings(int)
Ring.heteroRingCount()
Ring.heteroRingCount(int)
Ring.heteroRings()
Ring.heteroRings(int)
MListProp and
MHashProp objects.
ServiceDescriptor implementation
for HTTP POST/GET based servicesHTTPServiceDescriptor
Hydrogenize.addHAtoms(MoleculeGraph) and
Hydrogenize.removeHAtoms(MoleculeGraph)
"imageSaveFormat".
"imageSaveURL".
"imageShowURL".
"implicitH".
Hydrogenize.removeHAtoms(MoleculeGraph, int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(mol, f);
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(mol, atoms, f);
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean)
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.removeHAtoms(mol, atoms, f, check);
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean)
Hydrogenize.removeHAtoms(MoleculeGraph, MolAtom[], int, boolean)
"importConv".
"importEnabled".
MolImporter.importMol(String,String);
if you have a byte array, call MolImporter.importMol(byte[], String, String).
MolImporter.importMol(String, String);
if you have a byte array, call MolImporter.importMol(byte[], String, String, Molecule).
Document into the current
(main) Document.
inc( int fa, int fb, int dist ).
- inc(int, int, int, float[]) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- The fuzzy version of
inc( int fa, int fb, int dist ).
- inc(int) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Increments the content of the specified hitogram bin by one.
- incGrinvCC() -
Method in class chemaxon.struc.MoleculeGraph
- Increases the graph invariant change count and sets
grinv to null.
- incGrinvCCOnly() -
Method in class chemaxon.struc.MoleculeGraph
- Increases the graph invariant change count, but does not change grinv.
- INCHI -
Static variable in class chemaxon.formats.MFileFormat
- IUPAC InChI files.
- INCHIKEY -
Static variable in class chemaxon.formats.MFileFormat
- IUPAC InChIKey.
- INCLUDE_ALL_ATOMS -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Include all atoms: chemical atoms, explicit hydrogen, multicenter, lone pair and pseudo atoms in atom iterations.
- INCLUDE_ALL_BONDS -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Include all bonds: covalent and coordinate bonds in bond iteration.
- INCLUDE_CHEMICAL_ATOMS -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Deprecated. Replaced by
IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY.
- INCLUDE_CHEMICAL_ATOMS_ONLY -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Include only chemical atoms in iteration, skip multicenters, lone pairs and pseudo atoms.
- Incomplecule - Interface in chemaxon.struc
- Ancestor of molecule classes and interfaces.
- INCORRECT_AROMATIC_NITROGEN_REMARK -
Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
- Incorrect aromatic nitrogen remark.
- incQProp(String) -
Method in class chemaxon.struc.MolAtom
- Increments the value of a query property.
- incQueryAromaticity() -
Method in class chemaxon.struc.MolAtom
- Increments the value of the query aromaticity property.
- incRegenerateDescriptorTable(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Calculates missing lines in MD table
- incrementProperty(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Increments the value of property with the specified
key by one.
- incValenceProp() -
Method in class chemaxon.struc.MolAtom
- Increments the value of the valence property.
- index(int, int, int) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the index of the bin specified by the arguments.
- indexOf(MObject) -
Method in class chemaxon.struc.MDocument
- Searches for an object in the document or in the chemical structure that
belongs to the document.
- indexOf(MolBond) -
Method in class chemaxon.struc.MolAtom
- Returns the index of the specified bond in this atom.
- indexOf(Sgroup) -
Method in class chemaxon.struc.Molecule
- Gets the array index of an S-group.
- indexOf(MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the index of the specified atom.
- indexOf(MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Gets the index of the specified bond.
- indexOf(MolAtom) -
Method in class chemaxon.struc.RgMolecule
- Gets the index of the specified node in the graph union.
- indexOf(MolBond) -
Method in class chemaxon.struc.RgMolecule
- Gets the index of the specified edge in the graph union.
- indexOf(MolAtom) -
Method in class chemaxon.struc.RxnMolecule
- Gets the index of the specified node in the graph union.
- indexOf(MolBond) -
Method in class chemaxon.struc.RxnMolecule
- Gets the index of the specified edge in the graph union.
- indexOf(MolAtom) -
Method in class chemaxon.struc.Sgroup
- Gets the atom index in the S-group graph.
- indexOf(MolBond) -
Method in class chemaxon.struc.Sgroup
- Gets the bond index in the S-group graph.
- indexOf(int) -
Method in class chemaxon.util.IntArray
- Searches for the first occurence of the given argument.
- indexOf(int, int) -
Method in class chemaxon.util.IntArray
- Searches for the first occurence of the given argument, beginning
the search at
index.
- indexOfButtonB(AbstractButton) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the index of the button on the visible area of the viewer.
- indexOfButtonC(AbstractButton) -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the index of the checkbox in the visible area of the viewer.
- indexOfWithBinarySearch(int) -
Method in class chemaxon.util.IntArray
- Searches for the first occurence of the given number with binary search.
- indicesOf(String) -
Method in class chemaxon.formats.recognizer.RecognizerList
- Gets the level and the index of the specified format.
- INFO -
Static variable in class chemaxon.jchem.file.ProgressWriter
- Log level info
- init() -
Method in class chemaxon.descriptors.CDParameters
- This method is called by the constructors before processing the XML
configuration.
- init() -
Method in class chemaxon.descriptors.CFParameters
- This method is called by the constructors before processing the XML
configuration.
- init() -
Method in class chemaxon.descriptors.ECFPParameters
- This method is called by the constructors before processing the XML
configuration.
- init() -
Method in class chemaxon.descriptors.GenerateMD
- Initialize the generator object.
- init() -
Method in class chemaxon.descriptors.PFParameters
- Initializes the object.
- init() -
Method in class chemaxon.descriptors.RFParameters
- This method is called by the constructors before processing the XML
configuration.
- init() -
Method in class chemaxon.descriptors.SDParameters
- This method is called by the constructors before processing the XML
configuration.
- init(Element, Standardizer, String) -
Method in class chemaxon.fragmenter.CutBondReviser
- Initializes the reviser.
- init(RxnMolecule[], Standardizer, CutBondReviser) -
Method in class chemaxon.fragmenter.Fragmenter
- Initializes Fragmenter.
- init(Element, Standardizer, String) -
Method in class chemaxon.fragmenter.Recap
- Initializes the reviser.
- init() -
Method in class chemaxon.jchem.db.Importer
- Initialization, checking given number of lines for file format and fields.
- init(ConnectionHandler, int, String, String) -
Method in class chemaxon.jchem.db.UpdateHandler
- Initializes the object.
- init(MolPanel) -
Method in class chemaxon.marvin.beans.MarvinPane
- Initializes the content pane.
- init(MolPanel, boolean) -
Method in class chemaxon.marvin.beans.MarvinPane
- Initializes the content pane.
- init(GLAutoDrawable) -
Method in class chemaxon.marvin.space.GraphicScene
- Called by the drawable immediately after the OpenGL context is initialized for the first
time.
- initAction(Action, ResourceBundle, String, KeyStroke) -
Static method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.initAction
- initAction(Action, ResourceBundle, String, KeyStroke) -
Static method in class chemaxon.marvin.util.SwingUtil
- Initializes an action from information in a resource.
- initAll(Molecule, Molecule, StructureSearch) -
Method in class chemaxon.sss.search.MolComparator
-
- initBrackets() -
Method in class chemaxon.struc.Sgroup
- Initializes the list of brackets in this S-group.
- initButton(AbstractButton, ResourceBundle, String) -
Static method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.initButton
- initButton(AbstractButton, ResourceBundle, String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Utility method to initialize a button from information in a
resource.
- initButton(AbstractButton, ResourceBundle, String, boolean) -
Static method in class chemaxon.marvin.util.SwingUtil
- Utility method to initialize a button from information in a
resource.
- initCtrlShortcutForMac(JMenuItem) -
Static method in class chemaxon.marvin.util.SwingUtil
- Deprecated. does nothing.
- initDraw() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- initDraw() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Initializes gl related drawing variables, for example display lists.
- initEmbeddedMD() -
Method in class chemaxon.descriptors.ShapeParameters
- This method is called by the constructors before processing the XML
configuration.
- initFields() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Initialize field information before update.
- initGenerator() -
Method in class chemaxon.descriptors.CDParameters
- This method is void in this class as custom descriptors are opaque, their
internal structure is not known.
- initGenerator() -
Method in class chemaxon.descriptors.CFParameters
- Initializes the fingerprint generator.
- initGenerator() -
Method in class chemaxon.descriptors.ECFPParameters
- Initializes the fingerprint generator.
- initGenerator() -
Method in class chemaxon.descriptors.PFParameters
- Creates and initializes a
PFGenerator instance.
- initGenerator() -
Method in class chemaxon.descriptors.RFParameters
- Initializes the reaction fingerprint generator.
- initGenerator() -
Method in class chemaxon.descriptors.ShapeParameters
- Initializes the fingerprint generator.
- INITIAL_CAPACITY -
Static variable in class chemaxon.struc.MoleculeGraph
- Initial capacity of the atoms and bonds vectors.
- initialised -
Variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- initialize() -
Method in class chemaxon.checkers.ComponentChecker
- Empty default implementation
- initialize() -
Method in class chemaxon.reaction.ConcurrentReactorProcessor
- For internal use only.
- initInApplet() -
Static method in class chemaxon.marvin.util.SwingUtil
- Deprecated. does nothing.
- initMolImport(MolInputStream) -
Method in class chemaxon.marvin.io.formats.mdl.MolImport
- Initializes the import module.
- initMolImport(MRecord, String) -
Method in class chemaxon.marvin.io.MolImportModule
- Initializes the import module.
- initMolImport(MolInputStream) -
Method in class chemaxon.marvin.io.MolImportModule
- Initializes the import module.
- initParameters() -
Method in class chemaxon.descriptors.BCUTParameters
-
- initParameters() -
Method in class chemaxon.descriptors.CDParameters
- Initializes data members that depend on the XML configuration but
are not directly taken from it.
- initParameters() -
Method in class chemaxon.descriptors.CFParameters
- Initializes those data members that depend on the XML configuration but
are not directly taken from it.
- initParameters() -
Method in class chemaxon.descriptors.ECFPParameters
- Initializes those data members that depend on the XML configuration but
are not directly taken from it.
- initParameters() -
Method in class chemaxon.descriptors.MDParameters
- Initializes object after configuration parameters are loaded.
- initParameters() -
Method in class chemaxon.descriptors.PFParameters
- Initializes those data members that depend on the XML configuration but
are not directly taken from it.
- initParameters() -
Method in class chemaxon.descriptors.RFParameters
- Initializes those data members that depend on the XML configuration but
are not directly taken from it.
- initParameters() -
Method in class chemaxon.descriptors.scalars.HBParameters
-
- initParameters() -
Method in class chemaxon.descriptors.scalars.LDParameters
-
- initParameters() -
Method in class chemaxon.descriptors.SDParameters
- Initializes those data members that depend on the XML configuration but
are not directly taken from it.
- initVariables(boolean) -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
- After reading from byte[] with
AlignmentMolecule.create(byte[] bytes) initialize variables.
- InputProducer<V> - Interface in chemaxon.util.concurrent
- Source of the input data.
- inputProducers -
Variable in class chemaxon.util.concurrent.marvin.CompositeInputProducer
- The input producer array.
- INSERT -
Static variable in class chemaxon.jchem.db.UpdateHandler
- Row insertion with automatic
cd_id value.
- insert(int, String, MTextAttributes) -
Method in class chemaxon.struc.graphics.MTextDocument
- Inserts a string.
- INSERT_WITH_ID -
Static variable in class chemaxon.jchem.db.UpdateHandler
- Row insertion with
cd_id value set by
the application.
- insertAtom(int, MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Inserts the atom at the specified index.
- insertBond(int, MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Inserts the bond at the specified index.
- insertBondInOrder(MolBond, MolBond[]) -
Method in class chemaxon.struc.MoleculeGraph
- Insert a bond in the order specified as the second argument.
- insertEdge(int, MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.insertBond(int, MolBond).
- insertEdgeInOrder(MolBond, MolBond[]) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.insertBondInOrder(MolBond, MolBond[]).
- insertNode(int, MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.insertAtom(int, MolAtom).
- insertNullAtoms(int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Insert nulls into the atom array.
- insertNullAtoms(int, int) -
Method in class chemaxon.struc.RgMolecule
- Insert nulls into the atom array.
- insertNullBonds(int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Insert nulls into the bond array.
- insertNullBonds(int, int) -
Method in class chemaxon.struc.RgMolecule
- Insert nulls into the bond array.
- insertStringBeforeLineEnds(String, String) -
Static method in class chemaxon.util.HTMLTools
- Inserts the specified string before the ends of lines.
- insertText(String) -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Inserts the given string to textPane at caret position.
- insideLabel(double, double) -
Method in class chemaxon.struc.MolAtom
- Tests whether the specified point is inside the atom label.
- INSTABLE_TAUTOMERIC_FORM_REMARK -
Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
- Instable tautomeric form remark.
- INSTANT_JCHEM -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: Instant JChem
- INSTANT_JCHEM_VIZ -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: Instant JChem VIZ
- INSTANTIATION_ERROR -
Static variable in class chemaxon.util.ErrorHandler
-
- IntArray - Class in chemaxon.util
- The
IntArray class implements an array of
integers. - IntArray() -
Constructor for class chemaxon.util.IntArray
- Constructs an empty IntArray.
- IntArray(int) -
Constructor for class chemaxon.util.IntArray
- Constructs an empty IntArray with the specified block size.
- intDescr -
Variable in class chemaxon.descriptors.CustomDescriptor
- storage for the integer or binary descriptors
- INTEGER_DESCRIPTOR -
Static variable in class chemaxon.descriptors.CDParameters
-
- INTERBASE -
Static variable in class chemaxon.jchem.db.DatabaseConstants
-
- internalSize -
Variable in class chemaxon.descriptors.MDParameters
- required memory size of one descriptor instance
- intValue() -
Method in class chemaxon.struc.prop.MIntegerProp
- Gets the integer value.
- INVALID_LINKNODE_MESSAGE -
Static variable in class chemaxon.struc.MoleculeGraph
-
- invert() -
Method in class chemaxon.struc.CTransform3D
- Inverts the matrix.
- invertSelection(int) -
Method in class chemaxon.marvin.space.GraphicCell
- The previously picked part of the component will be selected
if it was unselected and vice versa.
- invertSelection() -
Method in class chemaxon.marvin.space.GraphicComponent
- Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
- invertSelection(ComponentElement) -
Method in class chemaxon.marvin.space.GraphicComponent
- Sets the the given part of the component to be selected if it was not set and vice versa.
- invertSelection(UOID) -
Method in class chemaxon.marvin.space.GraphicScene
- The previously picked part of the component will be selected
if it was unselected and vice versa.
- invertSelection() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Sets the previously picked but unprocessed element to be selected if it was not set and vice versa.
- invertSelection() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Sets the the given part of the component to be selected if it was not set and vice versa.
- INVISIBLE_SETS -
Static variable in class chemaxon.marvin.common.ParameterConstants
-
- invokeAndWait(Runnable) -
Method in interface chemaxon.marvin.view.TaskScheduler
- Enqueues a task on the scheduler's thread and waits for its completion.
- invokeLater(Runnable, int) -
Method in interface chemaxon.marvin.view.TaskScheduler
- Enqueues a task on the scheduler's thread.
- IO_ERROR -
Static variable in class chemaxon.util.ErrorHandler
-
- ionChargeOf(int) -
Static method in class chemaxon.struc.MolAtom
- Gets the ion charge.
- IonChargePlugin - Class in chemaxon.marvin.calculations
- Plugin class for charge calculation on ionized microspecies.
- IonChargePlugin() -
Constructor for class chemaxon.marvin.calculations.IonChargePlugin
- Constructor.
- ionizer -
Variable in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
- irm -
Variable in class chemaxon.marvin.space.GraphicComponent
- Inverse of the Rotation matrix represented by a GeomCalc matrix.
- is3d() -
Method in class chemaxon.struc.CTransform3D
- Tests whether the transformation is 3D.
- IS_SUPPORTED_JAVA -
Static variable in class chemaxon.marvin.VersionInfo
- Deprecated. The current JVM is supported or not.
- isAbsolutePlacement() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets whether the placement of this attached data is absolute or relative
to the objects it is attached.
- isAbsStereo() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the absolute stereoconfiguration flag.
- isAcceptableGraph(MoleculeGraph) -
Static method in class chemaxon.struc.sgroup.MultipleSgroup
- Decides whether the given molecule graph can be the graph of a multiple s-group.
- isAcceptablePolymerGraph(MoleculeGraph) -
Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Checks if the given molecular graph can be the graph of a polymer SRU
- isAcceptableRSRUGraph(MoleculeGraph) -
Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Checks if the given molecular graph can be the graph of an RSRU
- isAcceptableSru(String) -
Static method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
- isAcceptor(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAcceptor() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Checks if actual pharmacophore type includes
PharmacophorePoint.ACCEPTOR_TYPE.
- isActinideMetal(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is an actinide metal
Actinium is included.
- isActive() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns true if this cell is the active cell of the entire scene.
- isActiveCell(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if the cell having
cellIndex is the active cell of the scene.
- isAddServices() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- Returns
true if services are displayed in the popup list
- isAliphaticAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.isAliphaticAtom(int)
- isAliphaticAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns
true if aliphatic atom.
- isAliphaticRC(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAlkaliMetal(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is an alkali (group I.) metal.
- isAlkalineEarthMetal(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is an alkaline earth (group II.) metal.
- isAmbiguousStereo() -
Method in class chemaxon.struc.MolAtom
- Check if the atom has ambiguous stereo wedge configuration.
- isAnimated(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Selected cell is animated or not.
- isAnimSync() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the animation synchronization.
- isAnionic() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Check if actual pharmacophore type includes
PharmacophorePoint.ANIONIC_TYPE.
- isAntialiasEnabled() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if full-screen antialias is enabled.
- isApproximateCount() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns
true if count is approximate due to multiple position bonds with
multicenters of variable size, false otherwise.
- isAromatic(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAromatic() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Checks if actual pharmacophore type includes
PharmacophorePoint.AROMATIC_TYPE.
- isAromaticAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.isAromaticAtom(int)
- isAromaticAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns
true if aromatic atom.
- isAromaticityChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects aromaticity atom query
properties or not.
- isAromaticRC(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isAromaticSMILESSubset(int) -
Static method in class chemaxon.struc.MolAtom
- Is the atom can be aromatic according to the daylight specification:
Only atoms on the following list can be considered aromatic:
C, N, O, P, S, As, Se, and * (wildcard).
- isAromatize() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- isArrow() -
Method in class chemaxon.struc.graphics.MPolyline
- Checks if it is an arrow.
- isArrow() -
Method in class chemaxon.struc.MolBond
- Deprecated. As of Marvin 5.3,
- isArrowEnd() -
Method in class chemaxon.struc.MolAtom
- Deprecated. As of Marvin 5.3
- isAssigned(int) -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- isAsymmetric() -
Method in class chemaxon.descriptors.MDParameters
- Returns whether current parametrized metric is asymmetric or not.
- isAsymmetricAtom(int) -
Method in class chemaxon.calculations.stereo.Stereochemistry
- Determines if an atom is asymmetric or not.
- isAsymmetricAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Stereochemistry.isAsymmetricAtom(int)
- isAsymmetricAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns
true if asymmetric atom.
- isAtom() -
Method in class chemaxon.struc.MoleculeGraph
- Determines whether the structure represents only one atom and an
arbitrary number of bonds.
- isAtom() -
Method in class chemaxon.struc.RgMolecule
- Determines whether the structure represents only one atom and an
arbitrary number of bonds.
- isAtom() -
Method in class chemaxon.struc.RxnMolecule
- A reaction molecule cannot represent an atom.
- isAtomFaded(int) -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isAtomFaded(int) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Tells whether the atom is faded or not.
- isAtomMappingVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Determines the visibility of the atom mapping.
- isAtomMappingVisible() -
Method in class chemaxon.marvin.MolPrinter
- Returns true if atom mapping is visible.
- isAtomNumbersVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Determines the visibility of the atom numbers.
- isAtomNumbersVisible() -
Method in class chemaxon.marvin.MolPrinter
- Returns true if atom numbers are visible.
- isAtomPropertiesVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Tells wheter the atom properties are visible or not if exist.
- isAtomPropertiesVisible() -
Method in class chemaxon.marvin.MolPrinter
- Get the atom properties visibility
- isAtomSetColorModeSet() -
Method in class chemaxon.struc.MDocument
- Decides whether the atomset coloring mode is set.
- isAtomSymbolsVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Tests the visibility of the atom symbols in 3D.
- isAtomSymbolsVisible() -
Method in class chemaxon.marvin.MolPrinter
- Returns the atom symbol visibility of 3D mode.
- isAtomVisible(int) -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isAtomVisible(int) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns if the atom is visible or hidden.
- isAutoCheckStructure() -
Method in class chemaxon.marvin.common.UserSettings
- Tells whether the automatic structure checking is enabled or not
- isAutoHeight() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets if it is autoHeight.
- isAutomaticFogEnabled() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the state of automatic fog calculation mode.
- isAutoPopup() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- Returns the auto popup behaviour
- isAutoSize() -
Method in class chemaxon.struc.graphics.MTextBox
-
- isAvailable() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- isAvailable() -
Method in interface chemaxon.checkers.StructureChecker
- Returns true if the checker is available, and can be used
- isBarredAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Determines if an atom is is part of a certain functional group with high
rotational barrier (amides, thioamides, sulphonamides).
- isBold() -
Method in class chemaxon.struc.graphics.MFont
- Tests whether the font is bold.
- isBold() -
Method in class chemaxon.struc.MolBond
- Decides whether this bond is bold or not.
- isBond() -
Method in class chemaxon.struc.MoleculeGraph
- Determines whether the structure represents only one bond and zero or
two atoms.
- isBond() -
Method in class chemaxon.struc.RgMolecule
- Determines whether the structure represents only one bond and zero or
two atoms.
- isBond() -
Method in class chemaxon.struc.RxnMolecule
- A reaction molecule cannot represent a bond.
- isBondDraggedAlong() -
Method in class chemaxon.marvin.beans.MSketchPane
- Is the currently used bond shown at the mouse cursor?
- isBondDraggedAlong() -
Method in class chemaxon.marvin.common.UserSettings
- Is the currently used bond shown at the mouse cursor?
- isBondLengthVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the bond length display option.
- isBondLengthVisible() -
Method in class chemaxon.marvin.MolPrinter
- Return whether the bond length is visible or not.
- isBoundTo(MolAtom) -
Method in class chemaxon.struc.MolAtom
- Checks if this MolAtom is connected to another one or not.
- isBracketCrossingBond(MolBond) -
Method in class chemaxon.struc.Sgroup
-
- isBracketVisible() -
Method in class chemaxon.struc.Sgroup
- Tests whether the bracket is visible.
- isBracketVisible() -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Tests whether the bracket is visible.
- isBracketVisible() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Tests whether the bracket is visible.
- isBridgingRAllowed() -
Method in class chemaxon.sss.search.SearchOptions
- Returns
true if different undefined R-atoms can match the same group of atoms.
- isCached() -
Method in class chemaxon.reaction.Reactor
- Returns the "cached" property:
true if search and calculation results are to be cached and reused.
- isCacheIDRegistered(String) -
Method in class chemaxon.jchem.db.CacheRegistrationUtil
- Checks whether a cache identifier is currently registered or not.
- isCacheRegistrationNeeded() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Only for internal use!
- isCanceled() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- Returns the canceled
- isCanceled() -
Method in class chemaxon.jchem.file.ProgressWriter
- Indicates, if the progress was canceled.
- isCanceled() -
Method in class chemaxon.metabolizer.MetabolizerUtilities
- Return canceled status
- isCanceled() -
Method in interface chemaxon.util.Cancelable
-
- isCationic() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Check if actual pharmacophore type includes
PharmacophorePoint.CATIONIC_TYPE.
- isCell() -
Method in class chemaxon.marvin.space.CellOrComponentId
- Returns true if this id identifies a cell.
- isCellwiseWeights() -
Method in class chemaxon.descriptors.MDParameters
- Gets boolean telling whether cell weights are to be generated for
current parametrized metric.
- isCentralShown() -
Method in class chemaxon.clustering.JarvisPatrick
- Indicates whether central objects are displayed.
- isChainAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.isChainAtom(int)
- isChainAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns
true if chain atom.
- isChainBond(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.isChainBond(int)
- isChainBond(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines if a bond is a ring bond or a chain bond.
- isChargeCalc() -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Returns
true if pH-Charge calculation.
- isChecking() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
-
- isChecking() -
Method in interface chemaxon.checkers.runner.CheckerRunner
- This function identifies the state of the checker thread
- isChecking() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
- Deprecated.
- isChemTermColumnDefined() -
Method in class chemaxon.jchem.db.DatabaseProperties
- Retrieve whether at least one Chemical Term column is defined for any table or not.
- isChildOf(MObject) -
Method in class chemaxon.struc.graphics.MMidPoint
- Is this object a children of another one?
- isChildOf(MObject) -
Method in class chemaxon.struc.graphics.MRectanglePoint
- Is this object a children of another one?
- isChildOf(MObject) -
Method in class chemaxon.struc.MObject
- Is this object a children of another one?
- isChildOf(MObject) -
Method in class chemaxon.struc.MPoint
- Is this object a children of another one?
- isChiral() -
Method in class chemaxon.calculations.stereo.Stereochemistry
- Determines if the molecule contains an atom with R or S stereo
configuration.
- isChiral() -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Stereochemistry.isChiral()
- isChiralCenter(int) -
Method in class chemaxon.calculations.stereo.Stereochemistry
- Determines if an atom can be a tetrahedral stereogenic center.
- isChiralCenter(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Stereochemistry.isChiralCenter(int)
- isChiralCenter(int) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Determines if an atom can be a tetrahedral stereogenic center.
- isChiralCenter(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines if an atom can be a tetrahedral stereogenic center.
- isCleanable() -
Method in class chemaxon.formats.MolExporter
- Tests whether cleaning is meaningful for the chosen output format.
- isCleanable() -
Method in class chemaxon.marvin.io.MolExportModule
- Tests whether 2D or 3D cleaning is meaningful for this output format.
- isCleanHOptionEnabled() -
Method in class chemaxon.marvin.common.UserSettings
- Returns true if the H option for cleaning is enabled.
- isCleanNeeded() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns
true if clean is needed for GUI display.
- isClearClipboardBeforeExport() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Returns whether the subsystem clears the clipboard before a copy
operation.
- isCleaveAliphaticRingBonds() -
Method in class chemaxon.fragmenter.MoleculeFragmenter
- Returns true if fragmenter cut CCQ bonds in aliphatic rings, false otherwise
- isCleaveAromaticBonds() -
Method in class chemaxon.fragmenter.MoleculeFragmenter
-
- isClipped() -
Method in class chemaxon.marvin.space.SurfaceComponent
- Returns true if there are clipping planes enabled that will clip part
of the surface during drawing.
- isCloseEnabled() -
Method in class chemaxon.marvin.beans.MSketchPane
- Determines if the File->Close menu item is enabled or not.
- isCollinear(MolAtom) -
Method in class chemaxon.struc.MolBond
- Returns whether atom is collinear with the bond or not.
- isColorMapperEnabled() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- isComment(String) -
Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
- isCompatible(MTextAttributes, MTextAttributes, MFont) -
Method in class chemaxon.struc.graphics.MTextAttributes
- Tests whether two attribute sets are compatible.
- isComponent() -
Method in class chemaxon.marvin.space.CellOrComponentId
- Returns true if this id identifies a component.
- isComponentPart() -
Method in class chemaxon.marvin.space.ComponentElement
- Returns true if the if the component is a structured component.
- isComponentWise() -
Method in class chemaxon.descriptors.MDSimilarity
- Checks the component-wise flag.
- isConfirmExit() -
Method in class chemaxon.marvin.beans.MSketchPane
- Gets whether the confirmation dialog will be appear or not by exit.
- isConjugated() -
Method in class chemaxon.struc.MolBond
- Gets the conjugation state of the bond set by the conjugation modul.
- isConnected() -
Method in class chemaxon.calculations.TopologyAnalyser
- Determines if the molecule is a connected graph or not.
- isConnected(int, int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Determines if two atoms are members of a connected graph or not.
- isConnected(int, int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns
true if two atoms are in the same connected component,
false for atoms of disconnected structures.
- isConnected() -
Method in class chemaxon.util.ConnectionHandler
- Getter for property
connected.
- isConnectedGraph() -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines if the molecule is a connected graph or not.
- isConnectionAlive(Connection) -
Static method in class chemaxon.util.DatabaseTools
- Checks if JDBC connection to a database is alive or not.
- isConnectionCountChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects connection count atom
query properties or not.
- isContracted() -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Is this S-group contracted?
- isContracted() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Decides whether this S-group is contracted or not.
- isControllable(String) -
Method in class chemaxon.marvin.space.GraphicComponent
- A component must return true if it allows itself to be controlled
by the given type controller.
- isControllable(String) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) -
Method in class chemaxon.marvin.space.PharmacophoreArrow
- Returns whether controling by the given type of controller is allowed to the component.
- isControllable(String) -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Returns whether controling by the given type of controller is allowed to the component.
- isCoordDependent() -
Method in class chemaxon.struc.MProp
- Tests whether the property depends on the molecular coordinates.
- isCoordinate() -
Method in class chemaxon.struc.MolBond
- Tests whether the bond is coordinate.
- isCoordinative() -
Method in class chemaxon.struc.MolBond
- Deprecated. As of Marvin 5.0, replaced by
MolBond.isCoordinate()
- isCopolymerMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Specifies whether matching mode is copolymer.
- isCopyAsTransferable() -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- Determines whether the
MTransferable is appearing as an option in
the Copy As dialog.
- isCorrect(StructureCheckerResult) -
Method in class chemaxon.checkers.ReactionChecker
- This method determines if a component of the reaction correct or not.
- isCorrect(StructureCheckerResult) -
Method in class chemaxon.checkers.ReactionMapErrorChecker
-
- isCreateRingCenters() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- isCrossingBond(MolBond) -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Decides whether the bond is a crossing bond in a ladder-type polymer bracket.
- isCubeLine(String, int) -
Static method in class chemaxon.formats.MFileFormatUtil
- Deprecated. as of Marvin 5.0,
CubeRecognizer.isCubeLine(String, int)
must be used instead
- isCubeLine(String, int) -
Static method in class chemaxon.formats.recognizer.CubeRecognizer
- Checks if it is a cube line:
an integer followed by floats.
- isCurrentFontDefault() -
Method in class chemaxon.struc.graphics.MTextBox
- Tests whether the default font is used.
- isCurrentFontRegular() -
Method in class chemaxon.struc.graphics.MTextBox
- Tests whether the current font is regular.
- isCurrentLevelEnded() -
Method in class chemaxon.metabolizer.Metabolizer
- Returns true if the current level has more element to process
- isCutBond(int, int) -
Method in class chemaxon.fragmenter.Fragmenter
- Return
true if bond i - j is stored as cut-bond.
- isCxSMILESLine(String) -
Static method in class chemaxon.formats.recognizer.SMILESRecognizer
- Checks if a line is a ChemAxon Extended
SMILES/SMARTS format.
- isDatabaseReadonly() -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns whether database of the current JChem property table is readonly.
- isDataDetached() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets whether the data should be displayed close to the objects or
separately (detached).
- isDataFlavorSupported(DataFlavor) -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
-
- isDataFlavorSupported(DataFlavor) -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Checks whether the
MarvinTransferable.flavor equals with the given parameter.
- isDaylightFormat(String) -
Static method in class chemaxon.util.MolHandler
- Decides whether the given molecule format belongs to the Daylight family
of languages.
- isDefault() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns if config element is at default state
- isDefault() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Tests whether all attributes have default values.
- isDefaults() -
Method in class chemaxon.jchem.db.Exporter
- Gets if only default fields are to be exported.
- isDefaultSelected() -
Method in class chemaxon.marvin.util.OptionDescriptor
- Tests whether the option is selected by default.
- isDefaultTransferable() -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- Determines whether the
MTransferable instance should be used by
the default copy operation.
- isDehidrogenize() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- isDescendantOf(Sgroup) -
Method in class chemaxon.struc.Sgroup
- Decides wheter this is a descendant of another sgroup.
- isDetachable() -
Method in class chemaxon.marvin.beans.MViewPane
- Gets the detachable property.
- isDetectCumulatedDoubleBonds() -
Method in class chemaxon.checkers.RingStrainErrorChecker
- Returns the detectCummulatedDoubleBonds
- isDetectTooLongBonds() -
Method in class chemaxon.checkers.BondLengthChecker
-
- isDetectTooShortBonds() -
Method in class chemaxon.checkers.BondLengthChecker
-
- isDetectTransDoubleBonds() -
Method in class chemaxon.checkers.RingStrainErrorChecker
- Returns the detectTransDoubleBonds
- isDetectTripleBonds() -
Method in class chemaxon.checkers.RingStrainErrorChecker
- Returns the detectTripleBonds
- isDifferentIdsOnly() -
Method in class chemaxon.clustering.Compare
- Indicates whether compounds with different id-s compared only.
- isDirty() -
Method in class chemaxon.sss.search.SearchOptions
- Returns the dirty flag.
- isDisplayLabelsAndBoxes() -
Method in class chemaxon.util.HitColoringAndAlignmentOptions
- Gets whether bounding boxes and labels are to be displayed for
the components of the search.
- isDissimilarityThresholdExcluded() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get the dissimilarity threshold exclusion option.
- isDistancerangeSet() -
Method in enum chemaxon.marvin.alignment.AlignmentProperties
-
- isDistinctFirstAtomMatching() -
Method in class chemaxon.sss.search.MolSearchOptions
- Get option ensuring that upon the findNext() call the first atom must be
stepped as well.
- isDndTransferable() -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
- isDocumentExport() -
Method in class chemaxon.marvin.io.MolExportModule
- Tests if this export module is document export instead of a simple
molecule export.
- isDocumentImporter() -
Method in class chemaxon.marvin.io.MolImportModule
- Tests whether this module is a document importer or not.
- isDonor(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isDonor() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Checks if actual pharmacophore type includes
PharmacophorePoint.DONOR_TYPE.
- isDoodle() -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- Returns the isDoodle
- isDraggable() -
Method in class chemaxon.marvin.beans.MViewPane
- Determines whether mouse dragged evens are allowed or not.
- isDuplicateFilteringOption(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns the state of the Duplicate Filtering table option.
- isDuplicateImportAllowed() -
Method in class chemaxon.jchem.db.Importer
- Gets whether duplicate structures are allowed.
- isEditable() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns if config element is editable
- isEditable(int, Molecule, String) -
Method in class chemaxon.marvin.io.MFieldAccessor
- Tests whether a field is editable or not.
- isEditable() -
Method in class chemaxon.struc.graphics.MTextBox
- Determines if this text box's content can be edited by the user.
- isEmpty() -
Method in class chemaxon.jep.context.ReactionContext
- Returns
true if the context is empty.
- isEmpty() -
Method in class chemaxon.struc.graphics.MChemicalStruct
- A chemical structure object is empty if the molecule graph is empty.
- isEmpty() -
Method in class chemaxon.struc.graphics.MPolyline
- A polyline becomes empty if it has less than 2 points.
- isEmpty() -
Method in class chemaxon.struc.graphics.MTextBox
- A text box is empty if the string contains only whitespace.
- isEmpty() -
Method in class chemaxon.struc.MDocument
- Tests whether the document is empty:
the main molecule object in the document is empty
no graphic object is included (neither simple nor extra)
- isEmpty() -
Method in class chemaxon.struc.MObject
- An object may become empty if all the children are removed.
- isEmpty() -
Method in class chemaxon.struc.Molecule
- Tests whether the molecule is empty.
- isEmpty() -
Method in class chemaxon.struc.MoleculeGraph
- Tests whether the molecule graph is empty.
- isEmpty() -
Method in class chemaxon.struc.RgMolecule
- Ask if the molecule is empty or not.
- isEmpty() -
Method in class chemaxon.struc.RxnMolecule
- Ask if the reaction is empty or not.
- isEmpty() -
Method in class chemaxon.struc.Sgroup
- Is it an empty S-group?
- isEmpty() -
Method in class chemaxon.util.IntArray
- Tests if this IntArray has no components.
- isEnabledT(int, int) -
Method in class chemaxon.marvin.view.MDocStorage
- Tests whether a text field is enabled.
- isEnableTranslateAndRotate() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- isEndgroupMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get whether polymers end groups must match.
- isEndReached() -
Method in class chemaxon.formats.MolImporter
- Tests whether the end of input is already reached.
- isEndReached() -
Method in class chemaxon.marvin.io.ArrayMDocSource
- Tests whether the end of input is already reached.
- isEndReached() -
Method in class chemaxon.marvin.io.MDocSource
- Tests whether the end of input is already reached.
- isEndReached() -
Method in exception chemaxon.marvin.view.MDocStorage.RecordUnavailableException
- Tests whether the end of storage is reached.
- isExactBondMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Indicates whether bond types should match exactly - looking
for query bonds target.
- isExactFragment() -
Method in class chemaxon.sss.search.SearchOptions
- Deprecated. since 5.6, replaced by
SearchOptions.isFullFragment()
- isExactQueryAtomMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Returns whether exact matching of query atom information is set.
- isExcluded() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Check if actual pharmacophore type is
PharmacophorePoint.EXCLUDED_TYPE.
- isExcludedAtom(MolAtom) -
Method in class chemaxon.util.iterator.IteratorFactory
- By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to
exclude more atoms, than it would normally.
- isExcludedBond(MolBond) -
Method in class chemaxon.util.iterator.IteratorFactory
- By overriding this method, the inclusion pattern of IteratorFactory can be rewritten to
exclude more bonds, than it would normally.
- isExitCanceled() -
Method in class chemaxon.marvin.beans.MarvinPane
- Check whether exiting is allowed or not.
- isExpandable(int) -
Method in class chemaxon.struc.Molecule
- Tests if the molecule is expandable with the specified options.
- isExpanded() -
Method in interface chemaxon.struc.sgroup.Expandable
- Is this S-group expanded?
- isExpanded() -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Is this S-group expanded?
- isExpanded() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Is this S-group expanded?
- isExperimentalEnabled() -
Method in class chemaxon.marvin.beans.MarvinPane
- Tests whether experimental features are enabled.
- isExpertMode() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- Returns the expert mode
- isExplicitConnectionCountChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects explicit connection
count atom query properties or not.
- isExplicitHVisible() -
Method in class chemaxon.marvin.MolPrinter
- Deprecated. As of Marvin 5.5.1 this method always returns true.
This method will be removed in a future release.
- isExplicitizedOutput() -
Method in class chemaxon.fragmenter.MoleculeFragmenter
-
- isExtraObject(MObject) -
Method in class chemaxon.struc.MDocument
- Decides whether a graphic object belongs to the main chemical structure
of the document.
- isEZLabelsVisible() -
Method in class chemaxon.marvin.MolPrinter
- Returns the visibility state of absolute double bond stereo configuration labels.
- isEzVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the E/Z display option.
- isEZVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Are E/Z labels visible?
- isEzVisible() -
Method in class chemaxon.marvin.MolPrinter
- Deprecated. As of Marvin 5.2.2, replaced by
MolPrinter.isEZLabelsVisible()
- isFileSupportEnabled() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns
true if file loading support is enabled
- isFiltered() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Return
true if molecule filter is set.
- isFinished() -
Method in class chemaxon.jchem.db.Importer
- Returns
true if importing has finished, else returns false.
- isFinished() -
Method in class chemaxon.util.UploadThread
- Returns
true if uploading has finished, else returns false.
- isFirstResized() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns the firstResized
- isFixed(int) -
Method in class chemaxon.marvin.view.MDocStorage
- Tests whether a record is fixed.
- isFlagSet(long) -
Method in class chemaxon.formats.MFileFormat
- Checks whether the format has a given (set of) flag(s) set.
- isFlipped() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Decides whether this sgroup is flipped.
- isFontDefault(MFont) -
Method in class chemaxon.struc.graphics.MTextAttributes
- Tests whether the default font is used.
- isFontDefaultInRange(int, int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Tests whether the default font is used in the specified range.
- isFontRegular() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Tests whether the default font is used.
- isFontRegularInRange(int, int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Tests whether the default font is used in the specified range.
- isFractionQuicklyAvailable(double) -
Method in class chemaxon.marvin.view.MDocStorage
- Tests whether the specified fraction of the total (estimated) number
of records is quickly available.
- isFreeLegalAttachAtom(MolAtom) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Tests whether the specified atom is a legal attachment point with a
free valence.
- isFull() -
Method in class chemaxon.marvin.space.monitor.Monitor
- Returns true if the monitor is full and can measure.
- isFullFragment() -
Method in class chemaxon.sss.search.SearchOptions
- Get option whether heavy atoms can occur in target besides the returned
hit fragments.
- isFuzzyFingerprint() -
Method in class chemaxon.descriptors.PFParameters
- Gets whether the fuzzy fingerprints are used or not.
- isGaussianSmoothing() -
Method in class chemaxon.descriptors.PFParameters
- Gets if fuzzy smmoothing is based on normal distribution.
- isGaussLike() -
Method in enum chemaxon.marvin.alignment.AlignmentProperties.NodeType
-
- isGenerateDistanceRanges() -
Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
-
- isGeneratingSubstrates() -
Method in class chemaxon.metabolizer.Metabolizer
- Return generatingSubstrates
- isGeneric() -
Method in class chemaxon.struc.MolAtom
- Tests whether the atom is a generic atom.
- isGenericTautomerProtectsChirality(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns whether generic tautomer protects chirality in tautomer region.
- isGenNameShown() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Are IUPAC names shown in the table?
- isGLInitialized() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if the OpenGL canvas is already initialized.
- isGrabbingEnabled() -
Method in class chemaxon.formats.MolImporter
- Tests whether molecule file content grabbing is enabled.
- isGraphicComponent() -
Method in class chemaxon.marvin.space.GraphicComponent
-
- isGraphicComponent() -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- isGraphInvariantVisible() -
Method in class chemaxon.marvin.MolPrinter
- Return whether the graph invariant is visible or not.
- isGrinv() -
Method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 3.5, use isGrinvVisible() instead
- isGrinvCCValid() -
Method in class chemaxon.struc.MoleculeGraph
- Tests whether the graph invariant change count is valid.
- isGrinvCCValid() -
Method in class chemaxon.struc.SelectionMolecule
- Tests whether the graph invariant change count is valid.
- isGrinvVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Gets the visibility of the graph invariants.
- isGUIContracted() -
Method in class chemaxon.struc.Molecule
- Tests if the molecule has a GUI-contracted S-group or not.
- isH(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isHalogen(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is a halogen.
- isHaltOnError() -
Method in class chemaxon.jchem.db.Importer
- Gets if import should stop when an error occures.
- isHashed() -
Method in class chemaxon.struc.MolBond
- Decides whether this bond is hashed or not.
- isHierarchic() -
Method in class chemaxon.struc.MPropertyContainer
- Tests whether the property list contains subcollections like
MListProp and MHashProp.
- isHighlighted() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isHighlighted() -
Method in class chemaxon.marvin.space.MoleculeComponent
- This functionality is currently unavailable.
- isHighlighted() -
Method in class chemaxon.marvin.space.PharmacophoreArrow
- Returns true if the component is highlighted.
- isHighlighted() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Returns true if the component is highlighted.
- isHighlighted(MObject) -
Method in class chemaxon.struc.MDocument
- Is the specified object currently highlighted?
- isHinderedBiarylBridgeBond(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Determines if a bond bridges two aryl systems having more than two ortho
substituents.
- isHitIncludesRNodes() -
Method in class chemaxon.sss.search.MolSearchOptions
- Specifies the result format for R-group queries.
- isHomologyEnumerated() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Indicates if homology groups are enumerated or not.
- isHydrogenCountChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects hydrogen count atom
query properties or not.
- isHydrophobic(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isHydrophobic() -
Method in class chemaxon.marvin.space.PharmacophorePoint
- Checks if actual pharmacophore type includes
PharmacophorePoint.HYDROPHOBIC_TYPE.
- isIgnoreAlleneStereo() -
Method in class chemaxon.sss.search.SearchOptions
- Retrieves if allene stereo is ignored during searching.
- isIgnoreAxialStereo() -
Method in class chemaxon.sss.search.SearchOptions
- Retrieves if axial stereo is ignored during searching.
- isIgnoreCTExceptions() -
Method in class chemaxon.sss.search.SearchOptions
- Get whether only syntactical exceptions are thrown for chemical terms.
- isIgnoreDoubleBondStereo() -
Method in class chemaxon.sss.search.SearchOptions
- Retrieves if double bond stereo is ignored during searching.
- isIgnoreMissingLicense() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns
false when panel is set to mark elements without valid license
- isIgnoreSynAntiStereo() -
Method in class chemaxon.sss.search.SearchOptions
- Retrieves if syn-anti stereo is ignored during searching.
- isIgnoreTetrahedralStereo() -
Method in class chemaxon.sss.search.SearchOptions
- Retrieves if tetrahedral stereo is ignored during searching.
- isImplicitHcountImportant(MolAtom) -
Static method in class chemaxon.marvin.io.MolExportModule
- Checks whether the number of implicit hydrogens is important
information for an atom or not.
- isImplicitHcountImportant(MoleculeGraph) -
Method in class chemaxon.marvin.io.MolExportModule
- Checks whether the number of implicit hydrogens is important information
for the atoms of mol or not.
- isImplicitHydrogenCountChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects implicit hydrogen
count atom query properties or not.
- isImplicitizableH(int) -
Method in class chemaxon.struc.MolAtom
- Tests whether the hydrogen atom is implicitizable or not.
- isIn3D() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Returns
true if structures are returned in 3D.
- isIncompleteReaction() -
Method in class chemaxon.struc.RgMolecule
- Check whether the reaction is incomplete or not.
- isIncompleteReaction() -
Method in class chemaxon.struc.RxnMolecule
- Check whether the reaction is incomplete or not.
- isInfoToStdError() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property infoToStdError.
- isInputAvailable() -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Checks that the implementation supports input from clipboard.
- isInputAvailable() -
Method in interface chemaxon.marvin.modules.datatransfer.MTransferable
- Checks that the implementation supports input from clipboard.
- isInputMoleculeAromatized() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if the input molecule has aromatic bond.
- isInsertable(Molecule, int, boolean) -
Static method in class chemaxon.jchem.db.UpdateHandler
- Decides whether a molecule can be inserted into a table of a given type.
- isInternalSelectable() -
Method in class chemaxon.struc.MObject
- Is it a selection only internal object?
- isInternalSelectable() -
Method in class chemaxon.struc.MPoint
- Is it a selection only internal object?
- isIntType(int) -
Static method in class chemaxon.util.DatabaseTools
- Determines if an SQL type is an integer
- isItalic() -
Method in class chemaxon.struc.graphics.MFont
- Tests whether the font is italic.
- isJtfWithStructure() -
Method in class chemaxon.jchem.db.Exporter
- Gets, wheter exported JTF will contain structure
information.
- isKeepQueryOrder() -
Method in class chemaxon.sss.search.SearchOptions
- Get options for rearranging query atoms for better search performance.
- isLanthanideMetal(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is a lanthanide metal
Lanthanum is included.
- isLargeMolecule() -
Method in class chemaxon.struc.MoleculeGraph
- Returns
true if large molecule
(number of atoms exceeds 1000).
- isLastLine() -
Method in class chemaxon.formats.recognizer.Recognizer
- Tests whether it is the last line of file.
- isLastTaskClean() -
Method in class chemaxon.reaction.Standardizer
- Returns
true if last task is clean or there are no tasks
(final clean not needed before output to file).
- isLegalAttachment(MolAtom) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Tests whether the specified atom is attached to a legal attachment point.
- isLicensed() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns
true if the action represented
by this element with current license settings can be used
- isLicensed() -
Method in class chemaxon.calculations.TopologyAnalyser
-
- isLicensed() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- isLicensed() -
Method in class chemaxon.clustering.LibraryMCS
-
- isLicensed() -
Method in class chemaxon.descriptors.BCUT
- Returns information about the licensing of the product.
- isLicensed() -
Method in class chemaxon.descriptors.ECFP
- Returns information about the licensing of the product.
- isLicensed() -
Method in class chemaxon.descriptors.ECFPGenerator
- Returns information about the licensing of the product.
- isLicensed() -
Method in class chemaxon.descriptors.MDSimilarity
-
- isLicensed() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Returns information about the licensing of the product.
- isLicensed() -
Method in class chemaxon.descriptors.ShapeDescriptor
-
- isLicensed() -
Method in class chemaxon.fragmenter.Fragmenter
-
- isLicensed() -
Method in class chemaxon.fragmenter.MoleculeFragmenter
-
- isLicensed() -
Method in class chemaxon.jchem.db.JChemSearch
-
- isLicensed(String) -
Static method in class chemaxon.license.LicenseManager
- Returns true if the license manager recognizes the given product to be licensed.
- isLicensed() -
Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- isLicensed() -
Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
- isLicensed() -
Method in class chemaxon.marvin.calculations.ChargePlugin
- Returns
true if the plugin is licensed.
- isLicensed() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns
true if the plugin is licensed.
- isLicensed() -
Method in class chemaxon.marvin.calculations.HuckelAnalysisPlugin
- Returns
true if the plugin is licensed.
- isLicensed() -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
- isLicensed() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
- isLicensed() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Returns
true if the plugin is licensed.
- isLicensed() -
Method in class chemaxon.marvin.calculations.OrbitalElectronegativityPlugin
- Returns
true if the plugin is licensed.
- isLicensed() -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Returns
true if the plugin is licensed.
- isLicensed() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if the plugin is licensed.
- isLicensed() -
Method in class chemaxon.metabolizer.Metabolizer
-
- isLicensed() -
Method in class chemaxon.pharmacophore.PMapper
-
- isLicensed() -
Method in class chemaxon.reaction.Reactor
-
- isLicensed() -
Method in class chemaxon.reaction.Standardizer
-
- isLicensed() -
Method in class chemaxon.sss.search.MCES
- Returns information about the licensing of the product.
- isLicensed() -
Method in class chemaxon.sss.search.MCS
- Deprecated. Returns information about the licensing of the product.
- isLicensed() -
Method in class chemaxon.sss.search.MolSearch
- Gets whether searching is included in the user licence.
- isLicensed() -
Method in class chemaxon.sss.search.RGroupDecomposition
-
- isLicensed() -
Method in class chemaxon.util.HitDisplayTool
-
- isLigand() -
Method in class chemaxon.marvin.space.MoleculeComponent
-
- isLigandErrorVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Tells wheter the bond's ligand error is visible or not.
- isLigandErrorVisible() -
Method in class chemaxon.marvin.MolPrinter
- Gets the bond's ligand error visibility
- isLinkNode() -
Method in class chemaxon.struc.MolAtom
- The atom is a link node if the maximum number of repetitions is nonzero.
- isLoadedMolModified() -
Method in class chemaxon.marvin.beans.MSketchPane
- Determines whether the original molecule that is loaded in is modified
or not.
- isLoggingEnabled() -
Method in class chemaxon.jchem.db.UpdateHandler
- Shows whether logging is enabled during import.
- isLonePairAutoCalc() -
Method in class chemaxon.marvin.common.UserSettings
- Returns the state of the automatic lone pair calculation.
- isLonePairsAutoCalculated() -
Method in class chemaxon.marvin.MolPrinter
- Returns the state of the automatic calculation of lone pairs.
- isLonePairsVisible() -
Method in class chemaxon.marvin.MolPrinter
- Returns the visibility state of lone pairs.
- isLP(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isMacromoleculePart() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Tells whether this
MoleculeComponent is a visualizer of a ligand in a complex
or an independent small molecule.
- isMappable() -
Method in class chemaxon.struc.MolAtom
- Checks if this atom it a mappable.
- isMarkush -
Variable in class chemaxon.jchem.db.UpdateHandler.RowData
-
- isMarkushEnabled() -
Method in class chemaxon.sss.search.MolSearchOptions
- Specifies whether a target containing Markush features
should be treated as a Markush library.
- isMarkushQuery() -
Method in class chemaxon.sss.search.RGroupDecomposition
- Returns
true if query contains Markush features
which will be enumerated (all features except defined R-rgroups
and homologies).
- isMarkushScreeningEnabled() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Gets whether screening methods are used for Markush search before ABAS step.
- isMarvinCompMode() -
Method in class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
- Marvin compatibility mode.
- isMatchCountBetween(int, boolean, int, boolean) -
Method in class chemaxon.sss.search.Search
- Decides questions like "does the query match the target
between 2 and 5 times (inclusively)"
Makes this efficiently, which means it only searches
for the number of hits necessary to decide the question.
- isMatchCountHighLimitInclusive() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- isMatchCountIncludesZero() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- isMatchCountInRelation(String, int) -
Method in class chemaxon.sss.search.Search
- Decides questions like "does the query match the target
at least 3 times", "[] up to 5 times", "[] exactly
once".
- isMatchCountLowLimitInclusive() -
Method in class chemaxon.sss.search.MatchCountOptions
-
- isMatching() -
Method in class chemaxon.sss.formula.FormulaSearch
- Checks if the query formula matches the target formula
according to the formula search type.
- isMatching() -
Method in class chemaxon.sss.search.MolSearch
- Checks if the query structure matches a substructure in the molecule.
- isMatching() -
Method in class chemaxon.sss.search.Search
- Checks if the query
structure matches a substructure in the molecule.
- isMaxResultCountReached() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property maxResultCountReached.
- isMaxTimeReached() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property maxTimeReached.
- isMDTableValid(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Tests, if a given MD table is valid or not.
- isMDTableValidByAllIDs(String) -
Method in class chemaxon.jchem.db.MDTableHandler
- Tests, whether a given MD table is valid.
- isMergedComponent(MoleculeGraph) -
Method in class chemaxon.struc.RxnMolecule
- Check whether given molecule is reaction component with a set of intentionally merged fragments or not.
- isMetal(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Decides whether the element is a metal.
- isMetalloid(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is a metalloid.
- isMinimumHeightSet() -
Method in class chemaxon.struc.graphics.MTextBox
- Gets if it is minimumHeightSet.
- isMixSgroupMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get option whether search should consider consider COM, MIX and FOR
sgroups during search.
- isMolecular() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns
true if molecule output.
- isMolecularDescriptorDefined() -
Method in class chemaxon.jchem.db.DatabaseProperties
- Retrieve whether at least one MolecularDescriptor is defined for any table or not.
- isMolecule() -
Method in class chemaxon.struc.Molecule
- Checks if the object is an instance of Molecule or not.
- isMolecule() -
Method in class chemaxon.struc.MoleculeGraph
- Checks if the object is an instance of Molecule or not.
- isMolMovie() -
Method in class chemaxon.formats.MolImporter
- Are the imported molecules merged into one multi-set molecule?
- isMolNameShown() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Are molecule names shown in the table?
- isMsCalc() -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns
true if microspecies calculation.
- isMsCalc() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns
true if microspecies calculation.
- isMsCalc() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if microspecies calculation.
- isMSpaceDisplayLabelOnlyOnHeavyAtoms() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns if mspace should display label only on heavy atoms.
- isMultiChiral() -
Method in class chemaxon.struc.MoleculeGraph
- Returns the multiple chirality flag.
- isMultipleDisplay() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Returns
true if results for more molecules can be displayed
in a single component, false if each molecule should be displayed
in a separate component.
- isMultiSet() -
Method in class chemaxon.formats.MolImporter
- Are the imported molecules merged into one multi-set molecule?
- isMultiThreadedRunEnabled() -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- For internal use only.
- isMultiThreadedRunEnabled() -
Method in class chemaxon.marvin.calculations.MSAPlugin
- For internal use only.
- isMultiThreadedRunEnabled() -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- For internal use only.
- isMultiThreadedRunEnabled() -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- For internal use only.
- isMultiThreadedRunEnabled() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- For internal use only.
- isNegative(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isNegligible(double[]) -
Method in class chemaxon.marvin.calculations.pKaPlugin
-
- isNegligibleResult(Object, int, Object) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Returns whether the result can be ignored.
- isNegligibleResult(Object, int, Object) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns whether the result can be ignored.
- isNegligibleResult(Object, int, Object) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns whether the result can be ignored.
- isNobleGas() -
Method in class chemaxon.struc.MolAtom
- Deprecated. As of Marvin 5.4, replaced by
PeriodicSystem.isNobleGas(int z).
- isNobleGas(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is a noble gas.
- isNonPreferredStereoAtom(MoleculeGraph) -
Static method in class chemaxon.marvin.util.CleanUtil
- Check if the atoms in the molecule is in SP2 hybridization state and
has wedge whose getAtom1 is the specified atom, but wiggly
bonds next to double bonds are allowed.
- isNormalized() -
Method in class chemaxon.descriptors.MDParameters
- Returns whether current parametrized metric is normalized or not.
- IsoelectricPointPlugin - Class in chemaxon.marvin.calculations
- Plugin class for isoelectric point and pH - charge distribution calculation.
- IsoelectricPointPlugin() -
Constructor for class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Constructor.
- isOK() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if no calculation error,
false on error.
- isOK() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns
true if the calculation has run without error.
- isOkActionEnabled() -
Method in class chemaxon.marvin.plugin.gui.ParameterPanel
-
- isOkActionEnabled() -
Method in interface chemaxon.marvin.plugin.ParameterPanelHandler
- Returns
true if "OK" button is enabled.
- isolate(MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Isolates atom: a more efficient way of removing an atom
than
MoleculeGraph.removeAtom(chemaxon.struc.MolAtom), especially for large molecule graphs.
- isolate(MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Isolates bond: a more efficient way of removing a bond
than
MoleculeGraph.removeBond(chemaxon.struc.MolBond), especially for large molecule graphs.
- ISOMERS_PLUGIN_GROUP -
Static variable in class chemaxon.license.LicenseManager
- Identifier of plugin: Isomers Plugin Group
- isOnlyDissimilarListed() -
Method in class chemaxon.clustering.Compare
- Indicates whether only dissimilar objects are printed.
- isOnlyFirstAtomInStereoCalculation() -
Method in class chemaxon.struc.MoleculeGraph
- Get how parity module interpret wedes.
- isOnlyStat() -
Method in class chemaxon.clustering.Common
- Indicates if only statistics are produced.
- isOperationRequired -
Variable in class chemaxon.jchem.db.Updater.UpdateInfo
- Indicates whether the operation is required or not.
- isOptimizeQueries() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Get whether query should be optimized.
- isOptionsPaneLoaded(int) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Returns
true is options pane is loaded for plugin,
false otherwise.
- isOrderedComponentSgroup() -
Method in class chemaxon.struc.Sgroup
- Returns if the Sgroup is ordered component Sgroup.
- isOrderSensitiveSearch() -
Method in class chemaxon.sss.search.SearchOptions
- Indicates whether the search is order sensitive
- isOrderSimilarObjects() -
Method in class chemaxon.clustering.Compare
- Indicates, whether the list similar objects should be ordered by distance
(closest first).
- isOrigTargetMayBeMarkush -
Variable in class chemaxon.sss.search.MolSearch
- FS#9166
Should be set to 'false' to indicate that any bonds (Markush components)
occurred only after generating generic tautomer of target.
- isOtherMetal(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is an "other metal", group IIIa-Va metal.
- ISOTOPE_H -
Static variable in class chemaxon.struc.MolAtom
- Include Hydrogen isotope(s).
- ISOTOPE_MATCHING_DEFAULT -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant for default isotope searching (isotope query
matches only isotope target, nonisotope query matches all).
- ISOTOPE_MATCHING_EXACT -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant for exact isotope searching (isotope query
matches only isotope target, nonisotope query only matches nonisotope).
- ISOTOPE_MATCHING_IGNORE -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant for ignore isotope searching (isotope information
is ignored during searching).
- IsotopeChecker - Class in chemaxon.checkers
- IsotopeChecker detects isotopes (non-elemental atoms).
- IsotopeChecker() -
Constructor for class chemaxon.checkers.IsotopeChecker
- Default constructor
- isotopeComposition(int) -
Method in class chemaxon.calculations.ElementalAnalyser
- Gets the molecular composition (w/w%).
- isotopeComposition(int, boolean) -
Method in class chemaxon.calculations.ElementalAnalyser
- Gets the molecular composition (w/w%).
- IsotopeFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts the isotopes to non isotope atoms - IsotopeFixer() -
Constructor for class chemaxon.fixers.IsotopeFixer
-
- isotopeFormula() -
Method in class chemaxon.calculations.ElementalAnalyser
- Calculates the molecular formula (isotopes are separated).
- isotopeFormula(boolean) -
Method in class chemaxon.calculations.ElementalAnalyser
- Calculates the molecular formula (isotopes are separated).
- isotopeType(int, int) -
Static method in class chemaxon.struc.MolAtom
- Gets the type of an isotope.
- isOutputCleanable(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether the specified output format is cleanable.
- isOverflowCalculation() -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns
true if overflow calculation:
maximum number of ionizable atoms exceeded and protein ionization invoked.
- isPartSelected(MoleculeGraph) -
Method in class chemaxon.struc.Sgroup
- Decides if part of the sgroup is selected or not.
- isPassWithAllDescriptors() -
Method in class chemaxon.descriptors.MDSimilarity
- Tells whether filtering of target descriptor sets is set to pass only if
each descriptor in the set passes.
- isPassWithAllMetrics() -
Method in class chemaxon.descriptors.MDSimilarity
- Tells whether filtering of target descriptor sets is set to pass only if
dissimilarity calculated with each metric used with the descriptor
is under the required threshold.
- isPassWithOneDescriptor() -
Method in class chemaxon.descriptors.MDSimilarity
- Tells whether filtering of target descriptor sets is set to pass if
at least one descriptor in the set passes.
- isPassWithOneMetric() -
Method in class chemaxon.descriptors.MDSimilarity
- Tells whether filtering of target descriptor sets is set to pass if
dissimilarity calculated with at least one metric used with the descriptor
is under the required threshold.
- isPerfectSearchType() -
Method in class chemaxon.sss.search.SearchOptions
- Get whether search should match only if query and target are exact matches.
- isPermanent() -
Static method in class chemaxon.jchem.db.CacheRegistrationUtil
-
- isPhaseShiftedMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get option whether phase shifted polymer matches on the original.
- isPlainH(MolAtom) -
Static method in class chemaxon.util.MolHandler
- Decides if atom is a plain H atom.
- isPolymerMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get option whether to search consider polymer sgroups during search.
- isPositionVariation() -
Method in class chemaxon.struc.MolBond
- Decides whether this bond is a position variation bond.
- isPositive(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isPrintEnabled() -
Method in class chemaxon.marvin.beans.MarvinPane
- Determines if the File->Print menu item is enabled or not.
- isProgressMonitoringSupported -
Variable in class chemaxon.jchem.db.Updater.UpdateInfo
- Indicates whether update process supports progress monitoring.
- isPropertyRecord() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
- isPropertyRecord() -
Method in interface chemaxon.marvin.io.MRecordReader
-
- isPseudo() -
Method in class chemaxon.struc.MolAtom
- Tests whether if the atom is a pseudo atom.
- isQHomologyHandling() -
Method in class chemaxon.sss.search.SearchOptions
- Deprecated. since 5.6, use
SearchOptions.getHomologyNarrowTranslation()
- isQProp() -
Method in class chemaxon.struc.MolAtom
- Tests whether this object represents a query property.
- isQuery() -
Method in class chemaxon.struc.MolAtom
- Tests whether it is a query atom.
- isQuery() -
Method in class chemaxon.struc.MolBond
- Tests whether it is query bond or has query property:
any
single or double
single or aromatic
double or aromatic
smarts bond
ring or chain topology
For more information on smarts bond and query bonds, see
The JChem Query Guide
- isQuery() -
Method in class chemaxon.struc.MoleculeGraph
- Indicates if the molecule has query features: query atoms or query bonds.
- isQuery() -
Method in class chemaxon.struc.RgMolecule
- Indicates if the molecule has query features.
- isQueryAbsoluteStereo() -
Method in class chemaxon.sss.search.MolSearchOptions
- Returns whether the chiral flag is ignored or not for the query molecule.
- isQueryDisplay() -
Method in class chemaxon.util.HitColoringAndAlignmentOptions
- Gets whether the query should be displayed in
the upper left corner along with the hit.
- isQueryStandardizable -
Variable in class chemaxon.sss.search.MolSearch
-
- isRandomEnumeration() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns
true if random enumeration is requested.
- isReaction() -
Method in class chemaxon.struc.Molecule
- Checks if the structure represents a reaction or not.
- isReaction() -
Method in class chemaxon.struc.RgMolecule
- Checks if the structure represents a reaction or not.
- isReaction() -
Method in class chemaxon.struc.RxnMolecule
- Checks if the structure represents a reaction or not.
- isReactionArrow(MoleculeGraph) -
Method in class chemaxon.struc.MObject
-
- isReactionErrorVisible() -
Method in class chemaxon.marvin.beans.MSketchPane
- Deprecated. As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
Are reaction errors highlighted?
- isReactionErrorVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Deprecated. As of Version 5.3.2, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
Are reaction errors visible?
- isReactionMappingIncomplete() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Returns
true if reaction molecule was not mapped completely during reaction fingerprint generation.
- isReactionUnpairedMapMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get whether unpaired(orphan or widow) atom maps can match any atom.
- isRealAtomParent() -
Method in class chemaxon.struc.MoleculeGraph
- Can it be a real atom parent?
- isRealAtomParent() -
Method in class chemaxon.struc.RgMolecule
- R-group molecule objects cannot be real node parents.
- isRealAtomParent() -
Method in class chemaxon.struc.RxnMolecule
- Reaction molecules cannot be real node parents.
- isRealAtomParent() -
Method in class chemaxon.struc.SelectionMolecule
- Selection molecules are not real atom parents.
- isRealType(int) -
Static method in class chemaxon.util.DatabaseTools
- Determines if an SQL type is a non-integer number
- isRegeneration -
Variable in class chemaxon.jchem.db.Updater.UpdateInfo
- Deprecated. since 5.1.2 use
Updater.UpdateInfo.isProgressMonitoringSupported instead.
- isRegenerationNeeded(String, DatabaseProperties) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Check whether any regeneration type is needed for a table.
- isRegenerationNeeded(String, DatabaseProperties, int) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Check whether regeneration is needed for a table.
- isRegenerationNeeded(String, DatabaseProperties, Document, int) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Check whether regeneration is needed for a table or not.
- isRegenerationNeededExact(String, DatabaseProperties, Document, int) -
Static method in class chemaxon.jchem.db.RegenerationChecker
- Check whether a regeneration type is needed for a table or not.
- isRemovable() -
Method in class chemaxon.struc.Sgroup
- Decides whether an S-group should be ungrouped if its structure changes.
- isRemoveUnusedDefitions() -
Method in class chemaxon.util.HitColoringAndAlignmentOptions
- Gets whether unused definitions should be removed or not.
- isRepeatingUnitAtom(MolAtom) -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Checks if the specified atom object is in the paradigmatic repeating
unit or not.
- isReturnsNonHits() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Indicates if an inverse hit list is to be returned.
- isReverse() -
Method in class chemaxon.reaction.Reactor
- Returns
true if the reaction is to be processed in reversed direction.
- isRewindable() -
Method in class chemaxon.formats.MolImporter
- Tests whether rewinding (seeking backwards) is possible in the
underlying input stream.
- isRewindable() -
Method in class chemaxon.marvin.io.ArrayMDocSource
- Tests whether rewinding (seeking backwards) is possible.
- isRewindable() -
Method in class chemaxon.marvin.io.MDocSource
- Tests whether rewinding (seeking backwards) is possible.
- isRewindable() -
Method in class chemaxon.marvin.view.MDocStorage
- Tests whether the document storage is rewindable.
- isRgrouped(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if molecule with R-groups.
- isRgroupsVisible() -
Method in class chemaxon.marvin.beans.MarvinPane
- Determines the visibility of R-group defintions.
- isRing() -
Method in class chemaxon.struc.MoleculeGraph
- Tests whether the molecule graph represents a ring.
- isRingAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.isRingAtom(int)
- isRingAtom(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Returns
true if ring atom.
- isRingBond(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.isRingBond(int)
- isRingBond(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines if a bond is a ring bond or a chain bond.
- isRingBond(int) -
Method in class chemaxon.struc.MoleculeGraph
- Is this bond in ring?
- isRingBondCountChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects ring bond count atom
query properties or not.
- isRingCountChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects ring count atom query
properties or not.
- isRLogicVisible() -
Method in class chemaxon.marvin.MolPrinter
- Is R-logic visible?.
- isRotatableBond(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Determines if a bond is a rotatable or not
- isRotatableBond(int) -
Method in class chemaxon.marvin.alignment.RotatableBondDetector
- Not flexible if:
double, aromatic, triple bond
single bond neighboring a triple like at cyanide
chain end bonds
amide
thioamide: -C(=S)-NR2
sulphonamide R-S(=O)2-NR2
aniline N : C(aromatic)-N(sp3)
aromatic amidine : C(aromatic)-C(=NH)-NH2
aromatic nitroso : C(aromatic)-N=O
aromatic nitro : C(aromatic)-NO2 (although at some substituent position it may be rotatable)
C(aromatic)-N(amide) flexible
Warning there are three intentional but unexpected feature:
Ring bonds may be rotatable also.
- isRotatableBond(int) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Determines if a bond is a rotatable or not
- isRunning() -
Method in class chemaxon.jchem.db.JChemSearch
- Getter for property running.
- isSameParityClass(int, int, int, int, int, int, int, int) -
Static method in class chemaxon.struc.MolAtom
- Calculates if chirality centers in the structure and the query
belong to the same parity class.
- isSaveIniEnabled() -
Method in class chemaxon.marvin.beans.MarvinPane
- Automatically saves user settings to an initialization file.
- isScaled() -
Method in class chemaxon.descriptors.MDParameters
- Returns whether current parametrized metric is scaled or not.
- isSearchAll() -
Method in class chemaxon.checkers.RatomChecker
- Gets the option determining if the checker detects all R-atoms or not.
- isSearchContracted() -
Method in class chemaxon.checkers.AbbreviatedGroupChecker
- Returns if the checker is searching for contracted SGroups or not
- isSearchDefaultValence() -
Method in class chemaxon.checkers.ValencePropertyChecker
- Returns if the checker detects valence properties with the default
valence of the current atom type.
- isSearchDisconnected() -
Method in class chemaxon.checkers.RatomChecker
- Gets the option determining if the checker detects R-atoms not connected
to any other atoms or not.
- isSearchExpanded() -
Method in class chemaxon.checkers.AbbreviatedGroupChecker
- Returns if the checker is searching for expanded SGroups or not
- isSearchGeneric() -
Method in class chemaxon.checkers.RatomChecker
- Gets the option determining if the checker detects R-atoms without
identifier numbers or not.
- isSearchLinker() -
Method in class chemaxon.checkers.RatomChecker
- Gets the option determining if the checker detects R-atoms with more than
one connection or not.
- isSearchMissingRatom() -
Method in class chemaxon.checkers.RgroupReferenceErrorChecker
- Gets the option determining if the checker detects missing R-atoms or
not.
- isSearchMissingRgroup() -
Method in class chemaxon.checkers.RgroupReferenceErrorChecker
- Gets the option determining if the checker detects missing R-groups or
not.
- isSearchNested() -
Method in class chemaxon.checkers.RatomChecker
- Gets the option determining if the checker detects R-atoms within
R-groups or not.
- isSearchNonDefaultValence() -
Method in class chemaxon.checkers.ValencePropertyChecker
- Returns if the checker detects valence properties with a non-default
valence of the current atom type.
- isSearchSelfReference() -
Method in class chemaxon.checkers.RgroupReferenceErrorChecker
- Sets the option determining if the checker detects nested R-atoms
referencing to their own R-groups directly or in circularly or not.
- isSeekable() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Tests whether the record reader is seekable.
- isSeekable() -
Method in class chemaxon.marvin.io.MRecordImporter
- Tests whether the record reader is seekable.
- isSeekable() -
Method in interface chemaxon.marvin.io.MRecordReader
- Tests whether the record reader is seekable.
- isSeekable() -
Method in class chemaxon.marvin.io.PositionedInputStream
- Tests whether the stream is seekable.
- isSelectable() -
Method in class chemaxon.marvin.beans.MViewPane
- Are the cells selectable?
- isSelectableNow() -
Method in class chemaxon.struc.graphics.MMidPoint
-
- isSelectableNow() -
Method in class chemaxon.struc.graphics.MRectanglePoint
-
- isSelectableNow() -
Method in class chemaxon.struc.MObject
- Is the object selectable now?
- isSelected() -
Method in class chemaxon.marvin.space.GraphicComponent
- Tells whether the component is being selected or not.
- isSelected(ComponentElement) -
Method in class chemaxon.marvin.space.GraphicComponent
- Tells whether a part of the component is selected.
- isSelected() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isSelected(ComponentElement) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns true if the given item is selected.
- isSelected() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns true if the whole component is selected.
- isSelected() -
Method in class chemaxon.struc.MObject
- Is the object selected?
- isSelected() -
Method in class chemaxon.struc.MolAtom
- Tests whether this atom is selected.
- isSelected(MoleculeGraph) -
Method in class chemaxon.struc.Sgroup
- Is the sgroup or part of the sgroup selected?
- isSelectedAtom(int) -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isSelectedAtom(int) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns true if the atom with the given index is selected.
- isSelectedComponent(int) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the given component is selected.
- isSelfReference(MProp) -
Method in class chemaxon.struc.MoleculeGraph
- Tests whether the specified property is a self reference to the molecule.
- isSelfReference(MProp) -
Method in class chemaxon.struc.MPropertyContainer
- Tests whether a property is a self reference to the containing
molecule.
- isSelfReference(MProp) -
Method in class chemaxon.struc.RgMolecule
- Tests whether the specified property is a self reference to the molecule.
- isSetColoringEnabled() -
Method in class chemaxon.marvin.beans.MarvinPane
- Is the atom/bond set coloring enabled?
- isSetColoringEnabled() -
Method in class chemaxon.marvin.MolPrinter
- Returns true if atoms and bonds are colored according to the color
of the pre-defined set they belong to.
- isSetSwitchOffAllProtectionsForTDF(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns whether all protections for tautomer duplicate filtering is switched off.
- isSgroup() -
Method in class chemaxon.struc.Molecule
- Checks if the structure represents an S-group or not.
- isShape(int) -
Static method in class chemaxon.marvin.alignment.Pharmacophore3D
-
- isSimilarListed() -
Method in class chemaxon.clustering.Compare
- Indicates whether similar objects listed from the first set.
- isSimilarTo(MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Tests if the molecule graph is similar to another graph.
- isSimpleMolecule() -
Method in class chemaxon.struc.MDocument
- Tests whether the document is equivalent to a simple molecule.
- isSingle() -
Method in class chemaxon.reaction.Reactor
- Returns
true if single mode.
- isSingleCellLabelShown() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Tests whether label should be shown for a single cell.
- isSingleStepReaction() -
Method in class chemaxon.struc.RxnMolecule
- Decides wheter this reaction is a singlestep or multistep reaction.
- isSingletonNegative() -
Method in class chemaxon.clustering.JarvisPatrick
- Indicates whether singeltons get negative cluster id-s.
- isSingletonNegative() -
Method in class chemaxon.clustering.Ward
- Indicates whether singeltons get negative cluster id-s.
- isSizeFinal() -
Method in class chemaxon.marvin.view.MDocStorage
- Tests whether the storage size is final.
- isSketchWindowOpened(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Checks whether the molecule from the specified cell is opened in a
sketcher window or not.
- isSmallestRingSizeChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects smallest ring size
atom query properties or not.
- isSMILESShown() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Are SMILES strings shown in the table?
- isSmoothBackgroundEnabled() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if the background is enabled to be smooth, so that
it does not have a homogenous color.
- isSpecBeilsteinGeneric(String) -
Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
- Tests whether the specified symbol is a Beilstein Generic except
A, Q and X.
- isSpecIsotopeSymbolPreferred() -
Method in class chemaxon.struc.MolAtom
- Tests whether special symbol is used.
- isSpecIsotopeSymbolUsed() -
Method in class chemaxon.struc.MolAtom
- Tests whether special symbol is used.
- isStandardizationMandatory() -
Method in class chemaxon.descriptors.MDParameters
- Checks is Standardization of molecules is mandatory for the corresponding
MolecularDescriptor before descriptor generation.
- isStarAtom(MolAtom) -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Decides whether an atom is a star atom in this S-group.
- isStatNeeded() -
Method in class chemaxon.clustering.Common
- Indicates whether statistics are produced.
- isStreamOutput() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Returns
true if stream output.
- isStructuralChange -
Variable in class chemaxon.jchem.db.Updater.UpdateInfo
- Indicates whether the operation is required or not.
- isSubFormatOf(String, String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether a format is a sub-format of another format.
- isSubgraphSearch() -
Method in class chemaxon.sss.search.MolSearchOptions
- Returns whether currently subgraph or complete graph matching is
performed.
- isSubgraphSearch() -
Method in class chemaxon.sss.search.SearchOptions
- Returns the subgraph matching option.
- isSubsetChangable() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Returns whether startAt and maxSize can be changed.
- isSubSetOf(ChemicalFingerprint) -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Checks if this fingerprint is a subset of another fingerprint that is
passed as method parameter.
- isSubsetOf(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Checks if this fingerprint is a subset of another fingerprint that is
passed as method parameter.
- isSubSetOf(ReactionFingerprint) -
Method in class chemaxon.descriptors.ReactionFingerprint
- Checks if this fingerprint is a subset of another fingerprint that is
passed as method parameter.
- isSubstitutionCountChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects substitution count
atom query properties or not.
- isSuperstructureSearch() -
Method in class chemaxon.sss.search.SearchOptions
- True if the current search type is superstructure search.
- isSupportedTransferFormat(String) -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Checks whether the given format is available in the current environment
or not.
- isSupportedTransferFormat(String) -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- isSwitchOffAllProtectsForTDF() -
Method in class chemaxon.sss.search.MolSearchOptions
- Specifies whether all protects are switched off during generic tautomer
creation.
- isSymmetric() -
Method in class chemaxon.struc.MoleculeGraph
- Tests whether the molecule graph is symmetric.
- isSymmetricalFuzzy() -
Method in class chemaxon.descriptors.PFParameters
-
- isTargetAbsoluteStereo() -
Method in class chemaxon.sss.search.MolSearchOptions
- Returns whether the chiral flag is ignored or not for the target
molecule.
- isTargetStandardizable -
Variable in class chemaxon.sss.search.MolSearch
-
- isTautomerDuplicateFiltering() -
Method in class chemaxon.sss.search.SearchOptions
- Deprecated. since 5.5, replace with
SearchOptions.getTautomerSearch()
- isTautomerDuplicateFilteringEnabled(String) -
Method in class chemaxon.jchem.db.DatabaseProperties
- Returns whether tautomers are considered during duplicate filtering
for this table.
- isTerminalAtom() -
Method in class chemaxon.struc.MolAtom
- Determines whether it is a terminal atom or not.
- isTextType(int) -
Static method in class chemaxon.util.DatabaseTools
- Determines if an SQL type is a text type
- isThicknessSet() -
Method in class chemaxon.struc.graphics.MPolyline
- Checks if the line thickness is set.
- isThrowExceptionOnTimeout() -
Method in class chemaxon.sss.search.SearchOptions
- It search should throw exception upon timeout.
- isTotalSelected(MoleculeGraph) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Decides if the whole data sgroup is selected or not.
- isTotalSelected(MoleculeGraph) -
Method in class chemaxon.struc.Sgroup
- Decides if the whole sgroup is selected or not.
- isTotalSelected(MoleculeGraph) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Decides if the whole superatom sgroup is selected or not.
- isTransformable() -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Is it a transformable object?
- isTransformable() -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Is it a transformable object?
- isTransformable() -
Method in class chemaxon.struc.graphics.MRectanglePoint
-
- isTransformable() -
Method in class chemaxon.struc.MObject
- Is it a transformable object?
- isTransformationEnabled() -
Method in class chemaxon.marvin.common.UserSettings
- Gets the transformation enabled/disabled.
- isTransitionMetal(int) -
Static method in class chemaxon.struc.PeriodicSystem
- Checks if the given atom is a transition metal, IB-VIIIB.
- isTransparent() -
Method in class chemaxon.marvin.MolPrinter
- Returns the transparency state of the painting.
- isTransparentBackgroundEnabled() -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if the background is transparent.
- isUndecided(Object) -
Static method in class chemaxon.jep.ChemJEP
- Returns whether the result object is undecided.
- isUndefinedRAtomMatchingGroup() -
Method in class chemaxon.sss.search.SearchOptions
- Gets whether undefined R atom matches group of atoms.
- isUnitDisplayed() -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets whether the units string should be displayed.
- isUnsaturationChecking() -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
- Gets the option determining if the checker detects unsaturation atom
query properties or not.
- isUpdateNeededForTable(String) -
Method in class chemaxon.jchem.db.Updater
- Check whether structural upgrade is necessary for a particular table.
- isURL(String) -
Static method in class chemaxon.marvin.space.MSpaceEasy
- Tells whether the given path is an URL (Uniform Resource Locator) or not.
- isURLOrFileName(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether the specified string is an URL (absolute or relative)
or file name.
- isUsedMetric(int, int) -
Method in class chemaxon.descriptors.MDSimilarity
- Return if the given metric is used with the given molecular descriptor
in similarity calculations.
- isUsefulForQuery() -
Method in class chemaxon.sss.search.MolComparator
- Decides based on the query and the search object if the comparator
should be used or not.
- isUsefulForTarget() -
Method in class chemaxon.sss.search.MolComparator
- Decides based on the query, target and the search object if the
comparator should be used or not.
- isUsePreparedStatement() -
Method in class chemaxon.jchem.db.DatabaseProperties
-
- isValenceCheckEnabled() -
Method in class chemaxon.struc.MoleculeGraph
- Determines whether valence check is enabled on this molecule graph.
- isValenceErrorVisible() -
Method in class chemaxon.marvin.beans.MSketchPane
- Are valence errors highlighted?
- isValenceErrorVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Are valence errors visible?
- isValenceErrorvisible() -
Method in class chemaxon.marvin.MolPrinter
- Returns the visibility state of valence errors.
- isValenceErrorVisibleInView() -
Method in class chemaxon.marvin.beans.MViewPane
- Are valence errors highlighted?
- isValenceErrorVisibleInView() -
Method in class chemaxon.marvin.common.UserSettings
- Are valence errors visible in MarvinView?
- isValenceMatching() -
Method in class chemaxon.sss.search.SearchOptions
- Get the valence matching option
- isValencePropertyVisible() -
Method in class chemaxon.marvin.common.UserSettings
- Tells wheter the atom valence property is visible or not.
- isValencePropertyVisible() -
Method in class chemaxon.marvin.MolPrinter
- Gets the atom valence property visibility
- isValid() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns the current validity state
- isValid() -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- isValid() -
Method in interface chemaxon.checkers.StructureChecker
- Returns true if the checker's configuration is valid, false otherwise
- isValid() -
Method in class chemaxon.marvin.services.DynamicArgument
-
- isValid() -
Method in class chemaxon.marvin.services.ServiceArgument
- Returns
true if service argument is valid
- isValid() -
Method in interface chemaxon.marvin.services.ServiceDescriptorEditor
- Returns
true if editor represents a valid descriptor in current state
- isValid(MProp) -
Method in class chemaxon.struc.MPropertyContainer
- Tests whether a coordinate dependent property is still valid.
- isvalidateSgroupsAtCreation() -
Method in class chemaxon.marvin.common.UserSettings
- Is the validation of the possible sgroups and allow only the
chemically correct ones on sgroups creation and edit dialog.
- isValidConfiguration() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Returns true if configuration is valid
- isValidLinkNode(int, int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Checks whether the specified link atom is valid or not.
- isValidSourceAndSinkForMolecule(Object, Object, Molecule) -
Static method in class chemaxon.struc.graphics.MEFlow
- Checks if the given Objects can be a source and sink of a electron flow in the molecule.
- isValidSourceForMolecule(Object, Molecule) -
Static method in class chemaxon.struc.graphics.MEFlow
- Checks if the given Object can be a source of a electron flow in the molecule.
- isVerbose() -
Method in class chemaxon.marvin.space.GraphicCell
- Gets the verbose level.
- isVerbose() -
Method in class chemaxon.marvin.space.GraphicScene
- Gets the verbose level.
- isVerbose() -
Method in class chemaxon.sss.search.Search
- For debugging purposes only.
- isVerbose() -
Method in class chemaxon.sss.search.SearchOptions
- For debugging purposes only.
- isViewAtomMarkEnabled() -
Method in class chemaxon.marvin.common.UserSettings
- Returns true if atom mark and highlight is enabled in View.
- isViewWindowOpened(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Checks whether the view canvas of the specified cell is detached into a
separate window or not.
- isVisible() -
Method in class chemaxon.marvin.space.ComponentElement
- Returns true if the
ComponentElement is visible in the component.
- isVisible() -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns true if this component is allowed to be drawn.
- isVisible(ComponentElement) -
Method in class chemaxon.marvin.space.GraphicComponent
- Returns true if the specified part of the component is allowed to be drawn.
- isVisible() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns true if any of its visualizers is visible.
- isVisible(ComponentElement) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Returns true if the gien ComponentElement is visible.
- isVisible() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- isVisible() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns true if this component is allowed to be drawn.
- isVisible(ComponentElement) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Returns true if the given item is visible.
- isVisible() -
Method in class chemaxon.marvin.space.monitor.Monitor
- A monitor is visible if all of its selected components are visible,
and it is not hidden explicitly.
- isVisible(ComponentElement) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Returns true, because a PositionMonitor cannot be hidden.
- isVisible() -
Method in class chemaxon.struc.Sgroup
- Checks whether this group is 'visible' (all parents are expanded
in case of superatom S-groups) or not.
- isVolumeVisible() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Tells whether the volumetric data is shown or not.
- isWeighted() -
Method in class chemaxon.descriptors.MDParameters
- Returns whether current parametrized metric is weighted or not.
- ITALIC -
Static variable in class chemaxon.struc.graphics.MFont
- Italic font style.
- ITEM_COUNT -
Static variable in class chemaxon.marvin.space.monitor.Label
-
- items -
Variable in class chemaxon.marvin.plugin.gui.ParameterPanel
-
- IteratorFactory - Class in chemaxon.util.iterator
- The
IteratorFactory class provides implementations of Iterator
to ease the handling of atoms and bonds used in Molecule objects and its
descendants. - IteratorFactory(Molecule, int, int) -
Constructor for class chemaxon.util.iterator.IteratorFactory
- Constructs an iterator factory for the specified molecule with
a specified atom and bond related behavior.
- IteratorFactory(Molecule) -
Constructor for class chemaxon.util.iterator.IteratorFactory
- Constructs an iterator factory for the specified molecule with
default atom and bond related behavior to include all atoms and bonds.
- IteratorFactory.AtomIterator - Class in chemaxon.util.iterator
- The
AtomIterator class provides
an iterator for the atoms of the specified molecule of the factory
according to the atom related behavior set in the factory. - IteratorFactory.AtomIterator() -
Constructor for class chemaxon.util.iterator.IteratorFactory.AtomIterator
- Constructs an atom iterator for the specified molecule of the factory
according to the atom related behavior set in the factory.
- IteratorFactory.AtomNeighbourIterator - Class in chemaxon.util.iterator
- The
AtomNeighbourIterator class provides an iterator to process
the atoms connecting to a specified atom according to the atom and bond related
behavior of this factory. - IteratorFactory.AtomNeighbourIterator(MolAtom) -
Constructor for class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator
- Constructs an iterator to process the atoms connecting to the specified atom according
to the atom and bond related behavior of this factory.
- IteratorFactory.BondIterator - Class in chemaxon.util.iterator
- The
BondIterator class provides an iterator to process
the bonds of the specified molecule in this factory
according to the bond related behavior of this factory. - IteratorFactory.BondIterator() -
Constructor for class chemaxon.util.iterator.IteratorFactory.BondIterator
- Constructs an iterator to process
the bonds of the specified molecule in this factory
according to the bond related behavior of this factory.
- IteratorFactory.BondNeighbourIterator - Class in chemaxon.util.iterator
- The
BondNeighbourIterator class provides an iterator to
process the bonds connecting to the specified atom according to the atom
and bond related behavior of this factory. - IteratorFactory.BondNeighbourIterator(MolAtom) -
Constructor for class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
- Constructs an iterator to process the bonds connecting to the specified
atom.
- IteratorFactory.NeighbourIterator<E> - Class in chemaxon.util.iterator
- The
NeighbourIterator class provides an iterator to process the bonds connecting to the
specified atom according to the atom and bond related behavior of this factory. - IteratorFactory.NeighbourIterator(MolAtom) -
Constructor for class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
- Constructs an iterator to process the bonds connecting to the specified
atom.
- IteratorFactory.RgComponentIterator - Class in chemaxon.util.iterator
- The
RgComponentIterator class provides an iterator to process
the rgroup definition components in the specified molecule of
the factory. - IteratorFactory.RgComponentIterator() -
Constructor for class chemaxon.util.iterator.IteratorFactory.RgComponentIterator
- Constructs an iterator to process
the rgroup definition components, if the specified
molecule in the factory is an RgMolecule, the iterator is empty otherwise.
- IteratorFactory.RxnComponentIterator - Class in chemaxon.util.iterator
- The
RxnComponentIterator class provides an iterator to process
the components (reactant, product and agent components) in the reaction molecule of
the factory. - IteratorFactory.RxnComponentIterator() -
Constructor for class chemaxon.util.iterator.IteratorFactory.RxnComponentIterator
- Constructs an iterator to process
the components (reactant, product and agent components), if the specified
molecule in the factory is an RxnMolecule, the iterator is empty otherwise.
- IUPAC_NAMING_PLUGIN -
Static variable in class chemaxon.license.LicenseManager
- Identifier of plugin: IUPAC Naming Plugin
- IUPACNamingPlugin - Class in chemaxon.marvin.calculations
- IUPAC name generator plugin.
- IUPACNamingPlugin() -
Constructor for class chemaxon.marvin.calculations.IUPACNamingPlugin
-
JChemSearch.JChemSearchOptions.JChemSearchOptions(int)
UserSettings.getPropertyMap() instead.
Ring.largestRing()
Ring.largestRingSize()
Ring.largestRingSizeOfAtom(int)
Ring.largestRingSystem()
Ring.largestRingSystemSize()
"layout".
"layoutH".
LogD scalar descriptor class.LibraryMCS class computes the maximum common substructure (MCS)
of a set of compounds.ClusterEnumerator is the right way to obtain results of a LibraryMCS clustering."license".
"licenseFile".
"ligandErrorVisible".
LIGAND_ORDER_OFF
LIGAND_ORDER_ON
LIGAND_ORDER_ONLY_WITH_DEFINITION
"listenmouseevent".
"listenpropertychange".
"loadMols".
GraphicComponent
in its local coordinate system.- LocalLocationControl(Monitor) -
Constructor for class chemaxon.marvin.space.monitor.LocalLocationControl
- Creates a new instance of LocalLocationControl
- LocalOrientationControl - Class in chemaxon.marvin.space.monitor
- This control is to change the orientation say rotate a
GraphicComponent
in its local coordinate system. - LocalOrientationControl(Monitor) -
Constructor for class chemaxon.marvin.space.monitor.LocalOrientationControl
- Creates a new instance of LocalOrientationControl
- LocalServiceDescriptor - Class in chemaxon.marvin.services.localservice
- Service Descriptor for java based local services.
- LocalServiceDescriptor() -
Constructor for class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- locateCell(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the internal index of the cell under x,y position.
- locateCellId(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the id of the cell under x, y position.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the internal id of the component under x, y location,
or the id of the cell itself if there is no component in that location.
- locateObject(int, int, Class) -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the internal id of the given class component under x, y location,
or the id of the cell itself if there is no component in that location.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.GraphicComponent
- Picking action at x, y coordinates, returns the z coordinate of the nearest
picked item, or -1.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the identifire of the object under x,y position.
- locateObject(int, int, Class) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the identifire of the given class object under x,y position.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.monitor.Label
- Pickes the label in x, y position.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Pickes the control in x, y position.
- locationNearEdge(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Tells whether the given location is near to any edges of any cell.
- locationNearEdgeX(int, int) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the given location is near the vertical edges of the cell.
- locationNearEdgeX(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Tells whether the given location is near the vertical edges of any cell.
- locationNearEdgeY(int, int) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the given location is near the horizontal edges of the cell.
- locationNearEdgeY(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Tells whether the given location is near the horizontal edges of any cell.
- log(int, String, Throwable) -
Method in class chemaxon.jchem.file.ProgressWriter
- Log a message which needs to be retrieved for a "suppressed" event during
execution.
- LOG_FILE_PATH -
Static variable in class chemaxon.metabolizer.MetabolizerConstants
- the log file path property
- LogD - Class in chemaxon.descriptors.scalars
- Implements logD value as a scalar descriptor.
- LogD() -
Constructor for class chemaxon.descriptors.scalars.LogD
- Creates a new, empty logD descriptor.
- LogD(LDParameters) -
Constructor for class chemaxon.descriptors.scalars.LogD
- Creates a new instance according to the parameters given.
- LogD(String) -
Constructor for class chemaxon.descriptors.scalars.LogD
- Creates a new instance according to the parameters given.
- LogD(ScalarDescriptor) -
Constructor for class chemaxon.descriptors.scalars.LogD
- Copy constructor.
- logDPlugin - Class in chemaxon.marvin.calculations
- Plugin class for logD calculation.
- logDPlugin() -
Constructor for class chemaxon.marvin.calculations.logDPlugin
- Constructor.
- logException(Logger, String) -
Method in class chemaxon.sss.search.Search
- Writes on the logger output the shown message together with
a representation of the query and the target.
- LogP - Class in chemaxon.descriptors.scalars
- Implements LogP value as a scalar descriptor.
- LogP() -
Constructor for class chemaxon.descriptors.scalars.LogP
- Creates a new, empty logP descriptor.
- LogP(SDParameters) -
Constructor for class chemaxon.descriptors.scalars.LogP
- Creates a new instance according to the parameters given.
- LogP(String) -
Constructor for class chemaxon.descriptors.scalars.LogP
- Creates a new instance according to the parameters given.
- LogP(ScalarDescriptor) -
Constructor for class chemaxon.descriptors.scalars.LogP
- Copy constructor.
- logPPlugin - Class in chemaxon.marvin.calculations
- Plugin class for logP calculation.
- logPPlugin() -
Constructor for class chemaxon.marvin.calculations.logPPlugin
- Constructor.
- LONE_PAIR_TYPE -
Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- LONE_PAIRS_AUTO_CALCULATION -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"lonePairsAutoCalc".
- LONE_PAIRS_VISIBLE -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"lonePairsVisible".
- LONELY_H -
Static variable in class chemaxon.struc.MolAtom
- Include lonely Hydrogen atom(s).
- lowestEigenvalues -
Variable in class chemaxon.descriptors.BCUT
-
- lowPrecisions -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- LP -
Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
-
- LP -
Static variable in class chemaxon.struc.MolAtom
- "Atomic number" of the lonely pair.
- LP_AUTO_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Lone pair automatic calculation visible flag.
- LP_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Lone pair visibility flag.
MolecularDescriptor generator.
ConcurrentStandardizerProcessor.main(String[])
MarvinPane.addHelpMenu(java.awt.Container) should be used.
MarvinPane.addToolsMenu(java.awt.Container) should be used.
setReaction() and
setMap() in one method.
setReaction() and
setMap() in one method.
AbstractStructureFixer which maps the atoms of the molecule incrementallysetReaction() and
setMap() in one method.
AbstractStructureFixer which maps the reaction with AutoMapperRgMolecule output that covers the specified targets
with the specified scaffold.JChemSearch."maxscale".
MCES algorithm.MCES search termination.MCES insteadMDDBReader.MDDBReader(java.lang.String, chemaxon.util.ConnectionHandler, chemaxon.descriptors.MDSet, java.lang.String)
instead.
MDDBReader.MDDBReader(java.lang.String, chemaxon.util.ConnectionHandler, java.lang.String[], java.lang.String)
intead.
MDSet objects from a text file.MDSet file reader for reading
one single MolecularDescriptor.
MDSet file reader for reading
multiple MolecularDescriptor components.
MDSet)s into text files.MDFileWriter object that
stores MDSets in the named text files component-wise.
MDFileWriter object that
stores MDSets in the named text files component-wise.
MDFileWriter object that
stores MDSets that have the given number of components.
MDFileWriter object that
stores MDSets in the named text file.
MDFileWriter object that
stores MDSets in the named text file.
MDFileWriter object that
stores MDSets in the named SDfile.
MDFileWriter object that
stores MDSets in the named SDfile.
MDFileWriter object that
stores MDSets in the named SDfile.
MolecularDescriptor generators.MolecularDescriptor.generate()
interface.MDGeneratorException without detailed explanation.
MDGeneratorException with the specified detailed
message.
MDGeneratorException with the specified detail message and
cause.
MDGeneratorException with the specified cause.
MolecularDescriptor parameter settings.MDParametersException reports all kinds of parametrization
related failures.MDSet input streams.MDReader classes.MDReaderException without detailed explanation.
MDReaderException with the specified detailed
message.
MDReaderException with the specified detailed
message and the cause
MDset combines several MolecularDescriptors into
one entity.MDSet object.
MDSet object capable of stroring a given
number of MolecularDescriptor components.
MDSet object capable of stroring a given
number of MolecularDescriptor components and the given
number of user defined (external) data.
MDSet-s.MDSet (for example set of
chemical fingerprints and/or pharmacophore fingerprints).MDSimilarity.MDSimilarityResultWriter object.
MDSet output streams.MDWriter object which
handles the given number of MolecularDescriptors.
MDWriter class.MDWriterException without detailed explanation.
MDWriterException with the specified detailed
message.
MDWriterException with the specified message
and cause.
Monitor that measures something on its elements."menuconfig".
"menubar".
"mergedst".
MoleculeGraph.mergeFrags(int, int, int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.mergeFrags(id1, id2, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
MoleculeGraph.mergeAtoms(MolAtom, MolAtom).
Metabolizer classAbstractStructureFixer which converts a single incorrectly drawn
metallocene into multicenter based coordinate bond representation.Metrics class implements dissimilarity metrics for
MolecularDescriptors.MPropHandler.createMMoleculeProp(String)
MCS.MODE_EXACT and MCS.MODE_TURBO.
"molLoaderFinishedEvent".
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.Builder.build()
instead.
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.Builder instead.MolecularDescriptor with the given
parameters.
MolecularDescriptor passed as a parameter.
Molecule instance to check
"mol".
Molecule which will be transferred to the clipboard.
"molbg".
"molChanged".
"molFormat".
MoleculeComponent is the basic visualizer of simple molecules in MarvinSpace.MoleculeComponent from the given molecule.
MoleculeComponent from the given
HeteroComponent and MacroMoleculeComponent;
this class can be used as a visualizer of a ligand.
Molecule by cleave CCQ bonds.MoleculeFragmenter instance
MolExportExceptionMolExportModuleMolImporter object.MolSearch.MolSearchOptions.MolSearchOptions(int)
Monitor is for "watching" something in the scene.Monitor.
"moreEnabled".
Action implementation which performs config element move down
Action implementation which performs config element move up
TemplateHandler.MYTEMPLATES_GROUP_INDEX instead.
NameConverter
to indicate that even though a name cannot be converted to a structure,
it is the prefix of a valid name.String
Double.NaN.
"navmode".
MDSet instance constituted of the specified
components.
MDSet instance constituted of the specified
components.
MDSet instance constituted of the specified
components.
null
when there are no more accessible data.
MDSet object from the input source.
MDSet object passed as parameter.
IteratorFactory.AtomIterator.next() instead.
IteratorFactory.AtomNeighbourIterator.next() instead.
IteratorFactory.BondIterator.next() instead.
IteratorFactory.BondNeighbourIterator.next() instead.
IteratorFactory.RgComponentIterator.next() instead.
IteratorFactory.RxnComponentIterator.next() instead.
MolAtom.getAtomicNumber(String).
AlignmentSimilarity3D"param".
"paramH".
MolImporter.parseMRV(String)
Cleaner.partialClean(Molecule, Molecule[], String)
Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String)
Cleaner.partialClean(MoleculeGraph, int, int[], String)
PFGenerator class generates 2-dimensional pharmacophore
fingerprints for molecular graphs.PharmacophoreArrow provides an extension of
PharmacophorePoint to represent pharmacophores by introducing
directionality.PharmacophoreArrow.
PharmacophoreArrow at the position of the given
ComponentElement getting the coordinates by getCoordinates().
PharmacophoreArrow at the given position.
PharmacophoreFingerprint class implements 2D pharmacophoric fingerprints.PharmacophorePoint.
PharmacophorePoint at the position of the given ComponentElement
getting the coordinates by getCoordinates().
GraphicComponent.pickedItem to be the picked part of the component.
GraphicComponent.pickedItem to the
pharmacophore point.
Throwable and the plugin object which
has thrown the Throwable.String
"preload".
CustomDescriptor.
ChemicalFingerprint.
ECFP.
ReactionFingerprint.
ScalarDescriptor.
Shape.
String represents the name of the property which represents
the arom type String property
String represents the name of the configuration file property which is
responsible for searching contracted abbreviated groups
String represents the name of the property which is
responsible for searching too long bonds in the molecule
String represents the name of the property which is
responsible for searching too short bonds in the molecule
String represents the name of the configuration file property which is
responsible for searching expanded abbreviated groups
String represents the name of the configuration file property which is
responsible for searching too long bonds in the molecule
String represents the name of the property which is
responsible for searching all ratoms in the molecule
String represents the name of the property which is
responsible for searching contracted abbreviated groups
String represents the name of the property which is
responsible for searching disconnected ratoms in the molecule
String represents the name of the property which is
responsible for searching expanded abbreviated groups
String represents the name of the property which is
responsible for searching generic ratoms in the molecule
String represents the name of the property which is
responsible for searching linker ratoms in the molecule
String represents the name of the property which is
responsible for searching missing ratoms in the molecule
String represents the name of the property which is
responsible for searching missing rgroups in the molecule
String represents the name of the property which is
responsible for searching nested ratoms in the molecule
String represents the name of the property which is
responsible for searching self references in the molecule
String represents the name of the configuration file property which is
responsible for searching too short bonds in the molecule
String represents the name of the property which is
responsible for using the given aromatization type during the check mechanism.
Boolean
UserSettings.getPropertyMap(String)
method to get all properties that are stored.
UserSettings.getPropertyMap(String)
method to get the default properties.
UserSettings.getPropertyMap(String)
method to get the properties set by UserSettings.setProperty(String, String)
method or by the setter methods.
UserSettings.getPropertyMap(String)
method to get the properties that are being stored temporary, and will
not be saved to the properties file.
AtomChecker detecting pseudo atoms.MDSet object into the output files as
readable text.
MDSet object from the given molecular
structure and writes result.
MDSet for the given Molecule
and writes the descriptors into the output with the given identifier.
MDSet for the given Molecule
and writes the descriptors into the output with the given identifier.
UserSettings.setProperty(String, String) or
UserSettings.setProperty(String, String, boolean) instead.
StringSelection.
"queryAtoms".
AtomChecker detecting generic atoms or ones having query properties.BondChecker detecting query bonds."rgroupsVisible".
AtomChecker detecting radical atoms.AbstractStructureChecker detecting R-atoms.Reactor."reactionSupport".
null if not a reaction.
ReactionFingerprint class.ReactionChecker detecting reactions with invalid mapping.ParametrizedMetric nodes in the DOM tree.
Molecule object.
ServiceDescriptor objects from specified InputStream
MDParameters sub-class.
AbstractStructureFixer which rearomatize the moleculeMoleculeGraph.regenBonds().
Action implementation which performs config element remove
MoleculeGraph.removeAllBonds().
Sgroup.removeAtom(MolAtom, int) of
sg.
AbstractStructureFixer which removes the atoms of the molecule
signed in the resultAbstractStructureFixer which removes the atom maps from the moleculeAbstractStructureFixer which removes the atom value from the moleculeAbstractStructureFixer which removes the attached data from the moleculeAbstractStructureFixer which removes the bonds of the molecule
signed by the resultMoleculeGraph.removeBond(MolBond).
MoleculeGraph.removeBond(int).
PropertyChangeListener from element listener list
PropertyChangeListener from element listener list
Hydrogenize.removeLonePairs(MoleculeGraph)
str parameter from the inactive tasks list.
null atom entries in the atoms array
and sets the index fields appropriately.
null bond entries in the bonds array
and sets the index fields appropriately.
MoleculeGraph.removeAtom(MolAtom).
MoleculeGraph.removeAtom(int).
MoleculeGraph.removeAtom(MolAtom, int).
MoleculeGraph.removeAtom(int, int).
AbstractStructureFixer which removes the radicals from the
atoms of the moleculeRxnMolecule.removeComponent(int, int)
TransferableDescriptor to the MTransferable
Registry.
TransferableDescriptor to the MTransferable
Registry by name.
"rendering".
MoleculeGraph.replaceBond(MolBond, MolBond).
MolecularDescriptor stream.
MDSet input stream.
mark method was last called on this input stream.
GraphicComponent by changing the coordinates.Reactor.react()
will return the first product set.
MarkushTagger.getFeatureTable()
or the feature coverage table returned by MarkushTagger.getFeatureCoverageTable()
from its String representation.
true if the cut-bond is accepted, false otherwise.
true if the cut-bond is accepted, false otherwise.
ReactionFingerprint descriptor.AbstractStructureChecker detecting invalid
attachments in R-group definitions.AbstractStructureChecker detecting R-group definition
errors.Ring.ringAtomCount()
Ring.ringBondCount()
Ring.ringCount()
Ring.ringCount(int)
Ring.ringCountOfAtom(int)
Ring.rings(int)
Ring.rings(int)
Ring.ringSystemCount()
Ring.ringSystemCount(int)
Ring.ringSystems()
Ring.ringSystems(int)
"RLogicVisible" or "RLogic".
"rows".
RgDecompResults.hasResults())
JChemSearch.run() or
JChemSearch.setRunning(boolean) return immediately.
JChemSearch.run() or
JChemSearch.setRunning(boolean) return immediately.
JChemSearch.run() or JChemSearch.setRunning(boolean)
return only after all hits has been found.
UserSettings.save(String).
$HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or
$HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux).
"scale".
"script".
ScalarDescriptor parameters.SearchOptions.SearchOptions(int)
"selectable".
"selectedIndex".
"selection".
String
ServiceDescriptorServiceDescriptorEditor instances based on ServiceDescriptor classes.ServiceDescriptorsServiceDescriptorReader, ServiceDescriptorWriter and ServiceDialogProvider
implementations and various configuration data for services.ServiceDescriptorsDialog instances to provide argument editor and result view for ServiceDescriptorException for failure indication for services.ServiceException with specified message and cause
ServiceException with specified message
ServiceException with specified cause
index of this
IntArray to be the specified value.
"setColoringEnabled".
JChemProperties table.
MoleculeGraph.setAbsStereo(boolean) for the
component
20).
Standardizer.setInactiveTasks(String)
true if all hits to be processed,
false if first hit only.
MolPrinter.setAtomSize(double).
-10).
MarvinPane.setBondSpacing(double)
MolPrinter.setBondSpacing(double)
true if search and calculation results are to be cached and reused.
setModel(int)
UserSettings.setCleanHOptionEnabled(boolean)
true then resonants returned
by ResonancePlugin.getStructure(int) and ResonancePlugin.getStructures() methods are cleaned in 2D.
true then tautomers returned
by TautomerizationPlugin.getStructure(int) and TautomerizationPlugin.getStructures() methods are cleaned in 2D.
next() method.
Cl- concentration (default: 0.1).
Cl- concentration (default: 0.1).
MDSet component's type and corresponding
parameters.
MDSet component's type and corresponding
parameters.
MDSet evaluation mode.
connected.
Importer.setFieldConnections(String).
MDGenerator object.
i - j as cut-bond.
i - j as cut-bond.
ComponentElement that will
be returned by {#getDescription()}.
MDSet.
ServiceDescriptorEditor.getDescriptor() may NOT return same instance
MDSet.
MolPrinter.setDispopts(int), but affects only limited
display options using a mask.
MolPrinter.setDispoptsExt(int), but affects only limited
display options using a mask.
true then dominant tautomer
distribution is calculated.
draw property.
draw property.
draw property.
draw property.
PharmacophoreSphere.
driver.
DropTarget of the graphic canvas.
UpdateHandler.setDuplicateFiltering(int) method
JChemProperties table.
Importer.setDuplicateImportAllowed(int) method
MoleculeGraph.setBond(int, MolBond).
false does not import empty molecules.
SearchOptions.SearchOptions(int)
SurfaceComponent.setExclusiveColor(byte[]).
SurfaceComponent.setExclusiveColor(byte[]).
true if homology groups
should be replaced by matching R-groups.
true if extendable cut sets
should be included.
MolPrinter.setEZLabelsVisible(boolean)
setMCSMode(MCS.MODE_FAST) or setMCSMode(MCS.MODE_TURBO) instead, this method has no effect form version 5.0 of JChem.
setMode(MODE_TURBO) instead
true.
MDSet.
CalculatorPlugin.getResultAsString(int, Object)
CutBondReviser.fragmenter.
SearchOptions.SearchOptions(int)
MDSet object.
true, only syntactical exceptions will be thrown.
0: apply both rules (default)
Reactor.IGNORE_REACTIVITY: ignore reactivity rule
Reactor.IGNORE_SELECTIVITY: ignore selectivity rule
Reactor.IGNORE_TOLERANCE: ignore selectivity tolerance
Reactor.IGNORE_REACTIVITY | Reactor.IGNORE_SELECTIVITY:
ignore both rules
Reactor.IGNORE_REACTIVITY | Reactor.IGNORE_TOLERANCE:
ignore reactivity rule and selectivity tolerance
Standardizer.addInactiveTasks(String) instead
loginName.
MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes.
MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes.
MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes.
MacroMoleculeComponent can be set and in this case this will be a
visualizer of a ligand in the macromolecule.
RxnMolecule passed in
setReaction( final
RxnMolecule rm )mapId map.
MolAtom.setForSpecIsotopeSymbol(String)
pKaPlugin.MODEL_SMALL model, it
sets the maximum number of ionizable atoms to be considered
and uses simple calculation method to compute pKa values.
JChemProperties table.
setMCSMode instead.
Molecule of the MoleculeComponent to mol,
sets proper atomIterators, and computes the bounding box.
MolHandler.setMolecule(byte[])
MolHandler.setMolecule(String)
Na+, K+ concentration (default: 0.1).
Na+, K+ concentration (default: 0.1).
MDSet object.
MoleculeGraph.setAtom(int, MolAtom).
Notlist array.
Action to be invoked at open file event
MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie().
SDfile.
BCUT object.
BCUT object.
ChemicalFingerprint object.
CustomDescriptor
object.
ECFP object.
ECFP object.
MDSet.
MolecularDescriptor.
MolecularDescriptor.
PharmacophoreFingerprint object.
ReactionFingerprint object.
ScalarDescriptor object.
HAcc object.
HDon object.
HeavyAtomCount object.
LogD object.
LogP object.
Mass object.
TPSA object.
ShapeDescriptor object.
password.
Double.NaN then the input molecule is taken as it is.
Double.NaN then the input molecule is taken as it is.
0.0).
0.0).
1.0).
14.0).
14.0).
pKaPlugin.STATICpKaPREFIX)
STATIC pKa prefix: pKa's prefix does not depend on the submitted micro state
DYNAMIC pKa prefix: pKa's prefix does depend on the submitted micro state
PharmacophoreArrow.
ConcurrentStandardizerProcessor.setPreprocessor(MolTransformer)
null - all products).
Standardizer to standardize products.
AlignmentPlugin.run() to display progress status.
ConformerPlugin.run() to display progress
status.
IsoelectricPointPlugin.run() to display progress status.
MolecularDynamicsPlugin.run() to display progress
status.
pKaPlugin.run() to display progress status.
ResonancePlugin.run() to display progress status.
StereoisomerPlugin.run() to display
progress status.
TautomerizationPlugin.run() to display progress status.
CalculatorPlugin.run() to display progress status.
ProgressWriter
object to track the progress the actual importing.
JChemProperties table.
propertyTable.
true then all tetrahedral stereo
information is preserved by the tautomer generator.
true then aromatic bonds are not modified by the tautomer
generator.
true then the charge of charged atoms are not modified by the tautomer
generator.
true then the stereo configuration of double bonds
with preset stereo information will not be changed.
true then double bonds stereo information is preserved by
the tautomer generator.
true then ester groups are excluded from the tautomerization.
true then labeled tetrahedral stereo
centers are protected by the tautomer generator.
true then stereo configuration of
tetrahedral stereo centers with preset stereo information will not be changed.
SearchOptions.setHomologyNarrowTranslation(HomologyTranslationOption)
SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s)
and MolAtom.setQueryString(String)
SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options)
and MolAtom.setQueryString(String)
Reactor.setReactants(Molecule[] mols)
for this purpose).
REACTIVITY, EXCLUDE, SELECTIVITY, TOLERANCE.
REACTIVITY, EXCLUDE, SELECTIVITY, TOLERANCE.
UserSettings.setSaveGUIPropertiesInMRV(boolean). It will be removed in a future version of Marvin.
AlignRigidEasy.getReferenceAndRotatedFused() cannot be applied
rememberPassword.
PharmacophoreArrow.setRenderingQuality(int).
RENDERING_* constants.
PharmacophorePoint.setRenderingQuality(int).
GraphicComponent.RENDERING_QUALITY_HIGH constants.
true if the reaction is to be
processed in reversed direction, that is, the product and reactant sides
are swapped.
AlignRigidEasy.getReferenceAndRotatedFused() and AlignRigidEasy.getRotatedMolecule() cannot be applied
SearchOptions, see SearchOptions.setRLigandEqualityCheck(boolean)
and SearchOptions.setOption(java.lang.String, java.lang.String)
Action to be invoked at save file event
options.
options to the current
search object.
SearchOptions.SearchOptions(int)
Reaction.setSelectivityRule(String, double[], Evaluator) or
Reaction.setSelectivityRule(String, String, Evaluator) and set
tolerances parameter to null
true during import.
true during import.
MSketchPane.setBondDraggedAlong(boolean)
MolecularDescriptor components and the
number of user defined (external) data in the MDSet.
MolecularDescriptor components in the
MDSet.
MDSetParameters
object.
MDSetParameters object.
UserSettings.MAX_RECENT_FILE_LIST_SIZE then the size will be the value of
UserSettings.MAX_RECENT_FILE_LIST_SIZE
SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)
Palette.smoothColorToCutoffValues(boolean).
Standardizer to standardize reactants.
JChemProperties table.
ConcurrentStandardizerProcessor.getAppliedTaskIDs(), ConcurrentStandardizerProcessor.getAppliedTaskIndexes(),
ConcurrentStandardizerProcessor.getInputMolecule().
MSAPlugin.VAN_DER_WAALS or MSAPlugin.SOLVENT.
true then symmetrical structures
are filtered out, otherwise symmetrical structures are returned as duplicates.
true then symmetrical structures
are filtered out, otherwise symmetrical structures are returned as duplicates.
JChemProperties table.
logPPlugin.setConsiderTautomerization(boolean)
pKaPlugin.setConsiderTautomerization(boolean)
MDSet component.
SearchOptions.setTautomerSearch(int)
JChemProperties table.
298 Kelvin).
SearchOptions.setTimeoutLimitMilliseconds(int) instead
Standardizer.
CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
url.
PROPERTY_KEY_VALID property will be fired
if necessary.
- setValidateDescriptor(String, double, String) -
Method in class chemaxon.descriptors.GenerateMD
- Sets parameters for the Activity-seeded Structure-based clustering.
- setvalidateSgroupsAtCreation(boolean) -
Method in class chemaxon.marvin.common.UserSettings
- Set the validation of the possible sgroups and allow only the
chemically correct ones on sgroups creation and edit dialog.
- setValue(T) -
Method in class chemaxon.marvin.services.ServiceArgument
- Sets the service argument value
- setValueForAdditionalColumn(int, Object, int) -
Method in class chemaxon.jchem.db.UpdateHandler
- Sets values for an additional column.
- setValueForAdditionalColumn(int, Object) -
Method in class chemaxon.jchem.db.UpdateHandler
- Sets values for all additional columns
Type is defined automatically.
- setVerbose(boolean) -
Method in class chemaxon.jep.Evaluator
- Sets verbose mode.
- setVerbose(boolean) -
Method in class chemaxon.marvin.space.GraphicCell
- Sets the verbose level on/off.
- setVerbose(int) -
Method in class chemaxon.marvin.space.GraphicCell
- Sets the verbose level to the given level.
- setVerbose(boolean) -
Method in class chemaxon.marvin.space.GraphicScene
- Sets the verbose level on/off.
- setVerbose(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Sets the verbose level to the given level.
- setVerbose(boolean) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Sets whether writing technical details to console is enabled or not.
- setVerbose(boolean) -
Method in class chemaxon.pharmacophore.PMapper
- Sets verbose output.
- setVerbose(boolean) -
Method in class chemaxon.sss.search.Search
- For debugging purposes only.
- setVerbose(boolean) -
Method in class chemaxon.sss.search.SearchOptions
- For debugging purposes only.
- setVerboseFrequency(int) -
Method in class chemaxon.descriptors.MDSimilarityResultWriter
- Specifies how frequently the status report is printed.
- setVerbosePrinter(StructuralFrameworksPlugin.VerbosePrinter) -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
- Set or clear verbose printer
Verbose messages will be sent to the verbose printer to ease debugging
- setVerbosity(boolean) -
Method in class chemaxon.descriptors.MDSimilarityResultWriter
- Sets or clears verbose mode.
- setVerticalAlignment(int) -
Method in class chemaxon.struc.graphics.MTextBox
- Sets the vertical alignment.
- setViewAnyBond(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the default any bond drawing style in the viewer.
- setViewAtomMarkEnabled(boolean) -
Method in class chemaxon.marvin.common.UserSettings
- Sets atom mark and highlight visibility in Marvin View.
- setViewCarbonVisibility(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the default carbon visibility style in the viewer.
- setViewColorScheme(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the viewer's default color scheme.
- setViewExplicitH(boolean) -
Method in class chemaxon.marvin.common.UserSettings
- Deprecated. As of release 5.3, this method is deprecated and has no replacement. It will be removed in a future version of Marvin.
- setViewHandlerType(int) -
Method in class chemaxon.marvin.view.swing.TableOptions
- Sets the view handler type.
- setViewImplicitH(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the display method of implicit hydrogens for the viewer.
- setViewLayout(int) -
Method in class chemaxon.marvin.common.UserSettings
- Set the layout of MarvinView.
- setViewLigandOrderVisibility(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the default ligand order visibility style in the viewer.
- setViewLoadWorkingDir(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the load working directory for MarvinView load filechooser.
- setViewMolbg2d(Color) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the default molecule background color for the 2D viewer.
- setViewMolbg3d(Color) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the default molecule background color for the 3D viewer.
- setViewNavmode2d(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the navigation mode for the 2D viewer.
- setViewNavmode3d(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the navigation mode for the 3D viewer.
- setViewRecentFileListSize(int) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the recent file list requested size, if it is smaller than zero,
then the size will be zero, if it is more than 10 then the size will be
10.
- setViewRendering2d(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the rendering style for the 2D viewer.
- setViewRendering3d(String) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the rendering style for the 3D viewer.
- setViewSaveWorkingDir(String) -
Method in class chemaxon.marvin.common.UserSettings
- Not implemented, don't use it.
- setVisible(boolean) -
Method in class chemaxon.marvin.space.GraphicComponent
- Indicates whether the component will appear on the graphic scene
at the next draw or not.
- setVisible(boolean) -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- setVisible(boolean) -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- Sets all of the visualizers to visible/invisible.
- setVisible(boolean) -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Sets the surface to be visible/invisible.
- setVisible(boolean) -
Method in class chemaxon.marvin.space.MoleculeComponent
- Sets the component to be visible/invisible.
- setVisibleRows(int) -
Method in class chemaxon.marvin.beans.MViewParams
- Sets the nuber of visible rows.
- setWebServiceName(String) -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- Sets the webservice name
- setWeight(int, float) -
Method in class chemaxon.descriptors.MDSetParameters
- Sets the weight of an individual component.
- setWeightMode(int) -
Method in class chemaxon.marvin.space.SurfaceColoring
- Way of handling values when multiple atoms have effect on one surface vertex.
- setWeightOfMethods(double, double, double, double) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Sets the weight of logP calculation methods.
- setWeightOfMethods(double, double, double, double) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Sets the weight of logP calculation methods.
- setWeights(float[]) -
Method in class chemaxon.clustering.Common
- Sets descriptor weights used for distance calculation.
- setWeights(float[]) -
Method in class chemaxon.descriptors.MDParameters
- Sets the cell-wise weight factors for the current parametrized metric.
- setWeights(float[]) -
Method in class chemaxon.descriptors.MDSetParameters
- Sets the weights.
- setWeights(float[], float[]) -
Method in class chemaxon.descriptors.PFParameters
- Sets the cell-wise weight factors for the current parametrized metric.
- setWeights(double[]) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Sets the atom weights for location calculation.
- setWinScale(double) -
Method in class chemaxon.marvin.beans.MViewPane
- Sets the magnification in the zoom windows.
- setWireThickness(double) -
Method in class chemaxon.marvin.beans.MarvinPane
- Sets the line thickness for wireframe mode.
- setWireThickness(double) -
Method in class chemaxon.marvin.common.UserSettings
- Sets the bond thickness in wireframe mode.
- setWireThickness(double) -
Method in class chemaxon.marvin.MolPrinter
- Sets the line thickness for wireframe mode.
- setWithCondition(float, float, float) -
Method in class chemaxon.marvin.space.BoundingBox
- This is the best way of passing coordinates to the box.
- setWithCondition(BoundingBox) -
Method in class chemaxon.marvin.space.BoundingBox
- Extends the box with the given box, say gives the bounding box of the two boxes.
- setWithExpansion(int, int) -
Method in class chemaxon.util.IntArray
- Sets the element at the specified
index of this
IntArray to be the specified value.
- setWord(ByteBuffer, int, int) -
Method in class chemaxon.marvin.io.PositionedInputStream
-
- setWorkerThreadCount(int) -
Method in class chemaxon.reaction.ConcurrentReactorProcessor
- Sets the number of worker threads.
- setWorkerThreadCount(int) -
Method in class chemaxon.reaction.ConcurrentStandardizerProcessor
- Sets the number of worker threads.
- setWorkerThreadCount(int) -
Method in interface chemaxon.util.concurrent.ConcurrentProcessor
- Sets the number of worker threads used by this processor.
- setWorkOnBackground(boolean) -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Starts or stops the background worker thread and ensures the required
state for the type of work.
- setWorkUnits(WorkUnit[]) -
Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnit
- Sets the work units.
- setWsdlURI(String) -
Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- Sets the WSDL URI
- setX(double) -
Method in class chemaxon.struc.MolAtom
- Sets the X coordinate.
- setX(double) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Sets the X coordinate.
- setXState(int) -
Method in class chemaxon.struc.Sgroup
- Sets the expanded/contracted state.
- setXState(int, int) -
Method in class chemaxon.struc.Sgroup
- Sets the expanded/contracted state.
- setXState0(int) -
Method in class chemaxon.struc.Sgroup
-
- setXY(double, double) -
Method in class chemaxon.struc.MolAtom
- Sets the x and y coordinates.
- setXYZ(double, double, double) -
Method in class chemaxon.struc.MolAtom
- Sets the coordinates.
- setY(double) -
Method in class chemaxon.struc.MolAtom
- Sets the Y coordinate.
- setY(double) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Sets the Y coordinate.
- setZ(double) -
Method in class chemaxon.struc.MolAtom
- Sets the Z coordinate.
- setZero() -
Method in class chemaxon.struc.CTransform3D
- Sets all components to zero.
- SGROUP -
Static variable in class chemaxon.struc.MolAtom
- "Atomic number" of an Sgroup.
- Sgroup - Class in chemaxon.struc
- S-group.
- Sgroup(Molecule, int) -
Constructor for class chemaxon.struc.Sgroup
- Creates an S-group with the specified parent and type.
- Sgroup(Molecule, int, int) -
Constructor for class chemaxon.struc.Sgroup
- Creates an S-group with the specified parent and type.
- Sgroup(Sgroup, Molecule, Sgroup) -
Constructor for class chemaxon.struc.Sgroup
- Copy constructor.
- Sgroup(Sgroup, Molecule, Sgroup, int[]) -
Constructor for class chemaxon.struc.Sgroup
- Copy constructor.
- SGROUP_TYPE_COUNT -
Static variable in class chemaxon.struc.Sgroup
- Number of S-group types.
- SGROUP_TYPENAMES -
Static variable in class chemaxon.marvin.io.formats.mdl.MolfileUtil
- Array of S-group type names.
- SgroupAtom - Class in chemaxon.struc.sgroup
- S-group superatom.
- SgroupAtom(SuperatomSgroup) -
Constructor for class chemaxon.struc.sgroup.SgroupAtom
- Constructs a superatom for a superatom type S-group.
- SgroupCheckerResult - Class in chemaxon.checkers.result
- A descendant of
DefaultStructureCheckerResult for identifying Sgroup problems. - SgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) -
Constructor for class chemaxon.checkers.result.SgroupCheckerResult
- Constructor which initialize all the properties.
- SGROUPEND_H -
Static variable in class chemaxon.struc.MolAtom
- Hydrogen atom which have a neighbor is an an Sgroup
- sgroupGraph -
Variable in class chemaxon.struc.Sgroup
- The S-group's internal structure.
- sgroupType -
Variable in class chemaxon.struc.Sgroup
- The S-group type.
- SHAPE -
Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
-
- ShapeDescriptor - Class in chemaxon.descriptors
- Shape descriptor implements a 3D alignment based similarity calculation.
- ShapeDescriptor() -
Constructor for class chemaxon.descriptors.ShapeDescriptor
-
- ShapeDescriptor(ShapeParameters) -
Constructor for class chemaxon.descriptors.ShapeDescriptor
- Creates a new instance of ShapeDescriptor according to the parameters given.
- ShapeDescriptor(String) -
Constructor for class chemaxon.descriptors.ShapeDescriptor
- Creates a new instance of ShapeDescriptor according to the parameters given.s
- ShapeDescriptor(ShapeDescriptor) -
Constructor for class chemaxon.descriptors.ShapeDescriptor
- Copy constructor.
- ShapeGenerator - Class in chemaxon.descriptors
-
- ShapeGenerator() -
Constructor for class chemaxon.descriptors.ShapeGenerator
-
- SHAPELY_SCHEME -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Shapely color scheme in display option flags.
- SHAPELY_SCHEME_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Shapely color scheme.
- ShapeParameters - Class in chemaxon.descriptors
-
- ShapeParameters() -
Constructor for class chemaxon.descriptors.ShapeParameters
-
- ShapeParameters(File) -
Constructor for class chemaxon.descriptors.ShapeParameters
-
- ShapeParameters(String) -
Constructor for class chemaxon.descriptors.ShapeParameters
- Creates a new object based on a given configuration string.
- SHAREPOINT -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: SharePoint
- shift(double, double) -
Method in class chemaxon.marvin.space.GraphicCell
-
- shift(double, double) -
Method in class chemaxon.marvin.space.GraphicScene
- Sets the given shift factor in the active cell or in every cells
in case of synchronous mode.
- shift(int, int) -
Method in class chemaxon.marvin.space.monitor.Label
- A label can be shifted in x,y direction.
- shiftAnimated(double, double, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Sets the given shift factor dividing by n parts.
- shiftx -
Variable in class chemaxon.marvin.space.monitor.Label
- Relative position of the label of the component with respect to the reference
point of the labeled component.
- shifty -
Variable in class chemaxon.marvin.space.monitor.Label
- Relative position of the label of the component with respect to the reference
point of the labeled component.
- shininess -
Static variable in class chemaxon.marvin.space.monitor.Control
-
- SHORTCUTS -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"shortcuts".
- shortestPath(int, int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the shortest topological path (number of bonds) between two
atoms.
- SHOW_SETS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"showSets".
- showAllComponents() -
Method in class chemaxon.marvin.space.GraphicCell
- Sets all components to visible.
- showAllComponents(Class) -
Method in class chemaxon.marvin.space.GraphicCell
- Sets all components of the given class to visible.
- showAllComponents() -
Method in class chemaxon.marvin.space.GraphicScene
- Sets all invisible component of the active cell to visible.
- showAllComponents(Class) -
Method in class chemaxon.marvin.space.GraphicScene
- Sets all components of the given class in the active cell to be visible.
- showAllMonitors() -
Method in class chemaxon.marvin.space.GraphicCell
- Sets all monitor type components (labels as well) to visible.
- showAllMonitors() -
Method in class chemaxon.marvin.space.GraphicScene
- Sets all monitor component of the active cell to visible.
- showDialog() -
Method in class chemaxon.marvin.view.swing.TableOptions
- Bring up Table Options dialog box
- showErrorDialog(String, Throwable) -
Method in class chemaxon.marvin.beans.MarvinPane
- Show error dialog.
- showFaded() -
Method in class chemaxon.marvin.space.GraphicCell
- Sets all faded components to visible.
- showFaded() -
Method in class chemaxon.marvin.space.GraphicComponent
- A descendant should overwrite this method to have its faded part become visible.
- showFaded() -
Method in class chemaxon.marvin.space.GraphicScene
- Sets the drawing mode of all faded elements back to the original drawing mode.
- showFaded() -
Method in interface chemaxon.marvin.space.MacroMoleculeComponent.MoleculeVisualizer
-
- showFaded() -
Method in class chemaxon.marvin.space.MacroMoleculeComponent
- The faded visualizers will be fully visible again.
- showFaded() -
Method in class chemaxon.marvin.space.MoleculeComponent
- Faded atoms will be fully visible again.
- showFileDialog(String, Molecule) -
Method in class chemaxon.marvin.beans.MarvinPane
- Shows an Open or Save file dialog.
- showFileOpenDialog() -
Method in class chemaxon.marvin.beans.MarvinPane
- Shows file open dialog.
- showInsertFunctionDialog() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Shows the modal insert function dialog
- showManageFavoritesDialog() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Shows the modal favourite manager dialog
- showManageMacrosDialog() -
Method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Shows the modal macro manager dialog
- showSelectedNodes() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- showVolume(boolean) -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- For Gaussian Cube surfaces it can be enabled to visualize the volumetric data
from which the surface is generated.
- similarity -
Variable in class chemaxon.descriptors.MDSimilarityResultWriter
- the similarity object which the MDSimilarityResultWriter belongs to
- similarity(Molecule) -
Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- similarity(AlignmentMolecule) -
Method in class chemaxon.marvin.alignment.PairwiseAlignment
-
- similarity(Molecule) -
Method in interface chemaxon.marvin.alignment.PairwiseComparison
- Calculates the 3D similarity between the previously set query and the target.
- similarity(AlignmentMolecule) -
Method in interface chemaxon.marvin.alignment.PairwiseComparison
-
- similarity(Molecule) -
Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- similarity(AlignmentMolecule) -
Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
-
- Similarity - Class in chemaxon.sss.screen
- Calculates the similarity of two bit strings.
- Similarity(byte[], byte[]) -
Constructor for class chemaxon.sss.screen.Similarity
- Deprecated.
- SIMILARITY -
Static variable in interface chemaxon.sss.SearchConstants
- Similarity search.
- SIMILARITY -
Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
- The similarity score is shown and stored in the MPropertyContainer of the
Molecule.
- SIMILARITY_LABEL -
Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
- Label for the similarity score part of the hit.
- SIMILARITY_OFF -
Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
- The similarity score is neither shown nor stored in the
MPropertyContainer of the Molecule.
- SimilarityCalculator<T> - Class in chemaxon.descriptors
- Descriptor similarity calculation can be performed using SimilarityCalculator.
- SimilarityCalculator() -
Constructor for class chemaxon.descriptors.SimilarityCalculator
-
- SimilarityCalculatorFactory - Class in chemaxon.descriptors
- This factory creates a similarity calculator object according to the user defined parameters.
- SimilarityCalculatorFactory.Representation - Enum in chemaxon.descriptors
-
- similarityNode -
Variable in class chemaxon.descriptors.MDParameters
- node holding the similarity calculations related parameters
- similarityScoreDisplay -
Variable in class chemaxon.util.HitColoringAndAlignmentOptions
- Mode of similarity score display.
- SIMPLE_VIEW -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"simpView".
- simplifyIncompleteReactionToMolecule() -
Method in class chemaxon.struc.RxnMolecule
- Simplify a reaction to a molecule if possible.
- simplifyMolecule() -
Method in class chemaxon.struc.MDocument
- Simplifies the main molecule object if possible.
- simplifyToMolecule() -
Method in class chemaxon.struc.RxnMolecule
- Simplifies this RxnMolecule by moving the atoms and bonds from the
reactants, products, and agents to a Molecule.
- SINGLE_OR_AROMATIC -
Static variable in class chemaxon.struc.MolBond
- Single or aromatic query bond type.
- SINGLE_OR_DOUBLE -
Static variable in class chemaxon.struc.MolBond
- Single or double query bond type.
- SINGLE_THREADED -
Static variable in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- size() -
Method in class chemaxon.descriptors.MDArrayReader
- Gets number of MDSets in the reader
- size() -
Method in class chemaxon.descriptors.MDSet
- Gets the number of components constituting the
MDSet.
- size() -
Method in class chemaxon.descriptors.MDSetParameters
- Get the size of the associated
MDSet instance.
- size() -
Method in class chemaxon.formats.recognizer.RecognizerList
- Gets the total number of elements.
- size(int) -
Method in class chemaxon.formats.recognizer.RecognizerList
- Gets the size of list at the specified level.
- size -
Variable in class chemaxon.marvin.space.monitor.Control
-
- size() -
Method in class chemaxon.struc.MPropertyContainer
- Gets the total number of properties.
- size() -
Method in class chemaxon.struc.prop.MHashProp
- Gets the table size
- size() -
Method in class chemaxon.struc.prop.MListProp
- Gets the array size.
- size() -
Method in class chemaxon.util.IntArray
- Returns the number of components in this IntArray.
- sizeToString(double) -
Static method in class chemaxon.struc.graphics.MFont
- Converts an integer or fractional size to a string.
- sizeX -
Variable in class chemaxon.marvin.space.monitor.Label
-
- sizeY -
Variable in class chemaxon.marvin.space.monitor.Label
-
- sjep -
Variable in class chemaxon.reaction.Reaction
- Deprecated. The JEP object that evaluates the selectivity (measure) rule.
- SKETCH_ANY_BOND -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"sketchAnyBond".
- SKETCH_ARROW_HEAD_LENGTH -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"sketchArrowHeadLength".
- SKETCH_ARROW_HEAD_WIDTH -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"sketchArrowHeadWidth".
- SKETCH_ARROW_TAIL_LENGTH -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"sketchArrowTailLength".
- SKETCH_ARROW_TAIL_WIDTH -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"sketchArrowTailWidth".
- SKETCH_CARBON_VISIBILITY -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"sketchCarbonVisibility".
- SKETCH_HELP -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"sketchHelp".
- SKETCH_LIGAND_ORDER_VISIBILITY -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"sketchLigandOrderVisibility".
- SKETCH_QUICK_HELP -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"sketchQuickHelp".
- SKETCHABLE -
Static variable in class chemaxon.marvin.beans.MViewPane
- Editing mode identifier meaning the structures can be edited
with the Edit > Structure menu or double click and launches MarvinSketch in a new window.
- SketchCheckerRunner - Class in chemaxon.checkers.runner
- WARNING!
- SketchCheckerRunner(ConfigurationReader) -
Constructor for class chemaxon.checkers.runner.SketchCheckerRunner
- Initiate a
SketchCheckerRunner instance which will can execute StructureChecker instances read from
configurationReader
- SketchParameterConstants - Class in chemaxon.marvin.sketch
- Parameters of MarvinSketch Applet and Bean.
- SKIN -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"skin".
- skip(int) -
Method in class chemaxon.jchem.db.Importer
- Skips the given number of molecules.
- skip(long) -
Method in class chemaxon.marvin.io.PositionedInputStream
- Skips over and discards n bytes of data.
- SKIP_COORDINATE_BONDS -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Exclude coordinate bonds from bond iteration.
- SKIP_COVALENT_BONDS -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Exclude covalent bonds from bond iteration.
- SKIP_EXPLICIT_H -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Exclude explicit hydrogens from atom iteration.
- SKIP_LONE_PAIR -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Exclude lone pairs from atom iteration.
- SKIP_MULTICENTER -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Exclude multicenters from atom iteration.
- SKIP_PSEUDO_ATOM -
Static variable in class chemaxon.util.iterator.IteratorFactory
- Exclude pseudo atoms from atom iteration.
- skipLine() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Skips the next line.
- skipLine() -
Method in class chemaxon.marvin.io.PositionedInputStream
- Skips the next line.
- skipRecord() -
Method in class chemaxon.formats.MolImporter
- Skips the next molecule or document instead of reading it into memory.
- skipRecord() -
Method in class chemaxon.marvin.io.ArrayMDocSource
- Skips the next document.
- skipRecord() -
Method in class chemaxon.marvin.io.MDocSource
- Skips the next document.
- skipRecord() -
Method in class chemaxon.marvin.io.MRecordImporter
- Skips the next document.
- skipRecord() -
Method in interface chemaxon.marvin.io.MRecordReader
- Skips the next record.
- skipRecords(int, int, MProgressMonitor, int, Runnable) -
Method in class chemaxon.marvin.io.MDocSource
-
- skipToNext() -
Method in class chemaxon.formats.MolImporter
- Deprecated. As of Marvin 5.0, the record reading/molecule import
separation makes this method unusable
- SM_ATOM -
Static variable in class chemaxon.marvin.beans.MSketchPane
- Atom mode.
- SM_BOND -
Static variable in class chemaxon.marvin.beans.MSketchPane
- Bond mode.
- SM_DELETE -
Static variable in class chemaxon.marvin.beans.MSketchPane
- Delete mode.
- SM_FLAGS_OFF -
Static variable in class chemaxon.marvin.beans.MSketchPane
- Offset of flags in sketch mode.
- SM_MASK -
Static variable in class chemaxon.marvin.beans.MSketchPane
- Sketch mode mask.
- SM_SELECT -
Static variable in class chemaxon.marvin.beans.MSketchPane
- Select mode.
- SM_SELECT_LASSO -
Static variable in class chemaxon.marvin.beans.MSketchPane
- Lasso select mode.
- SMALL_FONT_SIZE -
Static variable in class chemaxon.marvin.space.monitor.Label
-
- smallestRing() -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.smallestRing()
- smallestRingSize() -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.smallestRingSize()
- smallestRingSizeOfAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.smallestRingSizeOfAtom(int)
- smallestRingSystem() -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.smallestRingSystem()
- smallestRingSystemSize() -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Ring.smallestRingSystemSize()
- smaps -
Variable in class chemaxon.reaction.Reaction
- Deprecated. Start map numbers: bond atom1.
- SMARTS -
Static variable in class chemaxon.formats.MFileFormat
- SMARTS.
- SMARTS_H_DAYLIGHT_COMP_MODE -
Static variable in class chemaxon.struc.MolAtom
- Option flag to express daylight-type smarts atom parsing of H.
- SMARTS_H_MARVIN_COMP_MODE -
Static variable in class chemaxon.struc.MolAtom
- Option flag to express marvin-pre-3.5-type smarts atom parsing of H.
- SmartsAtomQuerifier - Class in chemaxon.marvin.io.formats.smiles
- Class for partial interpretation of smarts atoms.
- SmartsAtomQuerifier() -
Constructor for class chemaxon.marvin.io.formats.smiles.SmartsAtomQuerifier
- Creates a new SmartsAtomQuerifier object.
- SMILES -
Static variable in class chemaxon.formats.MFileFormat
- SMILES.
- smiles -
Variable in class chemaxon.jchem.db.UpdateHandler.RowData
-
- SMILESRecognizer - Class in chemaxon.formats.recognizer
- SMILES/SMARTS/CxSMILES/CxSMARTS format recognizer.
- SMILESRecognizer(String) -
Constructor for class chemaxon.formats.recognizer.SMILESRecognizer
- Creates a SMILES, SMARTS, CxSMILES or CxSMARTS format recognizer.
- smol() -
Method in class chemaxon.struc.MoleculeGraph
- Gets a
Smolecule representation of this molecule.
- Smolecule - Interface in chemaxon.struc
- Array-based abstract molecule class.
- SMOOTH_STICKS -
Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- smoothStickColoring -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- SoapServiceDescriptor - Class in chemaxon.marvin.services.soap
- Service descriptor of SOAP type requests.
- SoapServiceDescriptor() -
Constructor for class chemaxon.marvin.services.soap.SoapServiceDescriptor
-
- SOLVENT -
Static variable in class chemaxon.marvin.calculations.MSAPlugin
- Surface area type: 3D solvent accessible surface area.
- sort() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel.LeftListModel
- Sorts the list
- sort(Sgroup[], int) -
Static method in class chemaxon.struc.Sgroup
- Sorts S-groups in parent-child or child-parent order.
- sort() -
Method in class chemaxon.util.IntArray
- Sorts the elements in ascending order.
- SORT_CHILD_PARENT -
Static variable in class chemaxon.struc.Sgroup
- Parent-child sort order.
- SORT_PARENT_CHILD -
Static variable in class chemaxon.struc.Sgroup
- Parent-child sort order.
- sortableFormula -
Variable in class chemaxon.jchem.db.UpdateHandler.RowData
-
- sortBondsAccordingTo(MolBond[]) -
Method in class chemaxon.struc.MoleculeGraph
- Sorts bonds in the same order as they appear in another chemical graph.
- sortBondsAccordingTo(MolBond[]) -
Method in class chemaxon.struc.RgMolecule
- Sort edges in the same order as they appear in the specified array.
- sortBondsAccordingTo(MolBond[]) -
Method in class chemaxon.struc.RxnMolecule
- Sort edges in the same order as they appear in the specified array.
- sortEdgesAccordingTo(MolBond[]) -
Method in class chemaxon.struc.MoleculeGraph
- Deprecated. As of Marvin 5.3, replaced by
MoleculeGraph.sortBondsAccordingTo(MolBond[]).
- sortSgroupXBonds() -
Method in class chemaxon.struc.Molecule
- Sorts superatom S-group crossing bonds in attachment point number
order.
- sortXBonds() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Sorts the crossing bonds in the parent molecule in attachment point
number order.
- SPACEFILL -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Spacefill rendering mode.
- SPACEFILL_RENDERING_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Spacefill rendering mode.
- spacefillPrecision -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- specular -
Static variable in class chemaxon.marvin.space.monitor.Control
-
- SPIN -
Static variable in class chemaxon.marvin.view.ViewParameterConstants
- Identifier of parameter:
"spin".
- SPLASH_SCREEN_IMAGE -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"splashScreenImage".
- splitAllDisconnectedComponents() -
Method in class chemaxon.struc.RxnMolecule
- Replaces all disconnected reaction components by its connected fragments
in the structure array.
- splitComponentParts(MoleculeGraph, int) -
Method in class chemaxon.struc.RxnMolecule
- Finds those component parts that are contained in the molecule graph m and
creates separate components from the fragments contained in m, splitting them from the previous merges.
- splitDisconnectedComponent(long) -
Method in class chemaxon.struc.RxnMolecule
- Replaces a disconnected reaction component by its connected fragments
in the structure array.
- splitDisconnectedComponent(int, int) -
Method in class chemaxon.struc.RxnMolecule
- Replaces a disconnected reaction component by its connected fragments
in the structure array.
- splitFileAndOptions(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Parses "file{options}" strings used in molecule file import.
- splitFormatAndOptions(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Parses "format:options" strings used in molecule file import and export.
- SQL_ERROR -
Static variable in class chemaxon.util.ErrorHandler
-
- sringsize() -
Method in class chemaxon.struc.MolAtom
- Calculate the size of smallest ring containing this atom.
- SST_ALTERNATING -
Static variable in class chemaxon.struc.Sgroup
- Alternating polymer S-group subtype.
- SST_BLOCK -
Static variable in class chemaxon.struc.Sgroup
- Block polymer S-group subtype.
- SST_RANDOM -
Static variable in class chemaxon.struc.Sgroup
- Random polymer S-group subtype.
- ST_ANY -
Static variable in class chemaxon.struc.Sgroup
- Any polymer S-group type.
- ST_COMPONENT -
Static variable in class chemaxon.struc.Sgroup
- Component S-group type.
- ST_COPOLYMER -
Static variable in class chemaxon.struc.Sgroup
- Copolymer S-group type.
- ST_CROSSLINK -
Static variable in class chemaxon.struc.Sgroup
- Crosslink S-group type.
- ST_DATA -
Static variable in class chemaxon.struc.Sgroup
- Data S-group type.
- ST_FORMULATION -
Static variable in class chemaxon.struc.Sgroup
- Formulation S-group type.
- ST_GENERIC -
Static variable in class chemaxon.struc.Sgroup
- Generic S-group type.
- ST_GRAFT -
Static variable in class chemaxon.struc.Sgroup
- Graft S-group type.
- ST_MER -
Static variable in class chemaxon.struc.Sgroup
- Mer S-group type.
- ST_MIXTURE -
Static variable in class chemaxon.struc.Sgroup
- Mixture S-group type.
- ST_MODIFICATION -
Static variable in class chemaxon.struc.Sgroup
- Modification S-group type.
- ST_MONOMER -
Static variable in class chemaxon.struc.Sgroup
- Monomer S-group type.
- ST_MULTICENTER -
Static variable in class chemaxon.struc.Sgroup
- Multicenter S-group type.
- ST_MULTIPLE -
Static variable in class chemaxon.struc.Sgroup
- Multiple group S-group type.
- ST_SRU -
Static variable in class chemaxon.struc.Sgroup
- SRU (Structural Repeating Unit: polymers and
repeating units with repetition ranges) S-group type.
- ST_SUPERATOM -
Static variable in class chemaxon.struc.Sgroup
- Superatom S-group type.
- STANDARD -
Static variable in class chemaxon.marvin.modules.AutoMapper
- good balance between speed and accuracy
- standardize(Molecule) -
Method in class chemaxon.descriptors.MDParameters
- Standardizes the
Molecule and returns the standardized
form.
- standardize(Molecule) -
Method in interface chemaxon.jep.Standardizer
-
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.AlignmentPlugin
-
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Expands sgroups.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Prevents default standardization: does nothing.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Expands sgroups.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Prevents default standardization: does nothing.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Expands sgroups.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.PredictorPlugin
-
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Clears enhanced stereo information.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
- Standardize input molecule
Standardization currently ungroups SGroups
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Standardizes the molecule.
- standardize(Molecule) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Expands sgroups.
- standardize(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Standardizes the molecule by performing the transformations necessary
to run the plugin (aromatize, dehydrogenize, bring nitro groups to
common form, ...).
- standardize() -
Method in class chemaxon.reaction.ConcurrentStandardizerProcessor
- Performs the standardization of the next input molecule, and returns the standardized molecule.
- standardize(Molecule) -
Method in class chemaxon.reaction.Standardizer
- Standardization for one input molecule:
performs the standardization actions according to the XML configuration.
- standardize(Molecule[]) -
Method in class chemaxon.reaction.Standardizer
- Deprecated. Use
Standardizer.standardize(Molecule).
- StandardizedMolSearch - Class in chemaxon.sss.search
- MolSearch subclass that standardizes (e.g. aromatizes) query and target
structures before searching.
- StandardizedMolSearch() -
Constructor for class chemaxon.sss.search.StandardizedMolSearch
- Constructs a StandardizedMolSearch object.
- standardizeIonicGroups(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Default standardization:
nitro groups:
[O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
- standardizeNeutralGroups(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Neutral -> ionic standardization:
[O:1]=[N:2] >> [O-:1][N+:2], [H:3][O:2][N:1] >> [NH1+:1][O-:2]
sulphynil group transformation: [#6][S:1]([#6])=[O:2] >> [#6][S+:1]([#6])[#8-:2]
- standardizer -
Variable in class chemaxon.descriptors.MDParameters
- transform molecules into standard form before descriptor generation
- Standardizer - Interface in chemaxon.jep
- Wrapper interface for chemaxon.reaction.Standardzier class.
- STANDARDIZER -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: Standardizer
- Standardizer - Class in chemaxon.reaction
- Performs the standardization actions determined by the XML config file, or simple config string.
- Standardizer(String) -
Constructor for class chemaxon.reaction.Standardizer
- Constructor.
- Standardizer(File) -
Constructor for class chemaxon.reaction.Standardizer
- Constructor.
- Standardizer(InputStream) -
Constructor for class chemaxon.reaction.Standardizer
- Constructor.
- Standardizer(Element, String) -
Constructor for class chemaxon.reaction.Standardizer
- Constructor.
- Standardizer(Element) -
Constructor for class chemaxon.reaction.Standardizer
- Constructor.
- standardizerConfig -
Variable in class chemaxon.jchem.db.StructureTableOptions
- Custom standardization configuration string (XML or simple action string).
- standardizerConfigurationNode -
Variable in class chemaxon.descriptors.MDParameters
- node defining the Standardizer configuration
- StandardizerException - Exception in chemaxon.reaction
- Standardizer Exception class.
- StandardizerException() -
Constructor for exception chemaxon.reaction.StandardizerException
- Constructs a new exception with
null as its detail message.
- StandardizerException(String) -
Constructor for exception chemaxon.reaction.StandardizerException
- Constructs a new exception with the specified detail message.
- StandardizerException(String, Throwable) -
Constructor for exception chemaxon.reaction.StandardizerException
- Constructs a new exception with the specified detail message and
cause.
- StandardizerException(Throwable) -
Constructor for exception chemaxon.reaction.StandardizerException
- Constructs a new exception with the specified cause and a detail
message of (cause==null ?
- STAR -
Static variable in class chemaxon.struc.MolAtom
- "Atomic number" of the star atom.
- start() -
Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- start(MDocSource, String) -
Method in class chemaxon.marvin.view.swing.TableSupport
- Starts loading molecules.
- start() -
Method in interface chemaxon.util.concurrent.ConcurrentProcessor
- Starts concurrently processing inputs returned by the
InputProducer instance using WorkUnit instances returned
by the WorkUnitFactory instance.
- startEMFGenerator() -
Static method in class chemaxon.util.ImageExportUtil
- Starts the initialization of the .NET based EMF generator on a background
thread.
- startGrabLines() -
Method in class chemaxon.marvin.io.PositionedInputStream
- Starts grabbing lines.
- startNow(MDocSource, String) -
Method in class chemaxon.marvin.view.swing.TableSupport
- Starts loading molecules immediately.
- startPermanentResources() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Starts all the permanent native resources that have to be started to do
fast and reliable copy in Marvin.
- STATICpKaPREFIX -
Static variable in class chemaxon.marvin.calculations.pKaPlugin
- pKa's prefix (acidic/basic) does not depend on the submitted micro state (default)
- STATUS_BAR -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"statusBar".
- step() -
Method in class chemaxon.clustering.LibraryMCS
- Adds one more level to the exsisting cluster hierarchy.
- step() -
Method in class chemaxon.descriptors.GenerateMD
- Fetches one structure from the input source and generates descriptors
as specified before initialization by the setter methods.
- STEP_DEFAULT -
Static variable in class chemaxon.marvin.calculations.AlignmentPlugin
-
- stepWedge() -
Method in class chemaxon.struc.MolBond
- Set the bond from 0 to
MolBond.UP or UP to MolBond.DOWN.
- stepWedge(MolBond[]) -
Static method in class chemaxon.struc.MolBond
- Flip the given bonds to the next state
ONLY 1 bond is set to chiral
starting from the last bond
- stereo(int) -
Method in class chemaxon.calculations.stereo.Stereochemistry
- Calculates absolute stereo configuration of the given atom.
- stereo(int, int) -
Method in class chemaxon.calculations.stereo.Stereochemistry
- Calculates absolute stereo configuration of the given double bond.
- stereo(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Stereochemistry.stereo(int)
- stereo(int, int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Stereochemistry.stereo(int, int)
- STEREO1_MASK -
Static variable in class chemaxon.struc.MolBond
- Single bond stereo mask.
- STEREO2_CARE -
Static variable in class chemaxon.struc.MolBond
- Cis/trans info of this bond is taken care of during
the SSS process if this flag is set - used only for query bonds.
- STEREO_DIASTEREOMER -
Static variable in interface chemaxon.sss.SearchConstants
- The diastereomers targets
of a given query structure are also matched.
- STEREO_ENANTIOMER -
Static variable in interface chemaxon.sss.SearchConstants
- The enantiomer targets
of a given query structure are also matched.
- STEREO_EXACT -
Static variable in interface chemaxon.sss.SearchConstants
- Equality is needed in stereochemistry.
- STEREO_IGNORE -
Static variable in interface chemaxon.sss.SearchConstants
- Stereo information is not considerd during searching.
- STEREO_MASK -
Static variable in class chemaxon.struc.MolBond
- Single and double bond stereo mask.
- STEREO_MODEL_COMPREHENSIVE -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant to use comprehensive stereo model, which combines
the advantages of local and global stereo models.
- STEREO_MODEL_DEFAULT -
Static variable in interface chemaxon.sss.SearchConstants
- For substructure search or query tables this is
SearchConstants.STEREO_MODEL_LOCAL.
- STEREO_MODEL_GLOBAL -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant to use global stereo information (global
parity, global double bond stereo configuration, etc).
- STEREO_MODEL_LOCAL -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant to use local stereo information only (local parity,
local double bond stereo configuration, etc).
- STEREO_SPECIFIC -
Static variable in interface chemaxon.sss.SearchConstants
- Stereo information is considered during searching.
- Stereochemistry - Class in chemaxon.calculations.stereo
- Central class for accessing functions analyzing the topology of a molecule.
- Stereochemistry() -
Constructor for class chemaxon.calculations.stereo.Stereochemistry
-
- stereoClean() -
Method in class chemaxon.struc.MoleculeGraph
- Reset the wedges of the molecule, based on the actual
parity information in 2D remove wedges in 3D.
- stereoClean() -
Method in class chemaxon.struc.RgMolecule
- Reset the wedges of the molecule, based on the actual
parity information in 2D remove wedges in 3D.
- stereoClean() -
Method in class chemaxon.struc.RxnMolecule
- Reset the wedges of the molecule, based on the actual
parity information in 2D remove wedges in 3D.
- StereoConstants - Interface in chemaxon.struc
- Constants for atom parity and double bond stereo.
- stereoDoubleBondCount() -
Method in class chemaxon.calculations.stereo.Stereochemistry
- Calculates the number of stereo double bonds.
- stereoDoubleBondCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Deprecated. as of release 5.5, replaced by
Stereochemistry.stereoDoubleBondCount()
- StereoisomerPlugin - Class in chemaxon.marvin.calculations
- Plugin class for stereoisomer calculation
- StereoisomerPlugin() -
Constructor for class chemaxon.marvin.calculations.StereoisomerPlugin
-
- stericEffectIndex(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates topological steric effect index (TSEI) of an atom from
covalent radii values and topological distances.
- STGRP_ABS -
Static variable in interface chemaxon.struc.StereoConstants
- Absolute stereo group type for enhanced stereo representation.
- STGRP_AND -
Static variable in interface chemaxon.struc.StereoConstants
- AND stereo group type for enhanced stereo representation.
- STGRP_NONE -
Static variable in interface chemaxon.struc.StereoConstants
- Empty stereo group type setting meaning no enhanced stereo label.
- STGRP_OR -
Static variable in interface chemaxon.struc.StereoConstants
- OR stereo group type for enhanced stereo representation.
- STICK_DISTANCE -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"stickdst".
- STICK_THICKNESS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"stickThickness".
- stickRadius -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- STICKS -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Sticks rendering mode.
- STICKS_RENDERING_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Sticks rendering mode.
- stickSlicePrecision -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- stop() -
Method in interface chemaxon.marvin.alignment.AlignmentMoleculeFactory.ProgressBarInterface
-
- stop() -
Method in class chemaxon.sss.search.MolSearch
- Tries to stop the running search as fast as possible.
- stop() -
Method in class chemaxon.sss.search.Search
- Tries to stop the running search as fast as possible.
- STOP_BADARGSINMODFUNC -
Static variable in class chemaxon.marvin.modules.AutoMapper
- bad paramters passed to
modfunc()
- STOP_FOUND -
Static variable in class chemaxon.marvin.modules.AutoMapper
- mapping stopped with an optimal solution
- STOP_NOTFOUND -
Static variable in class chemaxon.marvin.modules.AutoMapper
- no solution found
- STOP_STEPLIMIT -
Static variable in class chemaxon.marvin.modules.AutoMapper
- mapping stopped because maximum allowed step count reached, no optimal solution found
- STOP_TIMELIMIT -
Static variable in class chemaxon.marvin.modules.AutoMapper
- maximum allowed time exceeded, no optimum solution has been found
- STOP_UNKONW -
Static variable in class chemaxon.marvin.modules.AutoMapper
- mapping stopped for an unknown reason
- storageSizeChanged(MDocStorage, int, int) -
Method in interface chemaxon.marvin.view.MDocStorage.Listener
- Storage size changed.
- storageSizeFinalized(MDocStorage) -
Method in interface chemaxon.marvin.view.MDocStorage.Listener
- Final storage size determined.
- store(Element) -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- This method adds the xml representation of ConfigElement to the parent element
- store(Element, String) -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- This method adds the xml representation of ConfigElement to the parent element
with the specified name
- store() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Stores a new result item.
- store(Hashtable<MarkushFeature, int[]>) -
Static method in class chemaxon.sss.search.MarkushTagger
- Converts the feature table returned by
MarkushTagger.getFeatureTable()
or the feature coverage table returned by MarkushTagger.getFeatureCoverageTable()
to String.
- storeDoc(MDocument, int, String) -
Method in class chemaxon.marvin.view.MDocStorage
- Store new document and free the oldest accessed if the number of
documents is too much to fit in memory.
- storeDrawProperty(String, String) -
Method in class chemaxon.marvin.space.GraphicComponent
- Stores the given property.
- storeMainDoc(MDocument, int) -
Method in class chemaxon.marvin.view.MDocStorage
- Store new document and free the oldest accessed if the number of
documents is too much to fit in memory.
- storeTemporaryObject(String, Object) -
Method in class chemaxon.struc.MolAtom
- Stores an object temporarily.
- storeValuesToProperties(Properties) -
Method in class chemaxon.util.ConnectionHandler
-
- stringBuffer -
Variable in class chemaxon.marvin.io.MolExportModule
- This buffer can contain the molecule file contents, in case of a
text format.
- stringToArray(String, String, int, int) -
Static method in class chemaxon.marvin.io.MPropHandler
-
- stringToPage(String) -
Static method in class chemaxon.util.HTMLTools
- Creates an HTML page that displays the specified
HTML text.
- stringToScalar(String, String) -
Static method in class chemaxon.marvin.io.MPropHandler
-
- stringValue() -
Method in class chemaxon.struc.prop.MStringProp
- Gets the string value.
- StrucFPConfig - Class in chemaxon.sss.screen
- Utility class for assembling and parsing structural FP configurations.
- StrucFPConfig() -
Constructor for class chemaxon.sss.screen.StrucFPConfig
-
- STRUCTURAL_FRAMEWORKS_PLUGIN -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: Structural Frameworks Plugin
- StructuralFrameworksPlugin - Class in chemaxon.marvin.calculations
- Plugin class to calculate Bemis-Murcko and other structural scaffolds of input
molecules.
- StructuralFrameworksPlugin() -
Constructor for class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- StructuralFrameworksPlugin.FrameworkTypes - Enum in chemaxon.marvin.calculations
- FrameworkTypes represents the available calculations
- StructuralFrameworksPlugin.VerbosePrinter - Interface in chemaxon.marvin.calculations
- Verbose printer specification
- structuralKeyConfig -
Variable in class chemaxon.jchem.db.StructureTableOptions
- A structural key configuration.
- structure -
Variable in class chemaxon.naming.DocumentExtractor.Hit
- The chemical structure corresponding to the name.
- STRUCTURE_CHECKER -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: Structure Checker
- STRUCTURE_TO_NAME -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: Structure to Name
- StructureChecker - Interface in chemaxon.checkers
- General interface describing functions that are available for a chemical structure checker.
- StructureCheckerErrorType - Enum in chemaxon.checkers
- Enum containing possible error types for structure checkers.
- StructureCheckerResult - Interface in chemaxon.checkers.result
- An instance of
StructureCheckerResult identifies a molecule problem - structureColumnType -
Variable in class chemaxon.jchem.db.StructureTableOptions
- Specifies the type of the
cd_structure column.
- StructureFixer - Interface in chemaxon.fixers
- A
StructureFixer can fix a Molecule problem identified by a
StructureCheckerResult - StructureTableOptions - Class in chemaxon.jchem.db
- Class for storing options for structure table creation.
- StructureTableOptions() -
Constructor for class chemaxon.jchem.db.StructureTableOptions
-
- SUBFORMULA -
Static variable in class chemaxon.sss.formula.FormulaSearch
- Constant value specifying the sub formula search type.
- substring(int) -
Method in class chemaxon.struc.graphics.MTextDocument.Section
- Gets a substring.
- substring(int, int) -
Method in class chemaxon.struc.graphics.MTextDocument.Section
- Gets a substring.
- substring(int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets a substring of the document.
- substring(int, int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets a substring of the document.
- SUBSTRUCTURE -
Static variable in interface chemaxon.sss.SearchConstants
- Substructure search that applies both
screening and atom-by-atom search.
- subtract(DPoint3) -
Method in class chemaxon.struc.DPoint3
- Subtract the given v2 vector from this one.
- SUM_OF_VALUES -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Will the sum of the affecting properties be mapped onto the surface.
- sumConservedQuantities(MolAtom, int[], int) -
Method in class chemaxon.struc.MoleculeGraph
- For internal use only.
- sumConservedQuantities(MolAtom, int[], int) -
Method in class chemaxon.struc.RgMolecule
- For internal use only.
- sumDistanceSquare(MoleculeGraph, DPoint3) -
Static method in class chemaxon.marvin.util.CleanUtil
- Calculates the sum of the distance square for each atom from a point.
- sumNonEmptyPercent -
Variable in class chemaxon.descriptors.MDGenerator
-
- SuperatomSgroup - Class in chemaxon.struc.sgroup
- Superatom S-group.
- SuperatomSgroup(Molecule) -
Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
- Constructs a superatom S-group in expanded state.
- SuperatomSgroup(Molecule, boolean) -
Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
- Constructs a superatom S-group.
- SuperatomSgroup(SuperatomSgroup, Molecule, Sgroup, int[]) -
Constructor for class chemaxon.struc.sgroup.SuperatomSgroup
- Copy constructor.
- superGraph -
Variable in class chemaxon.struc.MoleculeGraph
- Parent of all parents.
- SUPERSTRUCTURE -
Static variable in interface chemaxon.sss.SearchConstants
- Superstructure search (Value=6)
- SURE -
Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
- Line is surely in the given format.
- SURE -
Static variable in class chemaxon.formats.recognizer.PDBRecognizer
- Line is surely in the given format.
- SURFACE_COLOR_GRID_MAPPING -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_PROPERTY_MAPPING -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_ATOMTYPE -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_B_FACTOR -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_CHAIN -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_CONSTANT -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_EP -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_RAINBOW -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_RESIDUE -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_COLOR_TYPE_SS -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_SIMPLIFICATION_ENABLED -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_SMOOTHNESS -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_TYPE_BLOBBY -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_TYPE_CONNOLLY -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_TYPE_GAUSSIAN -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_TYPE_SAS -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SURFACE_TYPE_VDW -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SurfaceColoring - Class in chemaxon.marvin.space
- SurfaceColoring is an easy-to-use tool to map different properties as colors
onto surfaces.
- SurfaceColoring(SurfaceComponent) -
Constructor for class chemaxon.marvin.space.SurfaceColoring
- The given surface is to be colored after the parametrization.
- SurfaceColoring(ArrayList, SurfaceComponent) -
Constructor for class chemaxon.marvin.space.SurfaceColoring
- The given surface of the given molecules is to be colored after the parametrization.
- SurfaceColoring(ArrayList, SurfaceComponent, float) -
Constructor for class chemaxon.marvin.space.SurfaceColoring
- The given surface of the given molecules is to be colored after the parametrization.
- surfaceColorType -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- SurfaceComponent - Class in chemaxon.marvin.space
- Class that represents a surface defined by its vertices, normal vectors and
polygons.
- SurfaceComponent(int) -
Constructor for class chemaxon.marvin.space.SurfaceComponent
- Creates a new instance of SurfaceComponent, sets its draw type to
FILLED_TYPE.
- SurfaceComponent(int, int) -
Constructor for class chemaxon.marvin.space.SurfaceComponent
- Creates a new SurfaceComponent, sets its draw type to
FILLED_TYPE.
- SurfaceComponent(int, int, int, int) -
Constructor for class chemaxon.marvin.space.SurfaceComponent
- Creates a new SurfaceComponent, sets its draw type to
FILLED_TYPE.
- surfaceGridPrecision -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- surfaceOf(GraphicComponent) -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Tells whether it is the molecular surface of the given component (molecule).
- surfaceSimplification() -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- Runs the (might be time-consuming) algorithm thst reduces the number of triangles
of the surface.
- surfaceSimplificationEnabled -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- surfaceSimplificationTolerance -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- surfaceSmoothnessFactor -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- surfaceType -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- svFuzzyIncrements -
Variable in class chemaxon.descriptors.PFParameters
- Fuzzy smoothing values for smoothing with user defined smoothing vector.
- SVG -
Static variable in class chemaxon.formats.MFileFormat
- Scalable Vector Graphics.
- swap() -
Method in class chemaxon.struc.MolBond
- Change orientation.
- swapAtoms(int, int) -
Method in class chemaxon.struc.SelectionMolecule
- Swap two atoms.
- swapHeadTail() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Swaps the head and tail bonds of this sru if both are set.
- SwingUtil - Class in chemaxon.marvin.util
- Swing utility functions.
- SwingUtil() -
Constructor for class chemaxon.marvin.util.SwingUtil
-
- SYBYLMOL -
Static variable in class chemaxon.formats.MFileFormat
- Tripos SYBYL molfiles.
- SYM_CX -
Static variable in class chemaxon.struc.MolAtom
- Atom symbol string for CxSMILES export.
- SYM_EXPLH -
Static variable in class chemaxon.struc.MolAtom
- Atom symbol string contains explicit H count if this flag is set.
- SYM_IMPLH -
Static variable in class chemaxon.struc.MolAtom
- Atom symbol string contains implicit H count is shown flag is set.
- SYM_MOLEX -
Static variable in class chemaxon.struc.MolAtom
- Atom symbol string for Molfile export.
- SYM_NEUTRAL -
Static variable in class chemaxon.struc.MolAtom
- Atom symbol string does not contain the charge if this flag is set.
- SYM_SMARTS -
Static variable in class chemaxon.struc.MolAtom
- Atom symbol string for SMILES export.
- SYM_SQBRACKETS -
Static variable in class chemaxon.struc.MolAtom
- Atom symbol is shown in square brackets if this flag is set.
- symbolOf(int) -
Static method in class chemaxon.struc.MolAtom
- Gets the element symbol for the specified atomic number.
- symbolOf(int, int) -
Static method in class chemaxon.struc.MolAtom
- Gets the special element symbol for the specified atomic and mass
numbers.
- SYN -
Static variable in interface chemaxon.struc.StereoConstants
- Non-CIP stereodescriptor, syn (relative configuration).
- szegedIndex() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the Szeged index of the molecule.
"tabScale".
"templateToolbarCustomizable".
"tmpls".
LibraryMCS.step()
AtomChecker detecting atoms having non-zero Z coordinates.MolecularDescriptor
object.
MolExporter.exportToBinFormat(Molecule, String)
BCUT object into a byte array.
CustomDescriptor object into a byte array.
ECFP object into a byte array.
MolecularDescriptor instance into an external format that
can be stored in a database.
PharmacophoreFingerprint object into a byte array.
ScalarDescriptor object into an array of bytes.
BCUT descriptor into a tab separated string.
ECFP fingerprint into a tab separated string.
MolecularDescriptor
object.
ECFP.toIdentiferSet().
BCUT descriptor
object.
CustomDescriptor
object.
ECFP fingerprint
object.
MolecularDescriptor
object.
MolecularDescriptor
object.
MolExporter.exportToFormat(Molecule, String)
Integer identifiers.
int identifiers.
MolExporter.exportToObject(Molecule, String)
"toolbarFloatable".
"ttmpls".
MolecularDescriptor
object.
CompnentElement.
Transferable which represents the clipboard data.
"transferButtonIcon".
"transferButtonText".
"transferButtonVisible".
TransferableDescriptor object.
AtomChecker detecting reaction schemes having more atoms
on one side of the reaction arrow than on the other."undetachByX".
"undo".
AbstractStructureFixer which ungroups all abbreviated groups
in the moleculecd_" prefix in their names) and
additional columns can be set using the class.null as its detail message.
JChemProperties table.
Updater.Updater(ConnectionHandler), but adds the ability for
the user to specify a list of tables to which to restrict the operation
of this Updater.
pKaPlugin.setCorrectionLibrary(String)
"usedJars".
"valenceCheckEnabled".
"valenceErrorVisible".
"valenceErrorVisibleInView".
"valencePropertyVisible".
MolAtom.valenceCheck().
AtomChecker detecting atoms with invalid valences.AbstractStructureFixer which fixes valence problem in the
molecule if it is possible with removing explicit hydrogens or by adding chargeAtomChecker detecting atoms having an
explicitly set valence property."viewAnyBond".
"viewCarbonVisibility".
"viewHelp".
"viewLigandOrderVisibility".
"viewonly".
"viewQuickHelp".
"visibleCols".
"visibleRows".
JChemSearch.RUN_MODE_ASYNCH_PROGRESSIVE.
BondChecker detecting double bonds havong wiggly bond ligands representing
unspecified double bond stereo configuration.AbstractStructureFixer which sets wiggly bond to crossed double bond"winScale".
"wireThickness".
Callable which returns a result in function of an input.WorkUnit instances.Molecules or not.
String
ConfigurationReader which can read CheckerRunner
configuration described ChemAxon's own
checker configuration XML format (schema in jar:
chemaxon/checkers/runner/configuration/reader/resoruce/checkerconfiguation.xsd)XMLBasedConfigurationReader instance with the given inputSteam with the configuration
ServiceDescriptor implementation for XML-RPC services.calculateXYZ() methods (in PharmacophoreFingerprint sub-classes) calculate
three numbers
(denoted by x,y and z), but methods in java cannot have output parameters.
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