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Smolecule.A_PARITY|Smolecule.A_CHIRALITY"abbrevgroups".
AbstractStructureChecker for detecting abbreviated groups."absLabelVisible" or "absLabel".
StructureFixer implementation which removes absolute stereo property from the molecule.ConfigElementEditor implementation with customizable
editor component.ConfigElement using MSketchPane as an external editor
by implementing ExternalEditorSupport interface.StructureFixer interfacetrue if molecule is accepted by the filter.
"addRemoveHatomsEnabled".
mainPanel
MDSet object.
PropertyChangeListener for element property changes
PropertyChangeListener for a specific element property change
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.
null, the property is deleted.
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.
TransferableDescriptor to the registry, and constructing it
by the given parameters.
Alchemist wizard frame
Alchemist wizard frame
Alchemist wizards.Alchemist wizard pagesAlchemist and AlchemistApplication
with fading capabilitiesAlchemist or AlchemistApplication
For internal use only!AlchemistProfile
ConfigElements or ConfigElementEditors implementing this
interface can store and restore persistent properties via ConfigBuilderPanelAlchemist wizard
For internal use only!AlchemistProgressLabel with given text and id
AlchemistProgressLabel with given text, id and
custom action
AbstractStructureChecker for detecting atoms with
aliases."animate".
"animDelay".
"animFPS".
"animSync".
DefaultStructureCheckerResult for identifying aromaticity problems, thus errorType property is StructureCheckerErrorType.AROMATICITYStructureCheckerErrorType.AROMATICITY by default.
MDocSource implementation for an array of documents or molecules."atomFont".
"atomMappingVisible".
"atomNumbersVisible".
"atomSet".
"atomSetColor".
"atomsize".
"atomStrings".
"atomSymbolsVisible".
AtomChecker for detecting atom maps.AtomProperty class provides access to chemical properties of
Molecule atoms by atom index.AtomChecker for detecting atoms with atom value.AbstractStructureChecker for detecting attached data in the moleculeMolAtom.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.setAttach(int).
MolAtom.setAttach(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."background".
"ballRadius".
BasicConfigElement objectsBCUT descriptor.BCUT descriptor generator object.
BCUT descriptor class."bondDraggedAlong".
"bondLengthVisible".
"bondSet".
"bondSetColor".
"bondSpacing".
BondChecker for checking incorrect bond angles in the moleculeComponentChecker for detecting bond problemsBondChecker for detecting bonds with incorrect length."border".
"buttonmenubar".
"cacheMols".
calcDissimilarity().
while(!
- calculate(int[]) -
Method in class chemaxon.util.MolAligner
-
- CALCULATIONS_PACK -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: Calculations Pack
- CalculatorPlugin - Class in chemaxon.marvin.plugin
- Common base class for calculator plugins.
- CalculatorPlugin() -
Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
- Constructor.
- CalculatorPluginDisplay - Class in chemaxon.marvin.plugin
- Common base class for calculator plugin displays.
- CalculatorPluginDisplay() -
Constructor for class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- CalculatorPluginOutput - Class in chemaxon.marvin.plugin
- Class providing plugin output in table form.
- CalculatorPluginOutput() -
Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
- Default constructor.
- CalculatorPluginOutput(CalculatorPlugin) -
Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
- Constructor that sets plugin.
- calcWidth() -
Method in class chemaxon.struc.MoleculeGraph
- Calculates the molecule width.
- call() -
Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
- Performs the calculation and returns the result
returned by
PluginWorkUnit.getResult().
- call() -
Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
- Performs the calculation and returns the result
returned by
ReusablePluginWorkUnit.getResult().
- call() -
Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnit
- Performs the work unit tasks in a linear fashion, one after the other.
- callback(String, Object) -
Method in class chemaxon.jep.ChemContext
- Implements
CallbackIface.
- callback(String, Object) -
Method in class chemaxon.jep.ChemJEP
- Delegates
CallbackIface.callback(String, Object)
to the context.
- callback(String, Object) -
Method in class chemaxon.jep.context.AtomContext
- Implements
CallbackIface.
- callback(String, Object) -
Method in class chemaxon.jep.context.MolContext
- Implements
CallbackIface.
- callback(String, Object) -
Method in class chemaxon.jep.context.ReactionContext
- Implements
CallbackIface.
- callback(String, Object) -
Method in class chemaxon.jep.context.SearchContext
- Implements
CallbackIface.
- callback(String, Object) -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- callback(String, Object) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Callback function to make avoiding direct calls easier.
- CAN_BE -
Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
- Line can be in the given format.
- CAN_BE -
Static variable in class chemaxon.formats.recognizer.PDBRecognizer
- Line can be in the given format.
- canBe1LetterPeptide(String) -
Static method in class chemaxon.formats.recognizer.PeptideRecognizer
- Tests whether a string can be one-letter-abbreviated
peptide name.
- canBe3LetterPeptide(String) -
Static method in class chemaxon.formats.recognizer.PeptideRecognizer
- Tests whether a string can be three-letter-abbreviated
peptide name.
- canBeAbbrevgroup(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Deprecated. as of Marvin 5.0,
AbbrevGroupRecognizer.testLine(String)
must be used instead
- canBeBase64(String) -
Static method in class chemaxon.formats.recognizer.Base64Recognizer
- Tests whether a string can be base64 encoded data.
- canBeBase64Line(String) -
Static method in class chemaxon.formats.recognizer.Base64Recognizer
- Tests whether a string can be base64 encoded data line.
- canBeChime(String) -
Static method in class chemaxon.formats.recognizer.ChimeRecognizer
- Tests whether a string can be Chime.
- canBeCT(int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Determines whether the bond between the specified atoms can be a
CIS/TRANS or not.
- canBeCT(int, int, boolean) -
Method in class chemaxon.struc.MoleculeGraph
- Determines whether the bond between the specified atoms can be a
CIS/TRANS or not.
- canBeJTF(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Deprecated. as of Marvin 5.0,
JTFRecognizer.canBeJTFHeader(String)
must be used instead
- canBeJTFHeader(String) -
Static method in class chemaxon.formats.recognizer.JTFRecognizer
- Determines if a String is valid as the first line of a JTF file.
- canBePDBRecord(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Deprecated. as of Marvin 5.0,
PDBRecognizer.testRecord(String)
must be used instead
- canBeReactionComponent() -
Method in class chemaxon.struc.Molecule
- Tests whether an object of this class can be a reaction component.
- canBeReactionComponent() -
Method in class chemaxon.struc.RgMolecule
- Tests whether an object of this class can be a reaction component.
- canBeReactionComponent() -
Method in class chemaxon.struc.RxnMolecule
- Tests whether an object of this class can be a reaction component.
- canBeSMARTS(String) -
Static method in class chemaxon.formats.recognizer.SMILESRecognizer
- Tests whether a string can be SMARTS.
- canBeSMILES(String) -
Static method in class chemaxon.formats.recognizer.SMILESRecognizer
- Tests whether a string can be SMILES.
- cancel() -
Method in interface chemaxon.checkers.runner.CheckerRunner
- Stops the background thread
- cancel() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
-
- cancel() -
Method in class chemaxon.jchem.db.Importer
- Stops the importing progress.
- cancel() -
Method in class chemaxon.metabolizer.MetabolizerUtilities
- Stops the calculation
- cancel() -
Method in interface chemaxon.util.Cancelable
-
- CANCEL_ACTION -
Variable in class chemaxon.alchemist.AlchemistController
- Cancel Action
- CANCEL_MOLECULE_EDIT_ACTION -
Variable in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor
- This method cancels performed molecule modification action
- Cancelable - Interface in chemaxon.util
- Represents a task/operation that can be cancelled.
- cancelChanges() -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor
- Cancel Changes action handler
- canceled -
Variable in class chemaxon.alchemist.AlchemistTask
- flag indicates task is canceled
- canceled() -
Method in class chemaxon.alchemist.configbuilder.AbstractSketchConfigElement
- This method is called after 'cancel' button pressed on external sketch editor.
- cancelPressed() -
Method in class chemaxon.alchemist.AlchemistController
- This method is called when cancel button is pressed
- canImport(JComponent, DataFlavor[]) -
Method in class chemaxon.alchemist.configbuilder.ConfigElementTransferHandler
-
- canRepeat() -
Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
-
- canRepeat() -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
- canRepeat() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if repeatedly running the same plugin object
while getting the results on the GUI is allowed, false otherwise.
- capacity() -
Method in class chemaxon.util.IntArray
- Returns the current capacity of this IntArray.
- carboaliphaticRingCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of carboaliphatic rings in the molecule (aliphatic
rings containing carbon atoms only).
- carboaromaticRingCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of carboaromatic rings in the molecule (aromatic
rings containing carbon atoms only).
- CARBON_VIS_INCHAIN -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Carbon-visibility is switched on in chain.
- CARBON_VIS_INCHAIN_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- String constant for switching on carbon-visibility in chain.
- CARBON_VIS_MASK -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Carbon-visibility mask.
- CARBON_VIS_OFF -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Carbon-visibility is switched off.
- CARBON_VIS_OFF_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- String constant for switching off carbon-visibility.
- CARBON_VIS_OFFSET -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Carbon-visibility offset.
- CARBON_VIS_ON -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Carbon-visibility is switched on.
- CARBON_VIS_ON_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- String constant for switching on carbon-visibility.
- CARBON_VIS_STYLES -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Array of carbon-visibility styles.
- carboRingCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of carbocyclic rings in the molecule (rings
containing carbon atoms only).
- carboRingCount(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of carbocyclic rings in the molecule (rings
containing at least a non-carbon atom).
- carboRings() -
Method in class chemaxon.calculations.TopologyAnalyser
- Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only).
- carboRings(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Identifies carbocyclic rings in the molecule (rings containing carbon
atoms only) having the given number of atoms.
- CARTRIDGE -
Static variable in class chemaxon.license.LicenseManager
- Identifier of product: JChem Cartridge
- cartridgeIndexTable -
Variable in class chemaxon.jchem.db.StructureTableOptions
- For internal use only.
- CATIONIC_TYPE -
Static variable in class chemaxon.marvin.space.PharmacophorePoint
-
- cbs -
Variable in class chemaxon.fragmenter.Fragmenter
- The CutBondSearch objects corresponding to the reactions.
- CCLENGTH -
Static variable in class chemaxon.struc.MolBond
- Default bond length.
- CDParameters - Class in chemaxon.descriptors
- Manages parameters the
CustomDescriptor class. - CDParameters() -
Constructor for class chemaxon.descriptors.CDParameters
- Creates an empty object.
- CDParameters(int) -
Constructor for class chemaxon.descriptors.CDParameters
- Creates an empty object of the given type.
- CDParameters(File) -
Constructor for class chemaxon.descriptors.CDParameters
- Creates a new descriptor configured from the given file.
- CDParameters(String) -
Constructor for class chemaxon.descriptors.CDParameters
- Creates a new object based on a given configuration string.
- CDX -
Static variable in class chemaxon.formats.MFileFormat
- ChemDraw CDX file.
- CDX_TRANSFERABLE_NAME -
Static variable in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- CDX Transfer name and identifier.
- CEdge - Interface in chemaxon.struc
- Deprecated. as of Marvin 5.3, please use
MolBond instead - CELL -
Static variable in class chemaxon.marvin.view.ViewParameterConstants
- Identifier of parameter:
"cell".
- CELL_RANGE -
Static variable in class chemaxon.marvin.space.GraphicScene
-
- CellOrComponentId - Class in chemaxon.marvin.space
- Class to identify cells and components.
- CellOrComponentId(int) -
Constructor for class chemaxon.marvin.space.CellOrComponentId
- Creates a cell id.
- CellOrComponentId(int, int) -
Constructor for class chemaxon.marvin.space.CellOrComponentId
- Creates an id.
- cellSize -
Variable in class chemaxon.descriptors.MDParameters
- size - number of bits - of one descriptor cell
- CELLSIZE -
Static variable in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- The default viewer cell size.
- cellwiseWeights -
Variable in class chemaxon.descriptors.MDParameters
- is cell weights for parametrized metrics
- center -
Variable in class chemaxon.marvin.space.monitor.Control
-
- center -
Variable in class chemaxon.marvin.space.monitor.DihedralControl
-
- centerx() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the x coordinate of the center of the box.
- centery() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the y coordinate of the center of the box.
- centerz() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the z coordinate of the center of the box.
- CFGenerator - Class in chemaxon.descriptors
- The
CFGenerator class generates topological fingerprints
of molecular graphs. - CFGenerator(Standardizer, int) -
Constructor for class chemaxon.descriptors.CFGenerator
- Deprecated. since 2.2
- CFGenerator(int) -
Constructor for class chemaxon.descriptors.CFGenerator
- Creates a new instance of
CFGenerator which can be used to
generate chemical fingerprints for an arbitrary number of molecules.
- CFNS -
Static variable in class chemaxon.jep.context.AtomContext
- The context function names.
- CFNS -
Static variable in class chemaxon.jep.context.MolContext
- The context function names.
- CFNS -
Static variable in class chemaxon.jep.context.ReactionContext
- The context function names.
- CFNS -
Static variable in class chemaxon.jep.context.SearchContext
- The context function names.
- CFParameters - Class in chemaxon.descriptors
- Manages fingerprint parameters.
- CFParameters() -
Constructor for class chemaxon.descriptors.CFParameters
- Creates an empty object.
- CFParameters(File) -
Constructor for class chemaxon.descriptors.CFParameters
- Creates a new object based on a given configuration file.
- CFParameters(String) -
Constructor for class chemaxon.descriptors.CFParameters
- Creates a new object based on a given configuration string.
- cfphistogram -
Static variable in class chemaxon.descriptors.ChemicalFingerprint
-
- CGraph - Interface in chemaxon.struc
- Deprecated. as of Marvin 5.3, please use
MoleculeGraph instead - chainAtomCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of chain atoms in the molecule excluding hydrogens.
- chainBondCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of chain bonds in the molecule excluding bonds of
hydrogen atoms.
- changeColorMapperColors(int) -
Method in class chemaxon.marvin.space.SurfaceColoring
- Switches to another built-in color palette and leaves minimum, maximum
and cutoff values unchanged.
- CHANGING -
Static variable in class chemaxon.marvin.modules.AutoMapper
- Only those atoms are mapped that have chaning bond.
- charAt(int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets a character of the document.
- CHARGE_MATCHING_DEFAULT -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant for default charge searching (charged query
matches only charged target, noncharged query matches all).
- CHARGE_MATCHING_EXACT -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant for exact charge searching (charged query
matches only charged target, noncharged query only matches noncharged).
- CHARGE_MATCHING_IGNORE -
Static variable in interface chemaxon.sss.SearchConstants
- Option value constant for ignore charge searching (charge information
is ignored during searching).
- CHARGE_ON_ATOMS -
Static variable in class chemaxon.struc.Sgroup
- Charge is located on atoms and displayed on atoms.
- CHARGE_ON_GROUP -
Static variable in class chemaxon.struc.Sgroup
- Charge is located on atoms but displayed on the whole group (bracket).
- CHARGE_PLUGIN_GROUP -
Static variable in class chemaxon.license.LicenseManager
- Identifier of plugin: Charge Plugin Group
- CHARGED_H -
Static variable in class chemaxon.struc.MolAtom
- Include charged Hydrogen atom(s).
- ChargePlugin - Class in chemaxon.marvin.calculations
- Plugin class for partial charge calculation.
- ChargePlugin() -
Constructor for class chemaxon.marvin.calculations.ChargePlugin
- Constructor.
- check(Molecule) -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.AliasChecker
-
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.AtomMapChecker
- Detects atom of the molecule has atom map.
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.AtomValueChecker
- Detects if the current atom of the molecule has atom value.
- check(Molecule, MolBond) -
Method in class chemaxon.checkers.BondAngleChecker
-
- check(Molecule, MolBond) -
Method in class chemaxon.checkers.BondLengthChecker
-
- check(Molecule, E) -
Method in class chemaxon.checkers.ComponentChecker
- Checks if the component with index i has problem
- check(Molecule, MolBond) -
Method in class chemaxon.checkers.CrossedDoubleBondChecker
- Examines if the bond is a crossed double bond.
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.IsotopeChecker
-
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.MissingAtomMapChecker
- Check the atom of the molecule with index i has no atom map.
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.MultiCenterChecker
-
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.OverlappingAtomsChecker
- Examines if an atom is closer to another than the given distance limit.
- check(Molecule, MolBond) -
Method in class chemaxon.checkers.OverlappingBondsChecker
- Detects bond of the molecule is crossing another bond or closer than the limit distance.
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.PseudoAtomChecker
-
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.QueryAtomChecker
- Detects atom of the molecule is a query atom.
- check(Molecule, MolBond) -
Method in class chemaxon.checkers.QueryBondChecker
-
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.RadicalChecker
- Detects if the current atom has free electrons.
- check() -
Method in interface chemaxon.checkers.runner.CheckerRunner
- Invoke a background thread which will run all checkers on the given molecule
- check() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
-
- check(Molecule) -
Method in interface chemaxon.checkers.StructureChecker
- Detects a specific error in the molecule.
- check(Molecule, MolAtom) -
Method in class chemaxon.checkers.ThreeDimensionChecker
-
- check(Molecule) -
Method in interface chemaxon.jep.MolCondition
- Deprecated. Returns
true if molecule should be processed,
false otherwise.
- check1(Molecule) -
Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
- check1(Molecule) -
Method in class chemaxon.checkers.AbstractStructureChecker
-
- check1(Molecule) -
Method in class chemaxon.checkers.AttachedDataChecker
- Detects attached data in the molecule
- check1(Molecule) -
Method in class chemaxon.checkers.BondAngleChecker
-
- check1(Molecule) -
Method in class chemaxon.checkers.BondLengthChecker
-
- check1(Molecule) -
Method in class chemaxon.checkers.ComponentChecker
- Iterate through the components and check every component.
- check1(Molecule) -
Method in class chemaxon.checkers.MoleculeChargeChecker
- Detects if molecule has charge
- check1(Molecule) -
Method in class chemaxon.checkers.ReactionChecker
-
- check1(Molecule) -
Method in class chemaxon.checkers.WigglyDoubleBondChecker
-
- checkAndWait() -
Method in interface chemaxon.checkers.runner.CheckerRunner
- Execute all the checker instances on the given molecule and return a
List of StructureCheckerResult
which contains all the identified problems
- checkAndWait() -
Method in class chemaxon.checkers.runner.CheckerRunnerImpl
-
- checkBeforeSave(Properties, Vector<String>) -
Method in class chemaxon.marvin.common.UserSettings
- Compares current user preferences file contents with settings stored in
this object.
- checkBondConsistency() -
Method in class chemaxon.struc.MoleculeGraph
-
- checkBondConsistency() -
Method in class chemaxon.struc.SelectionMolecule
- Empty implementation, edge consistency is not checked in case of
selections.
- CheckBoxList - Class in chemaxon.alchemist.utils
-
- CheckBoxList() -
Constructor for class chemaxon.alchemist.utils.CheckBoxList
-
- CheckBoxList.CellRenderer - Class in chemaxon.alchemist.utils
-
- CheckBoxList.CellRenderer() -
Constructor for class chemaxon.alchemist.utils.CheckBoxList.CellRenderer
-
- checkChemTermColValue(Object) -
Static method in class chemaxon.jchem.db.UpdateHandler
-
- checkConsistency() -
Method in class chemaxon.struc.Molecule
- Checks the internal consistency of the structure.
- checkConsistency() -
Method in class chemaxon.struc.MoleculeGraph
- Checks the internal consistency of the structure.
- checkConsistency() -
Method in class chemaxon.struc.RgMolecule
- Checks the internal consistency of the structure.
- checkDocumentVersion(String, String) -
Method in class chemaxon.descriptors.MDParameters
- Checks if the document is the right version
- checkError() -
Method in class chemaxon.util.ErrorHandler
- Throws the exception stored in the object.
- CheckerRunner - Interface in chemaxon.checkers.runner
- The descendant of CheckerRunner interface have to provide the functionality to run
StructureChecker instances automatically
on the given molecule and fixes the problems with the associated StructureFixer instances
Exmaple:
CheckerRunner can be used directly with checkAndWait method. - CheckerRunnerImpl - Class in chemaxon.checkers.runner
- The default implementation of
CheckerRunner interface. - CheckerRunnerImpl(ConfigurationReader) -
Constructor for class chemaxon.checkers.runner.CheckerRunnerImpl
- Initiate a
CheckerRunnerImpl instance which will can execute StructureChecker instances read from
configurationReader
- checkException() -
Method in class chemaxon.util.ErrorHandler
- Throws the exception stored in the object.
- checkFilter(String) -
Static method in class chemaxon.sss.search.MolSearch
- Checks the syntax of the filtering expression.
- checkFilter(String, File) -
Static method in class chemaxon.sss.search.MolSearch
- Checks the syntax of the filtering expression.
- checkLicense() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Checks the input molecule.
- checkRlogicRange(int, String) -
Method in class chemaxon.struc.RgMolecule
- Checks an R-logic occurence range string for syntax errors
and returns a "normalized" string.
- checkSgroupConsistency() -
Method in class chemaxon.struc.Molecule
- Checks the internal consisitency of S-groups.
- checkSgroupConsistency() -
Method in class chemaxon.struc.RgMolecule
- Checks the consistency of S-groups.
- checkSgroupConsistency() -
Method in class chemaxon.struc.RxnMolecule
- Checks the consistency of S-groups.
- checkType(String, String[]) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Checks result types.
- checkValidity(MDocument, Collection<MolAtom>) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) -
Method in class chemaxon.struc.graphics.MPolyline
- Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) -
Method in class chemaxon.struc.MObject
- Is it a valid object in the document?
- CHEMAXON -
Static variable in class chemaxon.marvin.modules.AutoMapper
- Reaction is mapped according to ChemAxon's style.
- chemaxon.alchemist - package chemaxon.alchemist
-
- chemaxon.alchemist.commonpages - package chemaxon.alchemist.commonpages
-
- chemaxon.alchemist.configbuilder - package chemaxon.alchemist.configbuilder
-
- chemaxon.alchemist.utils - package chemaxon.alchemist.utils
-
- chemaxon.calculations - package chemaxon.calculations
- Contains chemical computation modules.
- chemaxon.checkers - package chemaxon.checkers
-
- chemaxon.checkers.result - package chemaxon.checkers.result
-
- chemaxon.checkers.runner - package chemaxon.checkers.runner
-
- chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader
-
- chemaxon.clustering - package chemaxon.clustering
- Provides classes for clustering.
- chemaxon.descriptors - package chemaxon.descriptors
- Classes for virtual screening using Molecular Descriptors.
- chemaxon.descriptors.scalars - package chemaxon.descriptors.scalars
-
- chemaxon.fixers - package chemaxon.fixers
-
- chemaxon.formats - package chemaxon.formats
-
Provides miscellaneous utility classes for converting between various
molecule file formats, importing structures, and compressing Molfiles.
- chemaxon.formats.recognizer - package chemaxon.formats.recognizer
-
Provides classes to recognize files of various file formats.
- chemaxon.fragmenter - package chemaxon.fragmenter
-
- chemaxon.jchem.db - package chemaxon.jchem.db
- Provides classes for database operations.
- chemaxon.jchem.file - package chemaxon.jchem.file
-
- chemaxon.jchem.version - package chemaxon.jchem.version
-
- chemaxon.jchem.webservice - package chemaxon.jchem.webservice
-
- chemaxon.jep - package chemaxon.jep
- Chemical Terms Evaluator classes.
- chemaxon.jep.context - package chemaxon.jep.context
- Specific chemical terms evaluation contexts.
- chemaxon.license - package chemaxon.license
-
Classes related licenses, license handling, validating, GUI and
documentation.
- chemaxon.marvin - package chemaxon.marvin
- Contains utility classes for rendering molecules.
- chemaxon.marvin.alignment - package chemaxon.marvin.alignment
- The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
- chemaxon.marvin.beans - package chemaxon.marvin.beans
- Provides bean classes for creating Marvin based user interface.
- chemaxon.marvin.calculations - package chemaxon.marvin.calculations
- Provides specific plugin, plugin loader and table form output implementations.
- chemaxon.marvin.common - package chemaxon.marvin.common
- Contains a class for handling user settings.
- chemaxon.marvin.io - package chemaxon.marvin.io
-
Provides classes for molecule import and export through data streams.
- chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats
- Core package of any import/export module.
- chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl
- Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (ChemAxon) compressed molfile.
- chemaxon.marvin.modules - package chemaxon.marvin.modules
- Marvin modules.
- chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer
- Since Marvin 5.3 this package contains the clipboard handler
infrastructure in Marvin.
- chemaxon.marvin.paint - package chemaxon.marvin.paint
-
Defines display options constants.
- chemaxon.marvin.plugin - package chemaxon.marvin.plugin
- Contains the classes responsible for calculator plugin loading, parameter setting,
running and displaying mechanism.
- chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent
- Classes to achieve concurrent processing of calculator plugins.
- chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui
- Calculator plugin common GUI classes.
- chemaxon.marvin.sketch - package chemaxon.marvin.sketch
- Contains the sketcher's core classes and various sketching modes.
- chemaxon.marvin.space - package chemaxon.marvin.space
- Contains the core classes of MarvinSpace including the graphic canvas and the
basic visualizer classes.
- chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor
- Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
- chemaxon.marvin.util - package chemaxon.marvin.util
- Contains some utilities for example for molecule cleaning and Swing.
- chemaxon.marvin.util.codeassist - package chemaxon.marvin.util.codeassist
- Code completion utility for Chemical Terms.
- chemaxon.marvin.view - package chemaxon.marvin.view
- Control records in MarvinView.
- chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing
- Swing support for MarvinView tables.
- chemaxon.metabolizer - package chemaxon.metabolizer
-
- chemaxon.naming - package chemaxon.naming
-
- chemaxon.pharmacophore - package chemaxon.pharmacophore
- Classes for pharmacophore point perception, pharmacophore fingerprint generation
and pharmacophore dissimilarity calculations.
- chemaxon.reaction - package chemaxon.reaction
- Classes for reaction processing related tasks.
- chemaxon.sss - package chemaxon.sss
- Contains packages for structure search and screening.
- chemaxon.sss.screen - package chemaxon.sss.screen
- Classes for screeening.
- chemaxon.sss.search - package chemaxon.sss.search
- Provides structural search capabilities.
- chemaxon.struc - package chemaxon.struc
- Provides classes for implementing and manipulating chemical structures.
- chemaxon.struc.graphics - package chemaxon.struc.graphics
- Contains graphics MDocument elements.
- chemaxon.struc.prop - package chemaxon.struc.prop
-
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
- chemaxon.struc.sgroup - package chemaxon.struc.sgroup
- S-group related classes and interfaces.
- chemaxon.util - package chemaxon.util
- Provides utility classes.
- chemaxon.util.concurrent - package chemaxon.util.concurrent
- Provides utility classes for concurrent processing.
- chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
- Provides utility classes for concurrent processing in Marvin.
- chemaxon.util.concurrent.processors - package chemaxon.util.concurrent.processors
- Provides utility classes for concurrent processing.
- chemaxon.util.iterator - package chemaxon.util.iterator
-
Provides iterator classes for molecules and their components.
- ChemContext - Class in chemaxon.jep
- Common base class of expression evaluation contexts.
- ChemContext() -
Constructor for class chemaxon.jep.ChemContext
- Constructor.
- ChemicalFingerprint - Class in chemaxon.descriptors
- The
ChemicalFingerprint class implements topological fingerprints as a
type of MolecularDescriptors. - ChemicalFingerprint() -
Constructor for class chemaxon.descriptors.ChemicalFingerprint
- Creates a new, empty instance of ChemicalFingerprint without allocating internal
storage.
- ChemicalFingerprint(CFParameters) -
Constructor for class chemaxon.descriptors.ChemicalFingerprint
- Creates a new instance of ChemicalFingerprint according to the parameters given.
- ChemicalFingerprint(String) -
Constructor for class chemaxon.descriptors.ChemicalFingerprint
- Creates a new instance of ChemicalFingerprint according to the
parameters given.
- ChemicalFingerprint(ChemicalFingerprint) -
Constructor for class chemaxon.descriptors.ChemicalFingerprint
- Copy constructor.
- ChemicalTermsWS - Class in chemaxon.jchem.webservice
- This class is the service that provides Chemical Terms Evaluation
- ChemicalTermsWS() -
Constructor for class chemaxon.jchem.webservice.ChemicalTermsWS
-
- ChemJEP - Class in chemaxon.jep
- Expression parser and evaluator for chemical expressions.
- ChemJEP() -
Constructor for class chemaxon.jep.ChemJEP
- Constructor.
- ChemJEP(Class) -
Constructor for class chemaxon.jep.ChemJEP
- Constructor.
- chemTermColsConfig -
Variable in class chemaxon.jchem.db.StructureTableOptions
- Map having as keys the names of columns which
must be assigned a value (during structure import and update).
- chemTermColValues -
Variable in class chemaxon.jchem.db.UpdateHandler.RowData
-
- CHIME -
Static variable in class chemaxon.formats.MFileFormat
- MDL Chime format.
- ChimeRecognizer - Class in chemaxon.formats.recognizer
- Chime format recognizer.
- ChimeRecognizer(String) -
Constructor for class chemaxon.formats.recognizer.ChimeRecognizer
- Creates a Chime format recognizer.
- chiralCenterCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of chiral centers.
- chiralCenterCount() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Calculates the number of tetrahedral stereogenic centers.
- chiralCenters() -
Method in class chemaxon.calculations.TopologyAnalyser
- Determines the chiral center atoms.
- CHIRALITY_MASK -
Static variable in interface chemaxon.struc.StereoConstants
- Chirality mask in flags.
- CHIRALITY_R -
Static variable in interface chemaxon.struc.StereoConstants
- Chiral atom of R configuration.
- CHIRALITY_S -
Static variable in interface chemaxon.struc.StereoConstants
- Chiral atom of S configuration.
- CHIRALITY_SUPPORT -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"chiralitySupport".
- CHIRALITYSUPPORT_ALL -
Static variable in interface chemaxon.struc.StereoConstants
- R/S shown always.
- CHIRALITYSUPPORT_NONE -
Static variable in interface chemaxon.struc.StereoConstants
- R/S not shown for any molecule.
- CHIRALITYSUPPORT_SELECTED -
Static variable in interface chemaxon.struc.StereoConstants
- R/S shown only if chiral flag is set in molecule or
the atom's enhanced stereo type is absolute.
- CIS -
Static variable in interface chemaxon.struc.StereoConstants
- Cis double bond.
- CLASS_NOT_FOUND_ERROR -
Static variable in class chemaxon.util.ErrorHandler
-
- classifier -
Variable in class chemaxon.fragmenter.CutBondReviser
- The classifier object that performs the DFS algorithm and stores ring-bond data.
- classifier -
Variable in class chemaxon.fragmenter.Fragmenter
- The classifier object that performs the DFS algorithm and stores ring-bond data.
- clean(int) -
Method in class chemaxon.formats.MolConverter.Builder
- Enables cleaning.
- clean(int, String) -
Method in class chemaxon.formats.MolConverter.Builder
- Enables cleaning.
- clean(int, String, int, String, MProgressMonitor, String[]) -
Method in class chemaxon.marvin.view.MDocStorage
- Clean the specified cell.
- clean(int, String, MProgressMonitor) -
Method in class chemaxon.struc.Molecule
- Calculates atom coordinates.
- clean(int, String) -
Method in class chemaxon.struc.MoleculeGraph
- Calculates atom coordinates.
- clean(int, String, MProgressMonitor) -
Method in class chemaxon.struc.MoleculeGraph
- Calculates atom coordinates.
- clean(int, String, MProgressMonitor) -
Method in class chemaxon.struc.SelectionMolecule
- Calculates atom coordinates.
- clean(boolean, String) -
Method in class chemaxon.util.MolHandler
- Calculates 2D coordinates.
- CLEAN_H_OPTION -
Static variable in class chemaxon.marvin.common.UserSettings
-
- cleanAll(int, String, MProgressMonitor, String[]) -
Method in class chemaxon.marvin.view.MDocStorage
- Clean all cells.
- CleanFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which cleans the molecule in 2d - CleanFixer() -
Constructor for class chemaxon.fixers.CleanFixer
-
- CLEANING_2D_OPTIONS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"clean2dOpts".
- CLEANING_3D_OPTIONS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"clean3dOpts".
- CLEANING_DIMENSION -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"cleanDim".
- CLEANING_OPTIONS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"cleanOpts".
- cleanResults() -
Method in class chemaxon.jchem.db.JChemSearch
- Cleans stored search results.
- cleanSgroups(int, String) -
Method in class chemaxon.struc.Molecule
- Clean S-groups.
- cleanup(long) -
Method in interface chemaxon.util.concurrent.ConcurrentProcessor
- Awaits termination of worker threads executing on behalf of this
processor and releases any resource this processor has reserved.
- cleanup() -
Method in interface chemaxon.util.concurrent.ConcurrentProcessor
- Calls
ConcurrentProcessor.cleanup(long) with Long.MAX_VALUE.
- cleanupRemovedRgroupMember(MoleculeGraph, int) -
Method in class chemaxon.struc.RgMolecule
- Clean-up after R-group removal.
- CleanUtil - Class in chemaxon.marvin.util
- Utility methods for cleaning.
- CleanUtil() -
Constructor for class chemaxon.marvin.util.CleanUtil
-
- clear() -
Method in class chemaxon.alchemist.AlchemistProfile
- Removes all key-value mappings.
- clear() -
Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel
- Removes all the elements form the right list
- clear() -
Method in class chemaxon.alchemist.configbuilder.ConfigElementPresentationChooser
- Removes all key-value pairs from the presentation chooser
- clear() -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor
- This method clears the editor, and closes the input stream
- clear() -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeView
- This method clear the view
- clear() -
Method in class chemaxon.alchemist.utils.AlchemistFileChooser
- This method closes accessory
- clear() -
Method in class chemaxon.alchemist.utils.AlchemistMoleculeView
- This method clears model, and view,
and also closes the underlying stream
- clear() -
Method in class chemaxon.alchemist.utils.AlchemistMViewAccessory
- This method clears the accessory.
- clear() -
Method in class chemaxon.descriptors.BCUT
- Clears the descriptor, all values are set to zero.
- clear() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Clears the fingerprint: sets all bins to store zero value.
- clear() -
Method in class chemaxon.descriptors.CustomDescriptor
- Clears the descriptor: sets all cells to store zero value.
- clear() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Clears the fingerprint: sets all bins to store zero value.
- clear() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Clears the fingerprint: sets all bins to store zero value.
- clear() -
Method in class chemaxon.descriptors.ScalarDescriptor
- Clears the descritor: sets its value to zero value.
- clear() -
Method in class chemaxon.formats.MolConverter.Builder
- Clears all settings.
- clear(int, int) -
Method in class chemaxon.fragmenter.CutBondReviser
- Clears cut-bond.
- clear(int, int) -
Method in class chemaxon.fragmenter.Recap
- Clears cut-bond info in arrays.
- clear() -
Method in class chemaxon.jep.ChemContext
- Clears the context.
- clear() -
Method in class chemaxon.jep.context.AtomContext
- Clears the context.
- clear() -
Method in class chemaxon.jep.context.MolContext
- Clears the context.
- clear() -
Method in class chemaxon.jep.context.ReactionContext
- Clears the context.
- clear() -
Method in class chemaxon.jep.context.SearchContext
- Clears the context.
- clear() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Clears the display.
- clear() -
Method in class chemaxon.marvin.space.BoundingBox
- Clears all previously set coordinate from the box.
- clear() -
Method in class chemaxon.marvin.space.monitor.Monitor
- Deletes all items from selectedItems.
- clear() -
Method in class chemaxon.pharmacophore.PMap
- Sets every feature for every atom to
false
- clear() -
Method in class chemaxon.struc.MDocument
- Clears the document.
- clear() -
Method in class chemaxon.struc.MolAtom
- Clear query properties, charge, and hcount.
- clear() -
Method in class chemaxon.struc.Molecule
- Clears the molecule.
- clear() -
Method in class chemaxon.struc.MoleculeGraph
- Clears the molecule.
- clear() -
Method in class chemaxon.struc.MPropertyContainer
- Clears properties.
- clear() -
Method in class chemaxon.struc.MSelectionDocument
- Clears the document.
- clear() -
Method in class chemaxon.util.IntArray
- Sets the size to zero.
- clearAll(String) -
Method in class chemaxon.jchem.webservice.RelAdminWS
- Clear all meta data about relationships.
- clearCache() -
Static method in class chemaxon.jchem.db.JChemSearch
- Clears the cache that stores fingerprints and structures.
- clearCachedInfo(int) -
Method in class chemaxon.struc.MoleculeGraph
- Deletes the cached information depending on the given options.
- clearChangesInUserComparators() -
Method in class chemaxon.sss.search.SearchOptions
- Used in initializing searches.
- clearCheckerMarks() -
Method in class chemaxon.struc.MDocument
- Clears the checker marks
- clearChoosableFileFilters() -
Method in class chemaxon.alchemist.utils.AlchemistFileChooser
- Removes all choosable file filters.
- clearClipboard() -
Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Clears the clipboard by creating an empty Transferable and placing it on
the clipboard.
- clearClipboard() -
Static method in class chemaxon.marvin.util.ClipboardHandler
- Deprecated. see the documentation of the class
- clearComparators() -
Method in class chemaxon.sss.search.MolSearch
-
- clearCutBond(int, int) -
Method in class chemaxon.fragmenter.Fragmenter
- Clears the
i - j cut-bond.
- clearCutBonds() -
Method in class chemaxon.fragmenter.Fragmenter
- Clears the 'cutbond' array.
- clearExtraLabel() -
Method in class chemaxon.struc.MolAtom
- Clears the extra label.
- clearExtraLabels() -
Method in class chemaxon.struc.Molecule
- Clears extra atom labels.
- clearFeatures(int) -
Method in class chemaxon.pharmacophore.PMap
- Clears all features corresponding to the given atom index.
- clearForImport(String) -
Method in class chemaxon.struc.Molecule
- Initializes molecule for import.
- clearForImport(String) -
Method in class chemaxon.struc.MoleculeGraph
- Clears the edges vector, the properties, the flags, and sets the
origin coordinates to 0.
- clearForImport(String) -
Method in class chemaxon.struc.RgMolecule
- Clear the edges vector and the properties.
- clearForImport(String) -
Method in class chemaxon.struc.RxnMolecule
- Clear the edges vector and the properties.
- clearHistory() -
Method in class chemaxon.marvin.beans.MSketchPane
- Reset undo queue.
- clearHits() -
Method in class chemaxon.naming.DocumentExtractor
- Clears the list of hits.
- clearInactiveTasks() -
Method in class chemaxon.reaction.Standardizer
- Clears the inactive tasks list.
- clearMaps(RxnMolecule) -
Static method in class chemaxon.marvin.modules.AutoMapper
- Clears atom maps.
- clearMatch() -
Method in class chemaxon.sss.search.MolSearch
- Clears the extra prerequisites of the structure search specified using
addMatch calls.
- clearMatch() -
Method in class chemaxon.sss.search.Search
- Clears the extra prerequisites of the structure search specified using
addMatch calls.
- clearObjects() -
Method in class chemaxon.struc.Molecule
-
- clearObjects() -
Method in class chemaxon.struc.RgMolecule
-
- clearObjects() -
Method in class chemaxon.struc.RxnMolecule
- Deletes the graphical objects from this.
- clearObjects() -
Method in class chemaxon.struc.Sgroup
- Clears all MObject-s that belong to this S-groups.
- clearProperties() -
Method in class chemaxon.struc.Molecule
- Clears RDfile/SDfile properties.
- clearQProps() -
Method in class chemaxon.struc.MolAtom
- Clears query props.
- clearSelection() -
Method in class chemaxon.alchemist.utils.AlchemistLinearMoleculeView
- Clears the selection
- clearSelection(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Sets all components and parts of components to be unselected in the given cell.
- clearSelections() -
Method in class chemaxon.marvin.space.GraphicCell
- Sets all components and parts of components to be unselected.
- clearSets() -
Method in class chemaxon.struc.MDocument
- Clears the atomSets and the bondSets.
- CLIPBOARD_OPERATION_GET -
Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
- Flag that indicates an import operation
- CLIPBOARD_OPERATION_PUT -
Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
- Flag that indicates an export operation
- CLIPBOARD_OPERATION_UNDEFINED -
Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
- Undefined clipboard operation state identifier
- ClipboardHandler - Class in chemaxon.marvin.modules.datatransfer
-
Facade of the Clipboard handling in Marvin.
- ClipboardHandler - Class in chemaxon.marvin.util
- Deprecated. since Marvin 5.3 the class has been moved to
ClipboardHandler the
functionalities in this class will be unsupported after Marvin
5.4 - ClipboardHandler() -
Constructor for class chemaxon.marvin.util.ClipboardHandler
- Deprecated.
- clipboardOperation -
Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
- Clipboard operation type.
- clipSurface(BoundingBox) -
Method in class chemaxon.marvin.space.SurfaceComponent
- The bounding box of the surface can be used to determine 6 clipping planes
and clip (do not draw) parts lying outside of the box.
- clone() -
Method in class chemaxon.alchemist.AlchemistTask
-
- clone() -
Method in class chemaxon.alchemist.configbuilder.BasicConfigElement
-
- clone() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
-
- clone() -
Method in class chemaxon.descriptors.BCUT
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.CustomDescriptor
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.MDSet
- Clones the object.
- clone() -
Method in class chemaxon.descriptors.MolecularDescriptor
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.ReactionFingerprint
- Creates a copy with identical internal state.
- clone() -
Method in class chemaxon.descriptors.ScalarDescriptor
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.scalars.HAcc
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.scalars.HDon
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.scalars.Heavy
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.scalars.LogD
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.scalars.LogP
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.scalars.Mass
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.descriptors.scalars.TPSA
- Creates a new instance with identical internal state.
- clone() -
Method in class chemaxon.formats.MolConverter.Builder
- Clones the object.
- clone() -
Method in class chemaxon.marvin.util.MolImageSize
- Creates an identical copy.
- clone() -
Method in class chemaxon.pharmacophore.PMap
- Clones this PMap object.
- clone() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Makes an identical copy of this SearchObject.
- clone() -
Method in class chemaxon.sss.search.MolSearchOptions
-
- clone() -
Method in class chemaxon.sss.search.SearchOptions
- Makes an identical copy of this SearchObject.
- clone() -
Method in class chemaxon.struc.DPoint3
- Make an identical copy.
- clone() -
Method in class chemaxon.struc.graphics.MAtomSetPoint
-
- clone() -
Method in class chemaxon.struc.graphics.MBracket
-
- clone() -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Creates a clone.
- clone() -
Method in class chemaxon.struc.graphics.MEFlow
-
- clone() -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
- clone() -
Method in class chemaxon.struc.graphics.MEllipse
-
- clone() -
Method in class chemaxon.struc.graphics.MFont
- Creates a clone.
- clone() -
Method in class chemaxon.struc.graphics.MMidPoint
-
- clone() -
Method in class chemaxon.struc.graphics.MMidPoint.Sticky
-
- clone() -
Method in class chemaxon.struc.graphics.MPolyline
-
- clone() -
Method in class chemaxon.struc.graphics.MRectangle
-
- clone() -
Method in class chemaxon.struc.graphics.MRectanglePoint
-
- clone() -
Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
-
- clone() -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- clone() -
Method in class chemaxon.struc.graphics.MTextBox
-
- clone() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- clone() -
Method in class chemaxon.struc.MObject
- Creates a clone.
- clone() -
Method in class chemaxon.struc.MolAtom
- Clones the atom.
- clone() -
Method in class chemaxon.struc.MolBond
- Make a copy of this object.
- clone() -
Method in class chemaxon.struc.Molecule
- Makes an identical copy of the molecule.
- clone() -
Method in class chemaxon.struc.MoleculeGraph
- Make an identical copy of the molecule.
- clone() -
Method in class chemaxon.struc.MPoint
-
- clone() -
Method in class chemaxon.struc.MPropertyContainer
- Clones this object.
- clone() -
Method in class chemaxon.struc.prop.MBooleanProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MCollectionProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MDoubleProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MIntegerProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MMoleculeProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MObjectProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.prop.MStringProp
- Clones the object.
- clone() -
Method in class chemaxon.struc.QueryBond
- Make a copy of this object.
- clone() -
Method in class chemaxon.struc.SelectionMolecule
- Create a clone of the selection.
- clone() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Clones the S-group superatom.
- cloneBond(MolAtom, MolAtom) -
Method in class chemaxon.struc.MolBond
- Clones this bond.
- cloneBond(MolAtom, MolAtom) -
Method in class chemaxon.struc.QueryBond
- Clones this bond.
- cloneCollectionProp(Set) -
Method in class chemaxon.struc.prop.MCollectionProp
- Clones the object.
- cloneCollectionProp(Set) -
Method in class chemaxon.struc.prop.MHashProp
- Clones the object.
- cloneCollectionProp(Set) -
Method in class chemaxon.struc.prop.MListProp
- Clones the object.
- clonecopy(SearchOptions) -
Method in class chemaxon.sss.search.JChemSearchOptions
- Copies parameters to
other.
- clonecopy(SearchOptions) -
Method in class chemaxon.sss.search.MolSearchOptions
- Copies parameters to
other.
- clonecopy(SearchOptions) -
Method in class chemaxon.sss.search.SearchOptions
- Copies all parameters to the other object.
- clonecopy(MoleculeGraph) -
Method in class chemaxon.struc.Molecule
- Makes another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) -
Method in class chemaxon.struc.Molecule
- Copies the specified atoms and bonds of this graph to another one.
- clonecopy(MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Make another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Copies the specified nodes of this molecule graph to another one.
- clonecopy(MoleculeGraph) -
Method in class chemaxon.struc.RgMolecule
- Make another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) -
Method in class chemaxon.struc.RgMolecule
- Copies the specified atoms of this graph to another one.
- clonecopy(MoleculeGraph) -
Method in class chemaxon.struc.RxnMolecule
- Make another molecule identical to this one.
- clonecopy(int[], MoleculeGraph) -
Method in class chemaxon.struc.RxnMolecule
- Copies the specified nodes and edges of this graph to another one.
- clonecopy(MoleculeGraph) -
Method in class chemaxon.struc.SelectionMolecule
- Copies the clones of nodes and edges of this graph to another one.
- clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Copies the specified nodes and edges of this graph to another one.
- clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) -
Method in class chemaxon.struc.SelectionMolecule
- Copies the specified atoms and bonds of this graph to another one.
- clonecopyWithoutSgroups(Molecule) -
Method in class chemaxon.struc.Molecule
- Copies the all the contents except the S-groups into another molecule
object.
- cloneDocument() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- cloneDocument() -
Method in class chemaxon.struc.MSelectionDocument
- Creates a clone.
- cloneEdge(MolAtom, MolAtom) -
Method in class chemaxon.struc.MolBond
- Clones this edge.
- cloneElement() -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Returns a clone of the element, or null if clone not supported
- cloneFromSgroupCopy() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Clones the S-group superatom partially.
- clonelesscopy(MoleculeGraph) -
Method in class chemaxon.struc.Molecule
- Copies to selection.
- clonelesscopy(MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Copy to selection.
- clonelesscopy(MoleculeGraph) -
Method in class chemaxon.struc.RgMolecule
- Copy to selection.
- clonelesscopy(MoleculeGraph) -
Method in class chemaxon.struc.RxnMolecule
- Copy to selection.
- cloneMainMolecule() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- cloneMainMoleculeGraph() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- cloneMFont() -
Method in class chemaxon.struc.graphics.MFont
- Creates a clone.
- cloneMolecule() -
Method in class chemaxon.struc.Molecule
- Makes an identical copy of the molecule.
- cloneMolecule() -
Method in class chemaxon.struc.RgMolecule
- Make an identical copy of the molecule.
- cloneMolecule() -
Method in class chemaxon.struc.RxnMolecule
- Make an identical copy of the molecule.
- cloneMoleculeWithDocument() -
Method in class chemaxon.struc.Molecule
- Makes an identical copy of the molecule and its document.
- cloneProp() -
Method in class chemaxon.struc.MDocument.Prop
- Creates a clone.
- cloneProp() -
Method in class chemaxon.struc.MProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MBooleanProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MCollectionProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MDoubleProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MIntegerProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MMoleculeProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MObjectProp
- Clones the object.
- cloneProp() -
Method in class chemaxon.struc.prop.MStringProp
- Clones the object.
- cloneResult -
Variable in class chemaxon.descriptors.MDReader
- indicates if mdSet is cloned or not in
next()
- cloneSets(MDocument) -
Method in class chemaxon.struc.MDocument
- Clones the atom/bond sets from doc.
- cloneSgroup(Molecule, Sgroup) -
Method in class chemaxon.struc.Sgroup
- Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) -
Method in class chemaxon.struc.Sgroup
- Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets a new DataSgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets a new Sgroup instance.
- cloneStructure() -
Method in class chemaxon.struc.Sgroup
- Gets the clone of the structure stored.
- close() -
Method in class chemaxon.alchemist.utils.AlchemistMoleculeView
- This method closes the underlying stream
- close() -
Method in class chemaxon.alchemist.utils.AlchemistMViewAccessory
- This method closes the molimporter
- close() -
Method in class chemaxon.alchemist.utils.AlchemistProgressMonitor
-
- close() -
Method in class chemaxon.descriptors.GenerateMD
- Closes the generator, all output files or database connection.
- close() -
Method in class chemaxon.descriptors.MDArrayReader
- Closes the reader
- close() -
Method in class chemaxon.descriptors.MDDBReader
- Closes down the descriptor stream.
- close() -
Method in class chemaxon.descriptors.MDDBWriter
- Closes down the descriptor output stream.
- close() -
Method in class chemaxon.descriptors.MDFileReader
- Closes the reader.
- close() -
Method in class chemaxon.descriptors.MDFileWriter
- Closes the stream, after that no more operations are permitted.
- close() -
Method in class chemaxon.descriptors.MDReader
- Closes down the descriptor stream.
- close() -
Method in class chemaxon.descriptors.MDSimilarityResultWriter
- Closes output.
- close() -
Method in class chemaxon.descriptors.MDWriter
- Closes down the descriptor output stream.
- close() -
Method in class chemaxon.formats.MolConverter
- Closes the exporter and the output stream.
- close(int) -
Method in class chemaxon.formats.MolConverter
- Closes the exporter.
- close() -
Method in class chemaxon.formats.MolExporter
- Closes the
MolExportModule and the underlying stream.
- close(int) -
Method in class chemaxon.formats.MolExporter
- Closes the
MolExportModule and, optionally, the underlying stream.
- close() -
Method in class chemaxon.formats.MolImporter
- Close the underlying input stream.
- close() -
Method in class chemaxon.jchem.db.DatabaseProperties
- Should be called only if the use of prepared statements are enabled with
DatabaseProperties.setUsePreparedStatement(boolean).
- close() -
Method in class chemaxon.jchem.db.UpdateHandler
- Closes the handler (required to call).
- close() -
Method in class chemaxon.jchem.file.ProgressWriter
- Indicate that the operation is complete.
- close(String) -
Method in class chemaxon.jchem.webservice.ConnectionWS
- Closes the connection at the end of a session.
- close() -
Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
- Interrupts parsing.
- close() -
Method in class chemaxon.marvin.io.MDocSource
- Closes the underlying input stream(s).
- close() -
Method in class chemaxon.marvin.io.MolExportModule
- Close the stream.
- close() -
Method in class chemaxon.marvin.io.MRecordImporter
- Closes the input stream.
- close() -
Method in interface chemaxon.marvin.io.MRecordReader
- Closes the input stream.
- close() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Closes the output.
- close(int) -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Closes the output.
- close() -
Method in interface chemaxon.metabolizer.MetabolizerExporter
- Closes exporter.
- close() -
Method in class chemaxon.metabolizer.MetabolizerFileExporter
-
- close() -
Method in class chemaxon.metabolizer.MetabolizerFileImporter
-
- close() -
Method in interface chemaxon.metabolizer.MetabolizerImporter
- Closes importer.
- close() -
Method in class chemaxon.metabolizer.MetabolizerMemoryExporter
-
- close() -
Method in class chemaxon.metabolizer.MetabolizerMemoryImporter
-
- close() -
Method in class chemaxon.metabolizer.MetabolizerTemporaryFileStorage
-
- close() -
Method in class chemaxon.metabolizer.MetabolizerTemporaryMemoryStorage
-
- close() -
Method in interface chemaxon.metabolizer.MetabolizerTemporaryStorage
- Closes storage.
- close() -
Method in class chemaxon.util.concurrent.marvin.MolInputProducer
- Closes the importers.
- close() -
Method in class chemaxon.util.ConnectionHandler
- Closes the connection to the database.
- close_NE() -
Method in class chemaxon.util.ConnectionHandler
- Deprecated. since JChem 5.2 use
ConnectionHandler.close()
- CLOSE_RESULTS -
Static variable in class chemaxon.alchemist.commonpages.ProgressPanel
-
- CLOSED_FLAG -
Static variable in class chemaxon.struc.graphics.MPolyline
- Closed flag.
- closeSketcher(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Closes the sketcher window that belongs the the specified cell.
- closeTemporaryStorage() -
Method in class chemaxon.metabolizer.Metabolizer
- Closes temporary storage
- closeWindow(int) -
Method in class chemaxon.marvin.beans.MViewPane
- Closes the detached viewer window of the specified cell.
- closeWindows() -
Method in class chemaxon.marvin.beans.MarvinPane
- Closes all windows opened by this MarvinPane.
- CML -
Static variable in class chemaxon.formats.MFileFormat
- Chemical Markup Language.
- CNode - Interface in chemaxon.struc
- Deprecated. as of Marvin 5.3, please use
MolAtom instead - CodeAssistFactory - Class in chemaxon.marvin.util.codeassist
- Manages the creation of Chemical Terms related components, such as the Code Assist text field,
toolbars, favorite and macro handling components, and validation response component.
- COL_MOLECULE -
Static variable in class chemaxon.sss.search.RGroupDecomposition
- Constant for adding query-target column to ligand table.
- COL_SCAFFOLD -
Static variable in class chemaxon.sss.search.RGroupDecomposition
- Constant for adding scaffold column to ligand table.
- colDec -
Variable in class chemaxon.descriptors.PFParameters
- atom set colors
- collect(String, String, String, String, String[]) -
Method in class chemaxon.fragmenter.Fragmenter
- Initiates cleavage reaction data collecting.
- collect(String, String, String, String, String[], boolean) -
Method in class chemaxon.fragmenter.Fragmenter
- Deprecated. as of JChem 5.3, use
Fragmenter.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.
- collectStatisitcs(ConnectionHandler, String) -
Method in class chemaxon.jchem.db.TableStatistics
-
- colNum -
Variable in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeView
-
- color -
Variable in class chemaxon.marvin.space.GraphicComponent
-
- color -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- color -
Variable in class chemaxon.marvin.space.SurfaceComponent
-
- color() -
Method in class chemaxon.sss.search.Decomposition
- Colors ligands, scaffold, query and target by setting color data in atoms by calling
MolAtom.setSetSeq(int).
- color(Molecule) -
Static method in class chemaxon.sss.search.Decomposition
- Colors a molecule by setting color data in atoms by calling
MolAtom.setSetSeq(int).
- color(String) -
Method in class chemaxon.sss.search.Decomposition
- Colors ligands, scaffold, query and target by setting color data
in the specified molecule property (SDF tag).
- color(Molecule, String) -
Static method in class chemaxon.sss.search.Decomposition
- Colors a molecule by setting color data
in the specified molecule property (SDF tag).
- color(Molecule, Molecule, HitColoringAndAlignmentOptions) -
Static method in class chemaxon.util.HitDisplayUtil
- Performs hit coloring on the specified structure.
- color(Molecule, Molecule, int[], HitColoringAndAlignmentOptions) -
Static method in class chemaxon.util.HitDisplayUtil
- Performs hit coloring on the specified structure.
- color3 -
Variable in class chemaxon.marvin.space.SurfaceComponent
-
- COLOR_MAPPER_BLUE_TO_GREEN -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Built-in blue-cyan-green palette will be used.
- COLOR_MAPPER_BLUE_TO_RED -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Built-in blue-lightgray-red palette will be used.
- COLOR_MAPPER_FIRE -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Built-in "fire" palette will be used.
- COLOR_MAPPER_GREEN_TO_BLUE -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Built-in green-cyan-blue palette will be used.
- COLOR_MAPPER_RAINBOW -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Built-in rainbow palette will be used.
- COLOR_MAPPER_RED_TO_BLUE -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Built-in red-lightgray-blue palette will be used.
- COLOR_MAPPER_REVERSE_RAINBOW -
Static variable in class chemaxon.marvin.space.SurfaceColoring
- Built-in reverse rainbow palette will be used.
- COLOR_SCHEME -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"colorScheme".
- COLOR_SCHEMES -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Array of color schemes strings.
- coloring(boolean) -
Method in class chemaxon.marvin.space.SurfaceComponent
-
- coloring -
Variable in class chemaxon.util.HitColoringAndAlignmentOptions
- Specifies if substructure hit coloring should be used.
- COLORING_ALL -
Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Constant for setting all coloring options, currently scaffold and R-groups.
- COLORING_NONE -
Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Constant for no hit coloring.
- COLORING_RGROUPS -
Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Constant for R-group coloring.
- COLORING_SCAFFOLD -
Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Constant for scaffold coloring.
- COLORS_MASK -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Color scheme mask in display option flags.
- COLORS_OFFSET -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Color scheme offset in display option flags.
- colorType -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- COLS -
Static variable in class chemaxon.marvin.view.ViewParameterConstants
- Identifier of parameter:
"cols".
- columnComboBox -
Variable in class chemaxon.alchemist.utils.AlchemistMoleculeView
-
- Common - Class in chemaxon.clustering
- Common superclass for JKlustor tools.
- Common() -
Constructor for class chemaxon.clustering.Common
-
- Compare - Class in chemaxon.clustering
- Compares two sets of objects (like compound libraries)
using diversity and dissimilarity calculations.
- Compare() -
Constructor for class chemaxon.clustering.Compare
-
- compare(int, int, MDSet) -
Method in class chemaxon.descriptors.MDSimilarity
- Compares a target descriptor against all queries added prior to the call
of this method using the given metric of the given descriptor.
- compare(MDSet) -
Method in class chemaxon.descriptors.MDSimilarity
- Compares a target descriptor set (for instance from a database)
against all queries added prior to the call of this method.
- compare(MDReader) -
Method in class chemaxon.descriptors.MDSimilarity
- Compares a list of target descriptor sets (read by a molecular descriptor
reader) against all queries added prior to the call of this method the
same way as
compareQueries( MolecularDescriptor target ) but
for each target.
- compareAtoms(int, int) -
Method in class chemaxon.sss.search.MolComparator
- Compares atoms of indices a1 and a2.
- compareBonds(int, int) -
Method in class chemaxon.sss.search.MolComparator
- Compares bonds of indices b1 and b2.
- compareHit(int[], int) -
Method in class chemaxon.sss.search.MolComparator
- Checks a partial hit during the search algorithm.
- compareTo(TransferableDescriptor) -
Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- Comparison method which uses the priority field for ordering.
- compareTo(Object) -
Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- compile(String) -
Method in class chemaxon.jep.ChemJEP
- Compiles the expression string to an inner structure.
- compile(String) -
Method in class chemaxon.jep.Evaluator
- Compiles the expression, creates
ChemJEP object.
- compile(String, Class) -
Method in class chemaxon.jep.Evaluator
- Compiles the expression, creates
ChemJEP object.
- compile(String, Class, SymbolTable) -
Method in class chemaxon.jep.Evaluator
- Compiles the expression, creates
ChemJEP object.
- COMPLETE -
Static variable in class chemaxon.marvin.modules.AutoMapper
- all atoms in the reaction are mapped
- component -
Variable in class chemaxon.marvin.space.monitor.Control
-
- COMPONENT_RANGE -
Static variable in class chemaxon.marvin.space.GraphicScene
-
- COMPONENT_TYPE_ATOM -
Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- COMPONENT_TYPE_ATOM -
Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- COMPONENT_TYPE_BOND -
Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- COMPONENT_TYPE_BOND -
Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- COMPONENT_TYPE_ENTIRE -
Static variable in class chemaxon.marvin.space.GraphicComponent
- Indicates if the entire component is selected by picking.
- COMPONENT_TYPE_MOLECULE -
Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- COMPONENT_TYPE_MOLECULE -
Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- COMPONENT_TYPE_RESIDUE -
Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
-
- componentBecameSelected() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns true if a component became selected previously.
- componentBecameSelected(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if a component became selected previously in the given cell.
- componentBecameUnselected() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns true if a component became unselected previously.
- componentBecameUnselected(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if a component became unselected previously in the given cell.
- ComponentChecker<E> - Class in chemaxon.checkers
- A descendant of the abstract ComponentChecker class implements a checker which
iterate through components of the molecule and check every component for the specific error.
- ComponentChecker(StructureCheckerErrorType) -
Constructor for class chemaxon.checkers.ComponentChecker
- Constructor to create a Structure checker instance with the given errorType.
- ComponentElement - Class in chemaxon.marvin.space
- Class to identify parts of GraphicComponents mainly during selection.
- ComponentElement(GraphicComponent, int, int) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Creates a new instance of
ComponentElement of a simple
(not structured) GraphicComponent.
- ComponentElement(GraphicComponent, int, Integer) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Creates a new instance of
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.
- 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
-
- 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.
- 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, ImageIcon) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id, name and icon
- ConfigElement(String, String, ImageIcon, String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id, name, icon
and tooltip
- ConfigElement(String, String, ImageIcon, String, String) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElement
- Constructs a config element with the specified id, name, icon
and tooltip
- ConfigElement(String, String, ImageIcon, 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(Configuration) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementFactory
- Creates a
ConfigElementFactory based on Configuration
- ConfigElementListCellRenderer - Class in chemaxon.alchemist.configbuilder
- Cell renderer for ConfigElements
Renders an icon, and the name of the item.
- ConfigElementListCellRenderer() -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementListCellRenderer
- Constructs a ConfigElement renderer for a list
- ConfigElementListCellRenderer(boolean) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementListCellRenderer
- Constructs a ConfigElement renderer for a list
- ConfigElementPresentationChooser - Class in chemaxon.alchemist.configbuilder
- This class provides the presentation for
ConfigElement classes. - ConfigElementPresentationChooser() -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementPresentationChooser
- Constructs an empty ConfigElementPresentationChooser
- ConfigElementSketchEditor - Class in chemaxon.alchemist.configbuilder
- This is the default editor of
AbstractSketchConfigElement instances. - ConfigElementSketchEditor() -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementSketchEditor
-
- ConfigElementTransferHandler - Class in chemaxon.alchemist.configbuilder
- Custom
TransferHandler for ConfigElement instances used by ConfigBuilderPanel - ConfigElementTransferHandler(JList, JList, ConfigBuilderPanel) -
Constructor for class chemaxon.alchemist.configbuilder.ConfigElementTransferHandler
-
- 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. - ConfigurationReaderFactory - Class in chemaxon.alchemist.configbuilder
- A Factory class for creating instances based on
AbstractConfigurationReader
for variuous configurations - configure(Object) -
Method in class chemaxon.alchemist.AlchemistApplication.DefaultActionConfigurer
-
- 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(Graphics2D, CTransform3D, int, int, DPoint3, DPoint3, Stroke, double) -
Method in class chemaxon.struc.graphics.MPolyline
-
- connect() -
Method in class chemaxon.util.ConnectionHandler
- Connects to the database.
- 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(ConnectionHandler) -
Constructor for class chemaxon.util.ConnectionHandler
- Creates new ConnectionHandler based on the settings of an other
ConnectionHandler.
- ConnectionWS - Class in chemaxon.jchem.webservice
- This class represents the Connection Web Service
- ConnectionWS() -
Constructor for class chemaxon.jchem.webservice.ConnectionWS
-
- ConnectionWS(ContextAccess) -
Constructor for class chemaxon.jchem.webservice.ConnectionWS
-
- construct() -
Method in class chemaxon.alchemist.utils.SwingWorker
- Compute the value to be returned by the
get method.
- 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 graph contains the specified node.
- contains(MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Checks if the graph contains the specified node.
- contains(MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Checks if the graph contains the specified edge.
- contains(MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Does the 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.
- containsKey(String) -
Method in class chemaxon.alchemist.AlchemistProfile
- Returns true if there is mapping for specified key
- containsKey(Class<?>) -
Method in class chemaxon.alchemist.configbuilder.ConfigElementPresentationChooser
- Returns if mapping contains the specified key
- 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
-
- 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.
- contractExpandedSgroups() -
Method in class chemaxon.struc.Molecule
-
- 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() -
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(String, String) -
Method in class chemaxon.jchem.webservice.MolConvertWS
- Converts a molecule to a specified format.
- 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.
- convertSpecialInput(String, String, String) -
Method in class chemaxon.jchem.webservice.MolConvertWS
- Converts a molecule specified by the inputFormat to a specified
outputFormat.
- 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.
- 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(String, int) -
Method in class chemaxon.struc.MDocument.Prop
- Converts the molecule to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.MProp
- Converts the property to text format.
- convertToString(String) -
Method in class chemaxon.struc.MProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MBooleanProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MDoubleProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MHashProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MIntegerProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MListProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MMoleculeProp
- Converts the molecule to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MObjectProp
- Converts the property to text format.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MStringProp
- Converts the property to text format.
- 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.
- COPY_AS_FORMAT -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"copyAsFormat".
- COPY_AS_IMAGE_BITMAP -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated. replaced with ClipboardHandler.bitmapTransferableId
- COPY_AS_IMAGE_EMF -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated. replaced with ClipboardHandler.graphicsStreamTransferableId
- COPY_AS_OLE -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated. replaced with ClipBoardHandler.OLETransferableId
- COPY_AS_TEXT -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated. replaced with ClipboardHandler.stringTransferableId
- COPY_OPTIONS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"copyOpts".
- copyAttributes(ConfigElement) -
Method in class chemaxon.alchemist.configbuilder.AbstractSketchConfigElement
-
- copyAttributes(ConfigElement) -
Method in class chemaxon.alchemist.configbuilder.ConfigElement
- Copies the default attributes from
source
- 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 of the number of all enumerated structures,
no arithmetic overflow because counts in
BigInteger.
- 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.
- 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(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.
- createAboutDialog(String) -
Static method in class chemaxon.alchemist.utils.AboutDialogFactory
-
- createAboutDialog(String, String) -
Static method in class chemaxon.alchemist.utils.AboutDialogFactory
-
- 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.
- 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
- Creates a
JTextPane instance with code assist capabilities.
- 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
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(boolean, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, boolean, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) -
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) -
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
-
- 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.
- createDisabledImage() -
Method in class chemaxon.alchemist.AlchemistApplication
-
- createDisabledImage(Component) -
Static method in class chemaxon.alchemist.utils.AlchemistGraphicsUtilities
- Returns an image created by rendering the component and applying
a semi-transparent white layer on it
- 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.
- createFileFilter(String, String[]) -
Static method in class chemaxon.alchemist.configbuilder.FileFilterFactory
-
- 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
-
- 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.
- 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 major 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[]) -
Method in class chemaxon.reaction.Reactor
- Deprecated. use
Reactor.setResultType(int)
- createReaction(Molecule, DPoint3[], int) -
Static method in class chemaxon.struc.RxnMolecule
- Creates a reaction.
- createReaction(MoleculeGraph, DPoint3[]) -
Static method in class chemaxon.struc.RxnMolecule
-
- 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.
- createReactions(Molecule[]) -
Method in class chemaxon.reaction.Reactor
- Deprecated. Not used. Returns
null.
- 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.
- createRelationTree(String, String, String, String, String, String) -
Method in class chemaxon.jchem.webservice.RelAdminWS
- Create a relation tree which contains one table without relationships.
- createRelationTreeWithRelation(String, String, String, String, String, String, String, String, String, String, String, String, String) -
Method in class chemaxon.jchem.webservice.RelAdminWS
- Creates a relation between two tables and, if it does not exist already,
a new relation tree with the given label.
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AliasChecker
-
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AtomChecker
-
- createResult(Molecule, List<MolBond>) -
Method in class chemaxon.checkers.BondChecker
-
- createResult(Molecule, List<E>) -
Method in class chemaxon.checkers.ComponentChecker
- Creates a
StructureCheckerResult from an List contains indices of components.
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.PseudoAtomChecker
-
- createResult(Molecule, List<StructureCheckerResult>) -
Method in class chemaxon.checkers.ReactionChecker
-
- 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.
- 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.
- createStandardizerConfigurationReader(String) -
Static method in class chemaxon.alchemist.configbuilder.ConfigurationReaderFactory
- Returns a
StandardizerConfigurationReader instance
- createStandardizerConfigurationReader(File) -
Static method in class chemaxon.alchemist.configbuilder.ConfigurationReaderFactory
- Returns a
StandardizerConfigurationReader instance based on a File
- createStandardizerConfigurationReader(InputStream) -
Static method in class chemaxon.alchemist.configbuilder.ConfigurationReaderFactory
- Returns a
StandardizerConfigurationReader instance based on InputStream
- createStandardizerPanel() -
Static method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanelFactory
- 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 with 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
- 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
- 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.
- createTransferable(JComponent) -
Method in class chemaxon.alchemist.configbuilder.ConfigElementTransferHandler
-
- 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.
- CrossedDoubleBondChecker - Class in chemaxon.checkers
- A descendant of
BondChecker for the detection of crossed double bonds
(unspecified stereo) and for their correction by conversion. - 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.
- current -
Variable in class chemaxon.alchemist.AlchemistTask
- the current state of the task (
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
- currentRowNum -
Variable in class chemaxon.alchemist.utils.AlchemistMoleculeView
-
- currentTask -
Variable in class chemaxon.alchemist.commonpages.ProgressPanel
- current task working background
- 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.
- CUSTOM_STYLE -
Static variable in class chemaxon.alchemist.utils.AlchemistLabel
-
- 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.
- CXSMILES_TRANSFERABLE_NAME -
Static variable in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
- Chemaxon Extended Smiles Transfer name and identifier.
- 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) instead.
null as its detail message.
"debug".
RGroupDecomposition results.MolSearchOptions.clonecopy(SearchOptions) instead
SearchOptions.clonecopy(SearchOptions) instead
"defaultSaveFormat".
SearchConstants.DEFAULT_DISSIMILARITY_THRESHOLD instead
JChemSearch.DissimilarityMetrics.metricNames
JChemSearch.DissimilarityMetrics.metricNames, starting from 0.
StructureCheckerResultMoleculeGraph.implicitizeHydrogens(int)
with parameter MolAtom.ALL_H does the same.
JChemProperties table,
if it exists.
"detach".
"detachable".
refresh()
or redraw() instead.
"dispQuality".
SearchConstants.SIMILARITY instead
SurfaceColoring object in case of custom properties.
SurfaceColoring object in case of built-in properties.
"downWedge".
"draggable".
GraphicCell from the Jogl rendering thread and draws the molecule.
DOTTED_TYPE or FILLED_TYPE.
MolPrinter.paint(java.awt.Graphics,java.awt.Rectangle)
MolPrinter.paint(java.awt.Graphics,java.awt.Rectangle)
three quality modes.
MESH_TYPE or TRANSPARENT_TYPE.
"editable".
"elements".
"2dviewerEnabled".
"3dviewerEnabled".
null.
HitColoringAndAlignmentOptions.markushDisplayMode
MarkushEnumerationPlugintrue if this decomposition is equivalent to the specified decomposition.
"escapeChar".
boolean.
boolean[].
double.
double[].
SearchConstants.FULL
SearchConstants.FULL_FRAGMENT
SearchOptions.setFullFragment(boolean)
instead.
SearchOptions.setFullFragment(boolean)
instead.
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.
ConfigElements implementing this interface can use an
external editor provided by ConfigBuilderPanelAbstractStructureChecker for providing a super class for externally
implemented structure checkers.StructureCheckerResult that supports external StructureChecker developement"extraBonds".
"xtmpls".
"ezVisible".
MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie().
AlchemistPage for handling list of input filestrue if the hit is accepted by the filteringExpression.
0D molecules only.
RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process)
RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process)
setOrderSensitiveSearch(true) instead
RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process)
RGroupDecomposition.findFirstDecomposition() and
RGroupDecomposition.findNextDecomposition() to get decomposition results
(the current implementation ignores the hit parameter and uses
the latest groupHit found by the search process)
construct method has returned.
StructureChecker on the given molecule and after that fixes all identified problems with the first StructureFixer which associated with the current problem
StructureFixer which 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 fixerdouble[][] 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().
MolecularDescriptor object from its external
(database) representation.
PharmacophoreFingerprint from an external data
format, created by a previous call to toData().
toData().
toData().
BCUT descriptor from its float array representation
(generated by toFloatArray()).
BCUT descriptor from its string representation
created by toString().
toString().
toString().
toString().
toString().
toString().
MolecularDescriptor
object.
CFGenerator 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.
RgMolecule with the specified scaffold
(see MarkushGenerator.setQuery(chemaxon.struc.Molecule)) covering the specified targets
(see MarkushGenerator.setTargets(chemaxon.struc.Molecule[])).
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 geometrical properties calculations.
- GeometryPlugin() -
Constructor for class chemaxon.marvin.calculations.GeometryPlugin
- Constructor.
- get(String) -
Method in class chemaxon.alchemist.AlchemistProfile
- Returns the value specified by key
Returns null if no such key exists
- get(Class<?>) -
Method in class chemaxon.alchemist.configbuilder.ConfigElementPresentationChooser
- Returns the
ConfigElementEditor instance for the given key.
- get(int) -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor.MoleculeIndexArray
-
- get() -
Method in class chemaxon.alchemist.utils.SwingWorker
- Return the value created by the
construct method.
- 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
- Gets a property.
- 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
-
- getAbsoluteStereo() -
Method in class chemaxon.sss.search.JChemSearchOptions
- Returns 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.
- getADD_MOLECULE_ACTION() -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor
-
- 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.
- getAlchemist() -
Method in class chemaxon.alchemist.AlchemistController
- Returns the alchemist of this configuration instance.
- getAliasstr() -
Method in class chemaxon.struc.MolAtom
- Gets the alias string or pseudo atom type string for pseudo atoms.
- getAlignedCoordinates() -
Method in class chemaxon.marvin.alignment.FlexibleAlignment
-
- getAlignedCoordinates() -
Method in interface chemaxon.marvin.alignment.PairedAlign
-
- getAlignedCoordinates() -
Method in class chemaxon.marvin.alignment.RigidAlignment
-
- getAlignedMolecule() -
Method in class chemaxon.marvin.alignment.FlexibleAlignment
-
- getAlignedMolecule() -
Method in interface chemaxon.marvin.alignment.PairedAlign
-
- getAlignedMolecule() -
Method in class chemaxon.marvin.alignment.RigidAlignment
-
- getAlignmentType() -
Method in class chemaxon.marvin.alignment.Alignment
-
- 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)
- 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.
- getApplicationFrame() -
Method in class chemaxon.alchemist.AlchemistApplication
- This method returns the application frame instance
The contentPane should not be modified, components
should be handled via getContentPane()
- getApplicationState() -
Method in class chemaxon.alchemist.AlchemistApplication
- This function returns the main state object of the application
- getApplicationTitle() -
Method in class chemaxon.alchemist.AlchemistApplication
- Returns the application title
- 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.
- getAPPLY_MOLECULE_EDIT_ACTION() -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor
-
- 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.
- getArcRadius(CTransform3D) -
Method in class chemaxon.struc.graphics.MPolyline
- Gets the arc radius.
- 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.
- 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.
- 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.
- getAscent(Graphics, FontMetrics) -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the ascent of this portion.
- 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.
- 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(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
- getAsymmetricFBPA(PharmacophoreFingerprint) -
Method in class chemaxon.descriptors.PharmacophoreFingerprint
- Calculates the asymmetric FBPA convolution product based distasnce 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(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 interface chemaxon.struc.Incomplecule
- Gets the number of atoms.
- getAtomCount() -
Method in class chemaxon.struc.MoleculeGraph
- Gets the number of atoms.
- getAtomCount() -
Method in class chemaxon.struc.RgMolecule
- Gets the number of nodes in the root structure.
- getAtomCount() -
Method in class chemaxon.struc.RxnMolecule
- Returns the number of nodes in the graph union.
- 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.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
- Returns the sum of the implicit H logP increments for the specified atom.
- 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.
- 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.
- 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.
- getAttach() -
Method in class chemaxon.struc.MolAtom
- Gets 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.
- 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.
- 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.alchemist.utils.AlchemistLinearMoleculeView
-
- 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.
- getBackgroundImage() -
Method in class chemaxon.alchemist.utils.AlchemistWaitPanel
-
- 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.
- getBanner() -
Method in class chemaxon.alchemist.AlchemistApplication
- This function returns a banner instance for
this application.
- getBarBackgroundColor() -
Method in class chemaxon.alchemist.utils.AlchemistWaitPanel
-
- getBarHeight() -
Method in class chemaxon.alchemist.utils.AlchemistWaitPanel
-
- getBarHighColor() -
Method in class chemaxon.alchemist.utils.AlchemistWaitPanel
-
- getBarLowColor() -
Method in class chemaxon.alchemist.utils.AlchemistWaitPanel
-
- getBarStyle() -
Method in class chemaxon.alchemist.utils.AlchemistWaitPanel
-
- 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.
- 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.
- getBlockIncrement() -
Method in class chemaxon.alchemist.utils.AlchemistLinearMoleculeView
- Returns the scrollbar block increment
- 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.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 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.
- getBondList(MolAtom[], int) -
Static method in class chemaxon.struc.MoleculeGraph
- Gets the list of bonds for the specified atoms.
- getBonds() -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- getBonds() -
Method in interface chemaxon.checkers.result.StructureCheckerResult
-
- getBonds() -
Method in class chemaxon.struc.MDocument.CheckerMark
-
- 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.
- 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.
- 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.
- 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.
- 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.
- getBrightness() -
Method in class chemaxon.descriptors.ChemicalFingerprint
- 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
- Gets the edge (bond) table.
- getBtab() -
Method in class chemaxon.struc.RgMolecule
- Gets the bond table of the root structre.
- getBtab() -
Method in class chemaxon.struc.RxnMolecule
- Gets the bond table for the graph union.
- 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.
- getButtom() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the y coordinate of the buttom of the cell in pixels.
- 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.
- getCacheLock() -
Method in class chemaxon.marvin.view.MDocStorage
- Gets the synchronization lock for caching operations.
- 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.
- getCANCEL_MOLECULE_EDIT_ACTION() -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor
-
- 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.alchemist.utils.MoleculeTableCellEditor
-
- 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.
- 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.
- 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.
- 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.
- getChargeMatching() -
Method in class chemaxon.sss.search.SearchOptions
-
- 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
- Returns true if sp-hybridization state of the atoms should be considered,
false otherwise
- 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.
- getChild() -
Method in interface chemaxon.marvin.util.MProgressMonitor
- Gets the child of this progress monitor.
- 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 neighbouring 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
-
- getChiralitySupport() -
Method in class chemaxon.marvin.MolPrinter
- Returns the current chirality display mode.
- getClassifier() -
Method in class chemaxon.fragmenter.Fragmenter
- Returns the classifier object.
- 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.modules.datatransfer.ClipboardHandler
- Deprecated. see
ClipboardHandler.setWorkOnBackground(boolean)
- 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.
- getColCount() -
Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeView
- Returns the current column count
- getColCount() -
Method in class chemaxon.alchemist.utils.AlchemistMoleculeView
- Returns the current column count
- 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.
- getColoringAndAlignOptions() -
Method in class chemaxon.jchem.webservice.RelSearchWS.Query
-
- 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.
- 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.