A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

A_ALL - Static variable in class chemaxon.struc.graphics.MTextAttributes

All identifiers.

A_BOLD - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font's bold subattribute.

A_DX - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the x shift attribute.

A_DY - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the y shift attribute.

A_FONT - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font attribute.

A_FONT_BITS - Static variable in class chemaxon.struc.graphics.MTextAttributes

All font bits.

A_FONTFAMILY - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font family subattribute.

A_FONTSIZE - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font size subattribute.

A_FOREGROUND - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the color attribute.

A_ITALIC - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font's italic subattribute.

A_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the font scale attribute.

A_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes

Identifier of the subscript/superscript level attribute.

AAMAP_MASK - Static variable in class chemaxon.struc.MolAtom

Atom map mask in flags.

AAMAP_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum atom-atom mapping number.

AAMAP_OFF - Static variable in class chemaxon.struc.MolAtom

Atom map offset in flags.

ABBREVGROUP - Static variable in class chemaxon.formats.MFileFormat

ChemAxon SMILES Abbreviated Groups.

AbbrevGroupRecognizer - Class in chemaxon.formats.recognizer

AbbrevGroup format recognizer.

AbbrevGroupRecognizer(String) - Constructor for class chemaxon.formats.recognizer.AbbrevGroupRecognizer

Creates an AbbrevGroup format recognizer.

ABS_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts

Absolute stereoconfiguration label visibility flag.

ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.sss.SearchConstants

Option for absolute stereo matching.

absoluteStereo - Variable in class chemaxon.jchem.db.StructureTableOptions

Specifies if structures should eb treated as absolute stereo during database search.

AbstractAlchemistMoleculeEditor - Class in chemaxon.alchemist.utils

AbstractAlchemistMoleculeEditor(int, int, SwingPropertyChangeSupport, MSketchPane) - Constructor for class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor

Constructor from superclass

AbstractAlchemistMoleculeEditor(int, int, int, int, SwingPropertyChangeSupport, MSketchPane) - Constructor for class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor

AbstractAlchemistMoleculeEditor.MoleculeIndexArray - Class in chemaxon.alchemist.utils

AbstractAlchemistMoleculeEditor.MoleculeIndexArray(int) - Constructor for class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor.MoleculeIndexArray

AbstractAlchemistMoleculeView - Class in chemaxon.alchemist.utils

AbstractAlchemistMoleculeView(int, int) - Constructor for class chemaxon.alchemist.utils.AbstractAlchemistMoleculeView

Constructs view with the given size

AbstractAlchemistMoleculeView(int, int, boolean) - Constructor for class chemaxon.alchemist.utils.AbstractAlchemistMoleculeView

Constructs view with the given size.

AbstractConfigElementEditor - Class in chemaxon.alchemist.configbuilder

A ConfigElementEditor implementation with customizable editor component.

AbstractConfigElementEditor() - Constructor for class chemaxon.alchemist.configbuilder.AbstractConfigElementEditor

AbstractConfigurationReader - Class in chemaxon.alchemist.configbuilder

This is an abstract configuration reader class for reading configuration xml files for configbuilder

AbstractConfigurationReader(InputStream) - Constructor for class chemaxon.alchemist.configbuilder.AbstractConfigurationReader

AbstractConfigurationWriter - Class in chemaxon.alchemist.configbuilder

This is an abstract configuration xml file writer for configbuilder

AbstractConfigurationWriter(OutputStream) - Constructor for class chemaxon.alchemist.configbuilder.AbstractConfigurationWriter

AbstractMRecordReader - Class in chemaxon.marvin.io.formats

Abstract record reader class.

AbstractMRecordReader(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader

Constructs an abstract record reader.

AbstractSketchConfigElement - Class in chemaxon.alchemist.configbuilder

This is an abstract ConfigElement using MSketchPane as an external editor by implementing ExternalEditorSupport interface.

AbstractSketchConfigElement() - Constructor for class chemaxon.alchemist.configbuilder.AbstractSketchConfigElement

accept(Molecule) - Method in interface chemaxon.enumeration.MolFilter

Returns true if molecule is accepted by the filter.

accepted(Molecule) - Method in class chemaxon.alchemist.configbuilder.AbstractSketchConfigElement

This method is called after 'accept' button pressed on external sketch editor.

ACCEPTOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin

Acceptor sign displayed in GUI.

ACCEPTOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint

ACCUM_NUMBER - Static variable in class chemaxon.marvin.space.GraphicCell

ACIDIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin

Constant denoting acidic pKa.

ACTION_ID - Static variable in class chemaxon.alchemist.AlchemistApplication.ExitApplicationAction

ACTION_ID - Static variable in class chemaxon.alchemist.AlchemistApplication.LicenseManagerAction

ACTION_ID - Static variable in class chemaxon.alchemist.AlchemistApplication.NewDocumentAction

ACTION_ID - Static variable in class chemaxon.alchemist.AlchemistApplication.OpenDocumentAction

ACTION_ID - Static variable in class chemaxon.alchemist.AlchemistApplication.SaveDocumentAction

ACTION_ID - Static variable in class chemaxon.alchemist.AlchemistApplication.SaveDocumentAsAction

actionPerformed(ActionEvent) - Method in class chemaxon.alchemist.AlchemistApplication.ExitApplicationAction

actionPerformed(ActionEvent) - Method in class chemaxon.alchemist.AlchemistApplication.LicenseManagerAction

actionPerformed(ActionEvent) - Method in class chemaxon.alchemist.AlchemistApplication.NewDocumentAction

actionPerformed(ActionEvent) - Method in class chemaxon.alchemist.AlchemistApplication.OpenDocumentAction

actionPerformed(ActionEvent) - Method in class chemaxon.alchemist.AlchemistApplication.SaveDocumentAction

actionPerformed(ActionEvent) - Method in class chemaxon.alchemist.AlchemistApplication.SaveDocumentAsAction

actionPerformed(ActionEvent) - Method in class chemaxon.marvin.beans.MViewPane

Handles menu item actions.

actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane

Action handler.

actionPerformed(ActionEvent) - Method in class chemaxon.marvin.util.SwingUtil

activateContainerCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene

The containing cell of the GraphicComponent will be the active cell of the scene.

activateWithItem(ConfigItem) - Method in class chemaxon.alchemist.configbuilder.ConfigItemPanel

Deprecated. Activates panel with given item

ACTIVE - Static variable in class chemaxon.alchemist.AlchemistProgressLabel

active state of progress label

active - Variable in class chemaxon.marvin.space.GraphicComponent

Is this component selected or not.

add(MDSet) - Method in interface chemaxon.descriptors.MDHypothesisGenerator

Adds a MDSet component to be considered in the hypothesis.

add(Molecule) - Method in class chemaxon.reaction.synthesis.MoleculeSet

Deprecated. Adds a molecule this molecule set.

add(Molecule, int[], int, boolean) - Method in class chemaxon.reaction.synthesis.MoleculeSet

Deprecated. Adds a molecule to the set with origin codes.

add(Molecule, Standardizer) - Method in class chemaxon.reaction.synthesis.MoleculeSet

Deprecated. Adds an input molecule to this molecule set.

add(Molecule) - Method in class chemaxon.reaction.Synthesizer

Deprecated. Adds a molecule to the input molecule set.

add(Molecule, String) - Method in class chemaxon.reaction.Synthesizer

Deprecated. Adds a molecule to a molecule set.

add(File) - Method in class chemaxon.reaction.Synthesizer

Deprecated. Adds molecules to the input molecule set.

add(InputStream) - Method in class chemaxon.reaction.Synthesizer

Deprecated. Adds molecules to the input molecule set.

add(File, String) - Method in class chemaxon.reaction.Synthesizer

Deprecated. Adds molecules to a molecule set.

add(InputStream, String) - Method in class chemaxon.reaction.Synthesizer

Deprecated. Adds molecules to a molecule set.

add(CNode) - Method in class chemaxon.struc.CGraph

Adds a node to the graph.

add(CEdge) - Method in class chemaxon.struc.CGraph

Adds an edge to the graph.

add(CEdge) - Method in class chemaxon.struc.CNode

Add an edge if it had not been already added.

add(CEdge) - Method in class chemaxon.struc.MolAtom

Add an edge if it had not been already added.

add(MProp) - Method in class chemaxon.struc.prop.MListProp

Adds an element.

add(CNode) - Method in class chemaxon.struc.RgMolecule

Adds an atom to the root structure.

add(CEdge) - Method in class chemaxon.struc.RgMolecule

Adds a bond to the root structure.

add(CNode) - Method in class chemaxon.struc.RxnMolecule

Adds an atom to a reactant, product or agent structure.

add(CEdge) - Method in class chemaxon.struc.RxnMolecule

Adds a bond to a reactant, product, agent.

add(CEdge) - Method in class chemaxon.struc.SelectionMolecule

Adds an edge to the graph.

add(MolAtom) - Method in class chemaxon.struc.Sgroup

Adds a new atom to the S-group.

add(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup

Adds a new atom to the S-group.

add(CEdge) - Method in class chemaxon.struc.sgroup.SgroupAtom

Add an edge if it had not been already added.

add(int) - Method in class chemaxon.util.IntArray

Adds the specified component to the end of this IntArray, increasing its size by one.

ADD_MOLECULE_ACTION - Variable in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor

Action for perform add molecule to the editor.

addActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane

Adds an action listener.

addAll(IntArray) - Method in class chemaxon.util.IntArray

Appends all of the elements in the specified collection to the end of this vector, in the order that they are returned by the specified collection's iterator (optional operation).

addAtomsAndBondsTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph

Adds all atoms and bonds to the specified molecule.

addAttachAtom(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Adds an atom to the list of attachments.

addAttributeKeys(Vector) - Method in class chemaxon.struc.graphics.MBracket

addAttributeKeys(Vector) - Method in class chemaxon.struc.graphics.MPolyline

Adds the attribute names to the specified vector.

addAttributeKeys(Vector) - Method in class chemaxon.struc.graphics.MRectangle

Adds the attribute names to the specified vector.

addAttributeKeys(Vector) - Method in class chemaxon.struc.graphics.MTextBox

Adds the attribute names to the specified vector.

addAttributeKeys(Vector) - Method in class chemaxon.struc.MObject

Adds the attribute names to the specified vector.

addCanvas(Container) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace viewer to the container.

addCdataAttributeKeys(Vector) - Method in class chemaxon.struc.graphics.MTextBox

Adds attribute names to the specified vector.

addCdataAttributeKeys(Vector) - Method in class chemaxon.struc.MObject

Adds attribute names to the specified vector.

addChar(char) - Method in class chemaxon.struc.graphics.MTextBox

Adds a character to the text.

addChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup

Adds a child S-group.

addCommand(ConfigItem) - Method in class chemaxon.alchemist.configbuilder.ConfigBuilder

Deprecated. Adds a configuration item to the end of the list

addCommand(String, String, Object, String, Class) - Method in class chemaxon.marvin.plugin.CommandPlugger

Adds a plugin.

addComparator(MolComparator) - Method in class chemaxon.sss.search.MolSearch

addComponent(Component) - Method in class chemaxon.alchemist.utils.AlchemistComponentSet

Adds a component to the set

addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell

Adds a new component to this cell.

addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene

Adds a component to the active or to the first cell.

addComponent(GraphicComponent, int) - Method in class chemaxon.marvin.space.GraphicScene

Adds a component to the cell having the given index.

addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule

Adds a reactant, product or agent.

addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule

Adds a reactant, product or agent.

addComponents() - Method in class chemaxon.alchemist.configbuilder.AbstractConfigElementEditor

Creates and adds components for mainPanel

addComponents() - Method in class chemaxon.alchemist.configbuilder.BasicConfigElementEditor

addComponentToEmptyCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene

Adds a component to an empty cell.

addCoordinateSystem(int) - Method in class chemaxon.marvin.space.GraphicScene

Adds a dummy graphic component that represents the coordinate system.

addData(Molecule, MolAtom, String, String) - Method in class chemaxon.marvin.io.MolExportModule

Adds a data sgroup to the given atom in the given molecule with fieldName and value.

addDataLine(String) - Method in class chemaxon.struc.sgroup.DataSgroup

Adds a line to the data stored in the field.

addDefaultOpenFileFilters() - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds the choosable file filters for open dialog.

addDefaultSaveFileFilters() - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds the choosable file filters for save dialog.

addDescriptor(MolecularDescriptor) - Method in class chemaxon.descriptors.MDSet

Appends the next component to the MDSet object.

addDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent

Forces the component to set all drawing property stored in drawProperties, and leaves the old settings which are not overidden.

addEdge0(CEdge) - Method in class chemaxon.struc.CGraph

Adds an edge.

addEdge0(CEdge) - Method in class chemaxon.struc.SelectionMolecule

Adds an edge.

addEdgeWithoutChangingIt(CEdge) - Method in class chemaxon.struc.CGraph

Adds an edge without setting its parentGraph and index fields.

addElement(ConfigElement) - Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel

Adds the clone of the element to the right list

addElementPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel

Adds a PropertyChangeListener for element property changes

addElementPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.alchemist.configbuilder.ConfigBuilderPanel

Adds a PropertyChangeListener for a specific element property change

addExplicitHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph

Adds explicit H atoms instead of the current implicit ones.

addExplicitHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph

Adds explicit H atoms instead of the current implicit ones.

addExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph

Adds explicit lone pairs.

addFileFilters(FileFilter[]) - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds choosable file filters to the choosable file filter list.

addFolder(String, Class) - Method in class chemaxon.marvin.plugin.CommandPlugger

Adds a plugin folder.

addFunction(String, PostfixMathCommandI) - Method in class chemaxon.jep.ChemJEP

Adds a new function to the parser.

addGroup(String) - Method in class chemaxon.alchemist.configbuilder.ConfigElement

Sets this element as a member of given group

addGroupsToFile(String, List) - Static method in class chemaxon.alchemist.configbuilder.GroupEditor

Deprecated. Adds a group name List directly to group configuration file.

addHelpMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane

Adds the help menu to a parent menu.

addHydrogens(Molecule) - Static method in class chemaxon.sss.search.RGroupDecomposition

Adds explicit hydrogens to query molecule to force ligands to be attached at Rgroup atoms only.

addHydrogens() - Method in class chemaxon.util.MolHandler

Adds explicit H atoms instead of the current implicit ones.

addHydrogensToAromaticHeteroAtoms() - Method in class chemaxon.util.MolHandler

Adds the implicit Hydrogen atoms to heteroatoms in aromatic rings.

addItem(String) - Method in class chemaxon.alchemist.configbuilder.ConfigItemList

Deprecated. Adds an item to the list

addLabel(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a label component inside the MarvinView table.

addLabel(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a label component inside the MarvinView table.

addListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage

Adds a listener if it is not yet added.

addListSelectionListener(ListSelectionListener) - Method in class chemaxon.alchemist.utils.AlchemistLinearMoleculeView

Adds a list selection listener

addListSelectionListerer(ListSelectionListener) - Method in class chemaxon.alchemist.utils.AlchemistMoleculeView

Add a list selection listener to the view grid

addLogger(ProgressWriter.Logger) - Method in class chemaxon.jchem.file.ProgressWriter

Adds a ProgressWriter.Logger to retrieve suppressed (error) messages.

addMatch(int, int) - Method in class chemaxon.sss.search.MolSearch

Specifies an extra prerequisite of the structure search that queryAtom must match to targetAtom only.

addMatch(int[], int[], int) - Method in class chemaxon.sss.search.MolSearch

Specifies extra prerequisites of the structure search that queryAtoms[0] must match to targetAtoms[0] only AND queryAtoms[1] must match to targetAtoms[1], etc.

addMatch(int, int) - Method in class chemaxon.sss.search.Search

Specifies an extra prerequisite of the structure search that queryAtom must match to targetAtom only.

addMatch(int[], int[], int) - Method in class chemaxon.sss.search.Search

Specifies extra prerequisites of the structure search that queryAtoms[0] must match to targetAtoms[0] only AND queryAtoms[1] must match to targetAtoms[1], etc.

addMDConfig(String, String, String) - Method in class chemaxon.descriptors.GenerateMD

Adds a new parameter configuration to the descriptor.

addMDConfig(String, String, File) - Method in class chemaxon.descriptors.GenerateMD

Adds a new parameter configuration to the descriptor.

addMenuBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace menubar to the container.

addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane

Adds a menubar change listener.

addMessage(int, String, Throwable) - Method in interface chemaxon.jchem.file.ProgressWriter.Logger

addMetabolizerSaveFileFilters() - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds the choosable metabolizer file filters for save dialog

addMolecule() - Method in class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor

AddMolecule action handler

addMolecule(Molecule) - Method in class chemaxon.clustering.LibraryMCS

Adds a new molecule to the set of structures to be clustered.

addMolecule(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a molecule viewer component inside the MarvinView table.

addMolecule(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams

Defines a molecule viewer component inside the MarvinView table.

addMolecule(String) - Method in class chemaxon.marvin.space.MSpaceEasy

Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.

addMolecule(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds a Molecule object to the actual cell of the viewer.

addMoleculeTo(Molecule, int) - Method in class chemaxon.marvin.space.MSpaceEasy

Makes the given cell to be the active cell, and adds the molecule to it.

addMoleculeToEmptyCell(String) - Method in class chemaxon.marvin.space.MSpaceEasy

Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.

addMoleculeToEmptyCell(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.

addMoleculeWithoutChange(Molecule, boolean) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds a Molecule object to the actual cell of the viewer and resets the view only if required.

addNode0(CNode) - Method in class chemaxon.struc.CGraph

Adds a node.

addNode0(CNode) - Method in class chemaxon.struc.Molecule

Adds a node.

addNode0(CNode) - Method in class chemaxon.struc.SelectionMolecule

Adds a node.

addNodeWithoutChangingIt(CNode) - Method in class chemaxon.struc.CGraph

Adds a node without setting its parentGraph and index fields.

addNotify() - Method in class chemaxon.struc.graphics.MMidPoint

Point added to a document.

addNotify() - Method in class chemaxon.struc.graphics.MRectanglePoint

Point added to a document.

addNotify() - Method in class chemaxon.struc.MObject

Called when the object is added to a document.

addObject(MObject) - Method in class chemaxon.struc.MDocument

Adds an object to the document.

addObject(MObject) - Method in class chemaxon.struc.MSelectionDocument

Adds an object to the document.

addOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings

Adds an owner.

addPage(String, AlchemistPage) - Method in class chemaxon.alchemist.AlchemistController

Inserts an item to the end of progress list.

addParameters(String) - Method in class chemaxon.descriptors.MDParameters

Sets parameters from an XML string representation keeping all previous settings.

addParameters(File) - Method in class chemaxon.descriptors.MDParameters

Sets parameters from an XML config file keeping all previous settings.

addParametrizedMetric(String, String, String) - Method in class chemaxon.descriptors.MDParameters

Expands the set of parametrized metrics with a new item.

addParametrizedMetricNode(String, String, String) - Method in class chemaxon.descriptors.MDParameters

Adds a ParametrizedMetric node to the DOM tree.

addParametrizedMetricsNode() - Method in class chemaxon.descriptors.MDParameters

Adds the ParametrizedMetrics node to the DOM tree.

addPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy

Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)

addPopupMenu() - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace popup menu to the JPanel.

addProgressCustomComponent(JComponent) - Method in class chemaxon.alchemist.commonpages.ProgressPanel

Adds a JComponent after the last item in the progress panel for custom progress actions (For example show current operations)

addProperty(String, String) - Method in class chemaxon.jchem.db.DatabaseProperties

Inserts the property with the specified key and value If the specified value is null, the property is deleted.

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.alchemist.configbuilder.ConfigElement

Add a PropertyChangeListener to the listener list.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.alchemist.configbuilder.ConfigElement

Add a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MSketchPane

Adds a PropertyChangeListener for a specific property.

addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MViewPane

Adds a PropertyChangeListener for a specific property.

addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings

Add bean property change listener

addQueries(MDSet[]) - Method in class chemaxon.descriptors.MDSimilarity

Adds new query molecules as their set of descriptors from an array.

addQueries(MDReader) - Method in class chemaxon.descriptors.MDSimilarity

Adds new query molecules as their set of descriptors from a chemical descriptor reader.

addQuery(MDSet) - Method in class chemaxon.descriptors.MDSimilarity

Adds a new query molecule as its set of descriptors.

addReactionLibraryOpenFileFilters() - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds the choosable reaction library file filters for open dialog

addReactionLibrarySaveFileFilters() - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds the choosable reaction library file filters for save dialog

addReactionOpenFileFilters() - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds the choosable reaction file filters for open dialog 'All reaction files' will be initially selected

addReactionSaveFileFilters() - Method in class chemaxon.alchemist.utils.AlchemistFileChooser

This method adds the choosable reaction file filters for save dialog

addReactionStep(ArrayList, ArrayList, ArrayList, MRArrow, int) - Method in class chemaxon.struc.RxnMolecule

addResultWriter(MDSimilarityResultWriter) - Method in class chemaxon.descriptors.MDSimilarity

Adds a MDSimilarityResultWriter object.

addRgroup(int, Molecule) - Method in class chemaxon.struc.RgMolecule

Adds an R-group member.

addRGroups(Molecule) - Static method in class chemaxon.sss.search.RGroupDecomposition

Adds different rgroup atoms connected by any-bonds to query molecule in place of all implicit H-s.

addRGroups(Molecule, int) - Static method in class chemaxon.sss.search.RGroupDecomposition

Adds different rgroup atoms connected by the specified bond type to query molecule in place of all implicit H-s.

addRgroupsTo(Molecule) - Method in class chemaxon.struc.RgMolecule

Creates a read only RgMolecule from a simple molecule object.

addSelectionPanel(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace selection panel to the container.

addSelectionPanelAndProgressBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace selection panel to the container.

addSets(MoleculeSet[], MoleculeSet[]) - Method in class chemaxon.reaction.SynthesisAlgorithm

Deprecated. Adds reactant and product set IDs for the current step to the set list.

addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.Molecule

Adds an S-group to this object and its parent.

addSgroupClones(Molecule, Molecule, Molecule) - Method in class chemaxon.struc.Molecule

Adds the S-groups of a child molecule clone to the new parent molecule clone.

addSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule

Adds S-groups to this object and its parent.

addString(String) - Method in class chemaxon.struc.graphics.MTextBox

Adds a string to the text.

addStructure(Molecule, int) - Method in class chemaxon.struc.RxnMolecule

Deprecated. as of Marvin 4.1, replaced by RxnMolecule.addComponent(Molecule, int)

addStructure(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule

Deprecated. as of Marvin 4.1, replaced by RxnMolecule.addComponent(Molecule, int, boolean)

addTo(Properties) - Method in class chemaxon.marvin.common.UserSettings

Puts all properties into the specified Properties object.

addToolBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy

Adds the basic MarvinSpace toolbar to the container.

addToolsMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane

Adds the Tools menu.

addToSketchRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings

Add an element to marvinsketch's recent file list

addToViewRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings

Add an element to marvinview's recent file list

addUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions

Adds the given user-defined comparator to the search.

addWithLCKeysTo(Properties) - Method in class chemaxon.marvin.common.UserSettings

Puts all properties into the specified Properties object, with lower case names.

adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph

Checks whether the molecule has multiple chiral centres

AGENTS - Static variable in class chemaxon.struc.RxnMolecule

"Agent" structure type.

Alchemist - Class in chemaxon.alchemist

Alchemist(String, AlchemistController) - Constructor for class chemaxon.alchemist.Alchemist

This is the constructor

alchemist - Variable in class chemaxon.alchemist.AlchemistController

The Alchemist object of the controller instance

ALCHEMIST_BLUE - Static variable in class chemaxon.alchemist.utils.AlchemistUtilities

Deprecated. See predefined colors in AlchemistGraphicsUtilities

AlCHEMIST_DEFAULT_MVIEW_LAYOUT - Static variable in class chemaxon.alchemist.utils.AlchemistUtilities

ALCHEMIST_GRAY - Static variable in class chemaxon.alchemist.utils.AlchemistGraphicsUtilities

ALCHEMIST_GRAY - Static variable in class chemaxon.alchemist.utils.AlchemistUtilities

Deprecated. See predefined colors in AlchemistGraphicsUtilities

ALCHEMIST_ORANGE - Static variable in class chemaxon.alchemist.utils.AlchemistGraphicsUtilities

ALCHEMIST_ORANGE - Static variable in class chemaxon.alchemist.utils.AlchemistUtilities

Deprecated. See predefined colors in AlchemistGraphicsUtilities

ALCHEMIST_SIDEBAR_BGR_GRADIENT1 - Static variable in class chemaxon.alchemist.utils.AlchemistGraphicsUtilities

alchemist sidebar background gradient top

ALCHEMIST_SIDEBAR_BGR_GRADIENT2 - Static variable in class chemaxon.alchemist.utils.AlchemistGraphicsUtilities

alchemist sidebar background gradient bottom

ALCHEMIST_TOOLTIP_BGR - Static variable in class chemaxon.alchemist.utils.AlchemistGraphicsUtilities

the alchemist tooltip background color

ALCHEMIST_TOOLTIP_YELLOW - Static variable in class chemaxon.alchemist.utils.AlchemistGraphicsUtilities

Deprecated. use ALCHEMIST_TOOLTIP_BGR instead

ALCHEMIST_WIZARD_PROGRESS_ACTIVE_9 - Static variable in class chemaxon.alchemist.utils.AlchemistIconFactory

progress object image for active state

ALCHEMIST_WIZARD_PROGRESS_DISABLED_9 - Static variable in class chemaxon.alchemist.utils.AlchemistIconFactory

progress object image for disabled state

ALCHEMIST_WIZARD_PROGRESS_DONE_9 - Static variable in class chemaxon.alchemist.utils.AlchemistIconFactory

progress object image for done state

ALCHEMIST_YELLOW - Static variable in class chemaxon.alchemist.utils.AlchemistUtilities

Deprecated. See predefined colors in AlchemistGraphicsUtilities

AlchemistApplication - Class in chemaxon.alchemist

AlchemistApplication() - Constructor for class chemaxon.alchemist.AlchemistApplication

Constructor.

AlchemistApplication(String) - Constructor for class chemaxon.alchemist.AlchemistApplication

Constructor.

AlchemistApplication.ExitApplicationAction - Class in chemaxon.alchemist

Default Exit Application Action

AlchemistApplication.ExitApplicationAction() - Constructor for class chemaxon.alchemist.AlchemistApplication.ExitApplicationAction

AlchemistApplication.LicenseManagerAction - Class in chemaxon.alchemist

Default License Manager Action

AlchemistApplication.LicenseManagerAction() - Constructor for class chemaxon.alchemist.AlchemistApplication.LicenseManagerAction

AlchemistApplication.NewDocumentAction - Class in chemaxon.alchemist

Default New Doucment Action

AlchemistApplication.NewDocumentAction() - Constructor for class chemaxon.alchemist.AlchemistApplication.NewDocumentAction

AlchemistApplication.OpenDocumentAction - Class in chemaxon.alchemist

Default Open Document Action

AlchemistApplication.OpenDocumentAction() - Constructor for class chemaxon.alchemist.AlchemistApplication.OpenDocumentAction

AlchemistApplication.SaveDocumentAction - Class in chemaxon.alchemist

Default Save Document Action

AlchemistApplication.SaveDocumentAction() - Constructor for class chemaxon.alchemist.AlchemistApplication.SaveDocumentAction

AlchemistApplication.SaveDocumentAsAction - Class in chemaxon.alchemist

Default Save Document As Action

AlchemistApplication.SaveDocumentAsAction() - Constructor for class chemaxon.alchemist.AlchemistApplication.SaveDocumentAsAction

AlchemistApplicationInnerDialog - Class in chemaxon.alchemist.utils

AlchemistApplicationInnerDialog(AlchemistApplication, Action, Action) - Constructor for class chemaxon.alchemist.utils.AlchemistApplicationInnerDialog

Constructs an AlchemistApplicationInnerDialog instance with ok and cancel actions

AlchemistApplicationInnerDialog(AlchemistApplication, Action) - Constructor for class chemaxon.alchemist.utils.AlchemistApplicationInnerDialog

Constructs an AlchemistApplicationInnerDialog instance with close action

AlchemistApplicationLicenseHandlerInnerDialog - Class in chemaxon.alchemist.utils

AlchemistApplicationLicenseHandlerInnerDialog(AlchemistApplication, Action) - Constructor for class chemaxon.alchemist.utils.AlchemistApplicationLicenseHandlerInnerDialog

Constructs an instance of AlchemistApplicationLicenseHandlerInnerDialog for AlchemistApplication license handling in inner dialog

AlchemistBanner - Class in chemaxon.alchemist

AlchemistBanner(String, String, String, String) - Constructor for class chemaxon.alchemist.AlchemistBanner

Constructor.

AlchemistBrowserLauncher - Class in chemaxon.alchemist.utils

AlchemistBrowserLauncher() - Constructor for class chemaxon.alchemist.utils.AlchemistBrowserLauncher

AlchemistComponentSet - Class in chemaxon.alchemist.utils

AlchemistComponentSet() - Constructor for class chemaxon.alchemist.utils.AlchemistComponentSet

Creates a new AlchemistComponentSet The components in this set will be initialized as visible and enabled

AlchemistComponentSet(boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistComponentSet

Creates a new AlchemistComponentSet The components in this set will be initialized as visible, and will be enabled depending on parameter

AlchemistComponentSet(boolean, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistComponentSet

Creates a new AlchemistComponentSet The components in this set will be initialized as given in parameters

AlchemistController - Class in chemaxon.alchemist

AlchemistController(String) - Constructor for class chemaxon.alchemist.AlchemistController

Creates an AlchemistController instance.

AlchemistDashedBorder - Class in chemaxon.alchemist.utils

AlchemistDashedBorder(Color) - Constructor for class chemaxon.alchemist.utils.AlchemistDashedBorder

AlchemistDashedBorder(Color, int, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistDashedBorder

AlchemistDashedBorder(Color, int) - Constructor for class chemaxon.alchemist.utils.AlchemistDashedBorder

AlchemistError - Class in chemaxon.alchemist

AlchemistFileChooser - Class in chemaxon.alchemist.utils

AlchemistFileChooser() - Constructor for class chemaxon.alchemist.utils.AlchemistFileChooser

Constructor.

AlchemistFileChooser(boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistFileChooser

Construct a file chooser Sets a marvin view accessory depending on parameter

AlchemistFileChooser(File, FileSystemView) - Constructor for class chemaxon.alchemist.utils.AlchemistFileChooser

AlchemistFileChooser(File) - Constructor for class chemaxon.alchemist.utils.AlchemistFileChooser

AlchemistFileChooser(FileSystemView) - Constructor for class chemaxon.alchemist.utils.AlchemistFileChooser

AlchemistFileChooser(String, FileSystemView) - Constructor for class chemaxon.alchemist.utils.AlchemistFileChooser

AlchemistFileChooser(String) - Constructor for class chemaxon.alchemist.utils.AlchemistFileChooser

AlchemistFileTextBox - Class in chemaxon.alchemist.utils

AlchemistFileTextBox(int, AlchemistFileChooser, SwingPropertyChangeSupport, String, boolean, String) - Constructor for class chemaxon.alchemist.utils.AlchemistFileTextBox

Constructs an AlchemistFileTextBox

AlchemistFileTextBox(AlchemistFileChooser, SwingPropertyChangeSupport, String, boolean, String) - Constructor for class chemaxon.alchemist.utils.AlchemistFileTextBox

Constructs an AlchemistFileTextBox in OPEN_FILE_MODE

AlchemistGlassPage - Class in chemaxon.alchemist

AlchemistGlassPage() - Constructor for class chemaxon.alchemist.AlchemistGlassPage

AlchemistGraphicsUtilities - Class in chemaxon.alchemist.utils

AlchemistGraphicsUtilities() - Constructor for class chemaxon.alchemist.utils.AlchemistGraphicsUtilities

AlchemistIconFactory - Class in chemaxon.alchemist.utils

AlchemistLabel - Class in chemaxon.alchemist.utils

AlchemistLabel() - Constructor for class chemaxon.alchemist.utils.AlchemistLabel

AlchemistLabel(String) - Constructor for class chemaxon.alchemist.utils.AlchemistLabel

AlchemistLabel(String, String) - Constructor for class chemaxon.alchemist.utils.AlchemistLabel

AlchemistLabel(int) - Constructor for class chemaxon.alchemist.utils.AlchemistLabel

AlchemistLabel(String, int) - Constructor for class chemaxon.alchemist.utils.AlchemistLabel

AlchemistLabel(String, int, int) - Constructor for class chemaxon.alchemist.utils.AlchemistLabel

AlchemistLabel(String, int, int, String) - Constructor for class chemaxon.alchemist.utils.AlchemistLabel

AlchemistLaunchable - Interface in chemaxon.alchemist.utils

AlchemistLauncher - Class in chemaxon.alchemist.utils

AlchemistLauncher() - Constructor for class chemaxon.alchemist.utils.AlchemistLauncher

This is the default constructor

AlchemistLinearMoleculeView - Class in chemaxon.alchemist.utils

AlchemistLinearMoleculeView(int) - Constructor for class chemaxon.alchemist.utils.AlchemistLinearMoleculeView

Creates an AlchemistLinearMoleculeView

AlchemistMoleculeEditor - Class in chemaxon.alchemist.utils

AlchemistMoleculeEditor(int, int, boolean, SwingPropertyChangeSupport) - Constructor for class chemaxon.alchemist.utils.AlchemistMoleculeEditor

Constructor from superclass

AlchemistMoleculeEditor(int, int, int, int, boolean, SwingPropertyChangeSupport) - Constructor for class chemaxon.alchemist.utils.AlchemistMoleculeEditor

Constructor from superclass

AlchemistMoleculePainter - Class in chemaxon.alchemist.utils

AlchemistMoleculePainter() - Constructor for class chemaxon.alchemist.utils.AlchemistMoleculePainter

AlchemistMoleculeUtilities - Class in chemaxon.alchemist.utils

AlchemistMoleculeUtilities() - Constructor for class chemaxon.alchemist.utils.AlchemistMoleculeUtilities

AlchemistMoleculeView - Class in chemaxon.alchemist.utils

AlchemistMoleculeView(int, int, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistMoleculeView

Creates AlchemistMoleculeView

AlchemistMoleculeView(int, int, int, int, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistMoleculeView

Creates AlchemistMoleculeView

AlchemistMViewAccessory - Class in chemaxon.alchemist.utils

AlchemistMViewAccessory(JFileChooser) - Constructor for class chemaxon.alchemist.utils.AlchemistMViewAccessory

This is the default constructor.

AlchemistPage - Class in chemaxon.alchemist

AlchemistPage() - Constructor for class chemaxon.alchemist.AlchemistPage

AlchemistProfile - Class in chemaxon.alchemist

This is a Profile for various categorized property key-value pairs used by Alchemist based applications and components.

AlchemistProfile() - Constructor for class chemaxon.alchemist.AlchemistProfile

Constructs an empty AlchemistProfile

AlchemistProfileSupport - Interface in chemaxon.alchemist.configbuilder

ConfigElements or ConfigElementEditors implementing this interface can store and restore persistent properties via ConfigBuilderPanel

AlchemistProgressLabel - Class in chemaxon.alchemist

AlchemistProgressLabel(String, int) - Constructor for class chemaxon.alchemist.AlchemistProgressLabel

AlchemistProgressLabel(String, int, Action) - Constructor for class chemaxon.alchemist.AlchemistProgressLabel

AlchemistProgressMonitor - Class in chemaxon.alchemist.utils

AlchemistProgressMonitor() - Constructor for class chemaxon.alchemist.utils.AlchemistProgressMonitor

AlchemistProgressMonitor(long) - Constructor for class chemaxon.alchemist.utils.AlchemistProgressMonitor

AlchemistProgressObject - Class in chemaxon.alchemist

Deprecated. Use AlchemistProgressLabel instead

AlchemistProgressObject(String, int, Action) - Constructor for class chemaxon.alchemist.AlchemistProgressObject

Deprecated. Creates an instance of AlchemistProgressObject with a caption defined in itemText.

AlchemistSpinBox - Class in chemaxon.alchemist.utils

AlchemistSpinBox(int, int, int) - Constructor for class chemaxon.alchemist.utils.AlchemistSpinBox

Constructs an AlchemistSpinBox instance

AlchemistSplashScreen - Class in chemaxon.alchemist

AlchemistSplashScreen() - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Construct an empty splash screen

AlchemistSplashScreen(AlchemistProgressMonitor) - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Conststruct a splash screen

AlchemistSplashScreen(String) - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Constructs a splash screen

AlchemistSplashScreen(String, AlchemistProgressMonitor) - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Constructs a splash screen

AlchemistSplashScreen(Dimension) - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Constructs a splash screen

AlchemistSplashScreen(Dimension, AlchemistProgressMonitor) - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Constructs a splash screen

AlchemistSplashScreen(String, Dimension) - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Constructs a splash screen

AlchemistSplashScreen(String, Dimension, AlchemistProgressMonitor) - Constructor for class chemaxon.alchemist.AlchemistSplashScreen

Constructs a splash screen

AlchemistSplitPane - Class in chemaxon.alchemist.utils

Deprecated. is it no longer used, will be removed

AlchemistSplitPane(boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistSplitPane

Deprecated.

AlchemistSplitPane(int, boolean, Component, Component, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistSplitPane

Deprecated.

AlchemistSplitPane(int, boolean, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistSplitPane

Deprecated.

AlchemistSplitPane(int, Component, Component, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistSplitPane

Deprecated.

AlchemistSplitPane(int, boolean) - Constructor for class chemaxon.alchemist.utils.AlchemistSplitPane

Deprecated.

AlchemistState - Class in chemaxon.alchemist.utils

AlchemistState() - Constructor for class chemaxon.alchemist.utils.AlchemistState

AlchemistTableSizeConfigurerComponent - Class in chemaxon.alchemist.utils

AlchemistTableSizeConfigurerComponent(ActionListener) - Constructor for class chemaxon.alchemist.utils.AlchemistTableSizeConfigurerComponent

Creates an AlchemistTableSizeConfigurerComponent instance with a default 10x10 maximum size, and 1x1 initial size

AlchemistTableSizeConfigurerComponent(ActionListener, int, int) - Constructor for class chemaxon.alchemist.utils.AlchemistTableSizeConfigurerComponent

Creates an AlcemistTableSizeConfigurerWindow instance with given parameters

AlchemistTableSizeConfigurerComponent(ActionListener, int, int, int, int) - Constructor for class chemaxon.alchemist.utils.AlchemistTableSizeConfigurerComponent

Creates an AlcemistTableSizeConfigurerWindow instance with given parameters

AlchemistTask - Class in chemaxon.alchemist

AlchemistTask() - Constructor for class chemaxon.alchemist.AlchemistTask

Constructor.

AlchemistUtilities - Class in chemaxon.alchemist.utils

AlchemistUtilities() - Constructor for class chemaxon.alchemist.utils.AlchemistUtilities

algorithmElement - Variable in class chemaxon.reaction.SynthesisAlgorithm

Deprecated. The algorithm element.

align(Molecule, int[]) - Method in class chemaxon.util.MolAligner

Alignes (rotates) a specified molecule to the pattern molecule in 2D according to the specified atom pairs.

align(Molecule, int[]) - Method in class chemaxon.util.MolHandler

Alignes (rotates) a specified molecule realtive to the contained molecule according to the specified atom pairs.

ALIGN_BOTTOM - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to bottom of box.

ALIGN_CENTER - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to center of box.

ALIGN_LEFT - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to left edge of box.

ALIGN_RIGHT - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to right edge of box.

ALIGN_TOP - Static variable in class chemaxon.struc.graphics.MTextBox

Align text to top of box.

ALIGNMENT_OFF - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions

The structure is displayed with the original coordinates.

ALIGNMENT_PARTIAL_CLEAN - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions

The substructure part of the target will get the exact coordinates of the query, and new coordinates will be generated for the remainder of the structure.

ALIGNMENT_ROTATE - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions

The structure is rotated according to the substructure.

alignmentMode - Variable in class chemaxon.util.HitColoringAndAlignmentOptions

Specifies what form of alignment to