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.

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.

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

Returns true if molecule is accepted by the filter.

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.

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.

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

Is this component selected or not.

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_LP - Static variable in class chemaxon.marvin.modules.PDBReader

add one electron pairs too (independant from all ather modes but not a applicaple for HYDROGENIZE_NO

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

Adds an action listener.

addAtom(int, String, char, String, String, int, char, float, float, float, String, int, boolean, float) - Method in class chemaxon.marvin.modules.MacroMolecule

addAtom(int, String, int, char, float, float, float, String, int) - Method in class chemaxon.marvin.modules.MacroMolecule.HeteroComponent

Adds a new atom to the hetero group.

addAtom(int, int, int, int, char, float, float, float, float) - Method in class chemaxon.marvin.modules.MacroMolecule.NucleicAcid

addAtom(int, int, int, int, char, float, float, float, float) - Method in class chemaxon.marvin.modules.MacroMolecule.Polymer

Adds a residue atom to the chain.

addAtom(int, String, int, char, float, float, float, String, int) - Method in class chemaxon.marvin.modules.MacroMolecule.Water

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.

addAuthor(String) - Method in class chemaxon.marvin.modules.MacroMolecule

addBond(int[]) - Method in class chemaxon.marvin.modules.MacroMolecule

addBond(int, int) - Method in class chemaxon.marvin.modules.MacroMolecule.HeteroComponent

Connects two previously defined atoms by a single bond.

addBond(int, int) - Method in class chemaxon.marvin.modules.MacroMolecule.Water

Connects two previously defined atoms by a single bond.

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.

addChain(String) - Method in class chemaxon.marvin.modules.MacroMolecule

addChain(String) - Method in class chemaxon.marvin.modules.MacroMolecule.Compound

Adds a one letter chain identifier to the compond.

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

Adds a plugin.

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.

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

Adds a component to an empty cell.

addCompound(String) - Method in class chemaxon.marvin.modules.MacroMolecule

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.

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.

addExpData(String) - Method in class chemaxon.marvin.modules.MacroMolecule

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.

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.

addHeader(String, String, String) - Method in class chemaxon.marvin.modules.MacroMolecule

addHelix(int, String, String, int, char, int, char, int, int) - Method in class chemaxon.marvin.modules.MacroMolecule

addHelix(int, String, String, int, char, int, char, int, int) - Method in class chemaxon.marvin.modules.MacroMolecule.Protein

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

Adds the help menu to a parent menu.

addHet(String, String, int, char, int) - Method in class chemaxon.marvin.modules.MacroMolecule

addHetNam(String, String) - Method in class chemaxon.marvin.modules.MacroMolecule

addKeywords(String) - Method in class chemaxon.marvin.modules.MacroMolecule

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

Adds a listener if it is not yet added.

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.

addModelAtom(int, int, int, int, char, float, float, float, float) - Method in class chemaxon.marvin.modules.MacroMolecule.Polymer

addModRes(int, int, int) - Method in class chemaxon.marvin.modules.MacroMolecule.Polymer

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.

addMolId(int) - Method in class chemaxon.marvin.modules.MacroMolecule

addMolName(String) - Method in class chemaxon.marvin.modules.MacroMolecule

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.

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.

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

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

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

Adds an R-group member.

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.

addSeqNoRange(String, int, int) - Method in class chemaxon.marvin.modules.MacroMolecule

addSeqRange(int, int) - Method in class chemaxon.marvin.modules.MacroMolecule.Polymer

Specifies residue sequence number range within which residue sequence numbers in the ATOM records should fall.

addSeqres(String, int, String) - Method in class chemaxon.marvin.modules.MacroMolecule

addSeqres(int) - Method in class chemaxon.marvin.modules.MacroMolecule

addSequenceResidue(int) - Method in class chemaxon.marvin.modules.MacroMolecule.Polymer

Adds a new residue to the current chain.

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.

addSheet(int, String, String, int, char, int, char, int, int) - Method in class chemaxon.marvin.modules.MacroMolecule

addSheet(int, String, String, int, char, int, char, int, int) - Method in class chemaxon.marvin.modules.MacroMolecule.Protein

addSource(String) - Method in class chemaxon.marvin.modules.MacroMolecule

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)

addTer() - Method in class chemaxon.marvin.modules.MacroMolecule

addTitle(String) - Method in class chemaxon.marvin.modules.MacroMolecule

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

Puts all properties into the specified Properties object.

addToMolecule(Molecule) - Method in class chemaxon.marvin.modules.MacroMolecule.Component

Merges a molecule to the current Component.

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

addTurn(int, String, String, int, char, int, char) - Method in class chemaxon.marvin.modules.MacroMolecule

addTurn(int, String, String, int, char, int, char) - Method in class chemaxon.marvin.modules.MacroMolecule.Protein

addWater(String, int, int) - Method in class chemaxon.marvin.modules.MacroMolecule

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.

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_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 use for hit display.

ALIPHATIC - Static variable in class chemaxon.struc.MolAtom

Aliphatic query atom.

aliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.

aliphaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.

aliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of aliphatic ring systems of the molecule.

aliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.

ALL_H - Static variable in class chemaxon.struc.MolAtom

Include any Hydrogen atom.

ALPHA - Static variable in class chemaxon.marvin.modules.MacroMolecule.Protein.Helix

ambient - Static variable in class chemaxon.marvin.space.monitor.Control

angle2D(double, double) - Method in class chemaxon.struc.DPoint3

Calculates the absolute angle of the vector to the other point on the XY plane.

AngleMonitor - Class in chemaxon.marvin.space.monitor

Monitor for measuring angle between 3 components, the first 2 determines a line, the second 2 another.

AngleMonitor() - Constructor for class chemaxon.marvin.space.monitor.AngleMonitor

Creates a new instance of AngleMonitor

angles - Variable in class chemaxon.util.MolAligner.AlignmentResult

int[] rotation vectors for each fragment

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

ANTIPARALLEL - Static variable in class chemaxon.marvin.modules.MacroMolecule.Protein.Sheet

ANY - Static variable in class chemaxon.struc.MolAtom

"Atomic number" of the any atom A.

ANY - Static variable in class chemaxon.struc.MolBond

Any bond type.

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

Automatic any bond style setting.

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

String constant for automatic any bond style setting.

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

Any bond is dashed line.

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

String constant for dashed any bond style.

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

Any bond drawing style mask.

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

Any bond drawing style offset.

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

Any bond is solid line.

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

String constant for solid any bond style.

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

Array of any bond display styles.

append(String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument

Append text to end of document.

appendChars(int, char) - Method in class chemaxon.marvin.io.MolExportModule

Append a character n times to the string buffer.

appendLeft(String, int) - Method in class chemaxon.marvin.io.MolExportModule

Append a string to the buffer in %-ns format.

appendLine(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Appends line to string buffer with closing '\n' character.

appendLines(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader

Appends lines to string buffer with closing '\n' character if it is not yet present.

appendMEnd(Molecule) - Method in class chemaxon.marvin.io.formats.mdl.MolExport

Appends the "M END" line to the string buffer.

appendpHText(String) - Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay

Appends the pH text.

appendRight(String, int, char) - Method in class chemaxon.marvin.io.MolExportModule

Append a string to the buffer in the right hand side of an n-characters wide field.

appendRight(int, int, char) - Method in class chemaxon.marvin.io.MolExportModule

Append an integer to the buffer in the right hand side of an n-characters wide field.

applyRotationMatrices() - Method in class chemaxon.marvin.beans.MViewPane

Applies the rotation part of the viewing transformation matrix on the atom coordinates in all molecule cells.

applyRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane

Applies the rotation part of the viewing transformation matrix on the atom coordinates in the specified molecule cell.

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

Checks whether the child S-groups are visible.

areChildSgroupsVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup

Checks whether the child S-groups are visible.

arePopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane

Are popup menus enabled?

AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph

Basic aromatization.

AROM_CHEMAXON - Static variable in class chemaxon.struc.MoleculeGraph

Deprecated. please use AROM_BASIC instead. Chemaxon aromatization.

AROM_DAYLIGHT - Static variable in class chemaxon.struc.MoleculeGraph

Deprecated. please use AROM_GENERAL instead. Daylight aromatization (modified Huckel rule).

AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph

General (Daylight conform) aromatization.

AROMATIC - Static variable in class chemaxon.struc.MolAtom

Aromatic query atom.

AROMATIC - Static variable in class chemaxon.struc.MolBond

Aromatic bond type.

AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom

Aromatic or aliphatic query atom.

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

aromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of all aromatic atoms in the molecule.

aromaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of all aromatic bonds in the molecule.

aromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of all aromatic ring systems in the molecule (SSSR).

aromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.

aromatize - Variable in class chemaxon.marvin.io.MolExportModule

Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, dearomatize if -1, do nothing if 0.

aromatize(int, String, boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Aromatize or dearomatize molecule in the specified cell.

aromatize(int) - Method in class chemaxon.struc.Molecule

Aromatize molecule.

aromatize(boolean) - Method in class chemaxon.struc.MoleculeGraph

Aromatize (using the default general aromatization method) or dearomatize molecule.

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

Aromatize molecule using the default general aromatization method.

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

Aromatize molecule.

aromatize(int) - Method in class chemaxon.struc.RgMolecule

Aromatize molecule.

aromatizeAll(boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage

Aromatize or dearomatize molecules in all cells.

arrangeComponents(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil

Arranges molecule components (reactants, agents, products, R-group definitions) nicely.

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

Arranges molecule components (reactants, agents, products, R-group definitions) nicely.

arrangeMolecules(CGraph[], int, int) - Static method in class chemaxon.marvin.util.CleanUtil

Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice

arrangeReaction(RxnMolecule) - Static method in class chemaxon.marvin.util.CleanUtil

Arranges reaction components nicely

ARROW - Static variable in class chemaxon.struc.MolBond

Reaction arrow flag.

ARROW_BACK_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline

Arrow points back.

ARROW_HALF_LEFT - Static variable in class chemaxon.struc.graphics.MPolyline

Only the left half of the arrow head is drawn.

ARROW_HALF_MASK - Static variable in class chemaxon.struc.graphics.MPolyline

Unshifted mask of the half arrow option bits in flags.

ARROW_HALF_RIGHT - Static variable in class chemaxon.struc.graphics.MPolyline

Only the right half of the arrow head is drawn.

arrowFlags - Variable in class chemaxon.struc.graphics.MPolyline

Arrow flags.

associate(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent

The given component will depend on this component.

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

Strores components that depend on this component.

asymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of asymmetric atoms.

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

Show atom mapping flag.

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

Show atom numbers flag.

ATOM - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Calculation domain type: calculation refers to atoms.

atom - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator

The atom whose the neighbours are processed.

ATOM1 - Static variable in interface chemaxon.marvin.modules.MoleculeIterators.BondIteratorInterface

ATOM2 - Static variable in interface chemaxon.marvin.modules.MoleculeIterators.BondIteratorInterface

ATOM_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by mapping atom based property values to the surface.

ATOM_TYPE_COUNT - Static variable in class chemaxon.struc.MolAtom

Number of atom types in the elements array

ATOM_TYPE_MAX - Static variable in class chemaxon.struc.MolAtom

Maximum atom number.

atomA - Variable in class chemaxon.marvin.space.monitor.DihedralControl

atomB - Variable in class chemaxon.marvin.space.monitor.DihedralControl

AtomContext - Class in chemaxon.jep.context

Expression evaluation context containing an input molecule and an input atom.

AtomContext() - Constructor for class chemaxon.jep.context.AtomContext

Constructor.

atomCount() - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the number of atoms in the molecule.

atomCount(int) - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the number of atoms of a given element in the molecule (including its isotopes).

atomCount(int, int) - Method in class chemaxon.calculations.ElementalAnalyser

Calculates the number of atoms of a given element in the molecule.

atomCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of atoms in the molecule including implicit hydrogens.

atomCount - Variable in class chemaxon.marvin.modules.MacroMolecule.Component

atomCount - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent

AtomProperty - Class in chemaxon.marvin.space

The AtomProperty class provides access to chemical properties of Molecule atoms by atom index.

AtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty

AtomProperty.MoleculeAtomProperty - Class in chemaxon.marvin.space

AtomProperty.MoleculeAtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty

AtomProperty.StaticMoleculeAtomProperty - Class in chemaxon.marvin.space

AtomProperty.StaticMoleculeAtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty.StaticMoleculeAtomProperty

ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants

Either stereo atom type.

ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants

Stereo atom type mask.

ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants

No stereo atom type specified.

ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants

Specific stereo atom type.

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

Show atom symbols in 3D flag.

ATTACH1 - Static variable in class chemaxon.struc.MolAtom

Attachment point on first site.

ATTACH2 - Static variable in class chemaxon.struc.MolAtom

Attachment point on second site.

ATTACH_BOTH - Static variable in class chemaxon.struc.MolAtom

Attachment point on first and second site.

AUTO_RESOLUTION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent

AutoMapper - Class in chemaxon.marvin.modules

AutoMapper finds the best mapping from reactant side atoms to product side atoms of a reaction.

AutoMapper() - Constructor for class chemaxon.marvin.modules.AutoMapper

Creates a new instance of AutoMapper.

automaticSettingOfGridSize - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent

AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat

Image object (java.awt.Image).

B

B_FACTOR_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent

backBoneAtomCount - Variable in class chemaxon.marvin.modules.MacroMolecule.NucleicAcid

backBoneAtomIndex - Variable in class chemaxon.marvin.modules.MacroMolecule.NucleicAcid

BACKGROUND_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label

BACKGROUND_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label

backgroundColor - Variable in class chemaxon.marvin.space.monitor.Label

backgroundColorChanged - Variable in class chemaxon.marvin.space.monitor.Label

backgroundColorMode - Variable in class chemaxon.marvin.space.monitor.Label

balabanIndex() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.

ballPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent

ballRadius - Variable in class chemaxon.marvin.space.MoleculeComponent

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

Balls & sticks rendering mode.

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

Balls & sticks rendering mode.

BASE64 - Static variable in class chemaxon.formats.MFileFormat

BASE64 encoded file.

Base64Recognizer - Class in chemaxon.formats.recognizer

BASE64 format recognizer.

Base64Recognizer(String) - Constructor for class chemaxon.formats.recognizer.Base64Recognizer

Creates a Base64 format recognizer.

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

Constant denoting basic pKa.

beginHourglass() - Method in class chemaxon.marvin.beans.MarvinPane

Changes the cursor to hourglass at the beginning of a long operation.

beginModel(int) - Method in class chemaxon.marvin.modules.MacroMolecule

BEST - Static variable in class chemaxon.marvin.modules.AutoMapper

slowest maping but better quality mapping

bFactor - Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer.Model

bit - Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer.BondIterator

BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Constant storing the blue rgb value (the basic pKa result color).

BOLD - Static variable in class chemaxon.struc.graphics.MFont

Bold font style.

bond - Variable in class chemaxon.marvin.space.monitor.DihedralControl

BOND_DRAW_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent

BOND_DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent

BOND_DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent

bondCount() - Method in class chemaxon.calculations.TopologyAnalyser

Calculates the number of bonds in the molecule including bonds of implicit hydrogens.

bondCount - Variable in class chemaxon.marvin.modules.MacroMolecule.Component

bondDistance - Variable in class chemaxon.marvin.space.MoleculeComponent

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

Show bond lengths flag.

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

Calculate the regular bond length for the unified structure.

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

Calculates the regular bond length.

bondRadius - Variable in class chemaxon.marvin.space.MoleculeComponent

bondSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent

bondType(int) - Method in class chemaxon.calculations.TopologyAnalyser

Determine the type of a bond (aromatic bonds are automatically recognized)

bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom

Calculates the average of the bond unit vectors pointing out of this atom.

bondWidth - Variable in class chemaxon.marvin.space.MoleculeComponent

BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor

Boolean option.

booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp

Gets the boolean value.

BORDER_MODE_BRIGHTER_FOREGROUND - Static variable in class chemaxon.marvin.space.monitor.Label

BORDER_MODE_FOREGROUND_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label

BORDER_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label

BORDER_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label

borderColor - Variable in class chemaxon.marvin.space.monitor.Label

borderColorChanged - Variable in class chemaxon.marvin.space.monitor.Label

borderColorMode - Variable in class chemaxon.marvin.space.monitor.Label

BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin

BoundingBox - Class in chemaxon.marvin.space

Class for representing a bounding box of any component in the 3D space.

BoundingBox() - Constructor for class chemaxon.marvin.space.BoundingBox

Creates a new instance of BoundingBox but does not set anything.

BoundingBox(float, float, float, float, float, float) - Constructor for class chemaxon.marvin.space.BoundingBox

Creates a bounding box with the given coordinates, computes the center and radius of the box.

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

The smallest box containing the graphic component.

btab - Variable in class chemaxon.struc.CGraph

Bond table.

bufincRead() - Method in class chemaxon.marvin.io.PositionedInputStream

Reads a character and writes into the buffer.

BUILD_DATE - Static variable in class chemaxon.marvin.VersionInfo

The date of the compilation of the Marvin release.

BUILT_IN_CHAIN_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in chain colors.

BUILT_IN_CPK_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in cpk colors.

BUILT_IN_RAINBOW_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in rainbow colors.

BUILT_IN_RESIDUE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in residue colors.

BUILT_IN_SECONDARY_STRUCTURE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring

Coloring by built-in secondary structure colors.

C

C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter

Close the underlying stream.

C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter

Flush the output stream and force any buffered output bytes to be written out.

CACHE_REMOVE_ALL - Static variable in class chemaxon.struc.CGraph

Cache removal option for clearing all cached info.

CACHE_REMOVE_AROMATAMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in aromatization.

CACHE_REMOVE_CACHEMEMORY - Static variable in class chemaxon.struc.CGraph

Cache removal option for cacheMemory.

CACHE_REMOVE_GRINVMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in graph invariant calculation.

CACHE_REMOVE_PARITYMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in parity calculation.

CACHE_REMOVE_SSSRMODULE - Static variable in class chemaxon.struc.MoleculeGraph

Cache removal option for remove module used in sssr.

cacheMemory - Variable in class chemaxon.struc.CGraph

calcArrowHeads(DPoint3, DPoint3, double, double, DPoint3[], DPoint3[], double[], double[], double[]) - Method in class chemaxon.struc.graphics.MPolyline

Calculate arrow coordinates.

calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil

Calculates a "badness" value for the atomic coordinates.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle

Calculates the geometrical center.

calcCenter() - Method in class chemaxon.struc.MDocument

Calculates the geometrical center.

calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject

Calculates the geometrical center.

calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the geometrical center.

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

Calculates the geometrical center.

calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint

Calculates the geometrical center.

calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph

Calculates the graph invariants with the assumption that hydrogens are removed.

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

Calculates the molecule height.

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

Calculates and sets hybridazation state for each atom.

calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin

Returns the logD value at fixed pH.

calcOrderFromLength() - Method in class chemaxon.struc.MolBond

Calculate the bond order from the atomic distances.

calcOrderFromValence() - Method in class chemaxon.struc.MolBond

Calculate bond order from the types and charges of the two atoms.

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

Calculates the outer rectangle.

calcOutRect(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

Calculates the outer rectangle.

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

Calculates the center of the outer rectangle.

calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph

CALCRGB_OFF - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin

Calculator rgb offset.

calcStereo2() - Method in class chemaxon.struc.MolBond

Computes the stereochemistry of the bond based on the atomic coordinates.

calcStereo2(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond

Computes the stereochemistry of the bond based on the atomic coordinates.

calculate(int[]) - Method in class chemaxon.util.MolAligner

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.MFileFormatUtil

Deprecated. as of Marvin 5.0, PeptideRecognizer.canBe1LetterPeptide(String) must be used instead

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.MFileFormatUtil

Deprecated. as of Marvin 5.0, PeptideRecognizer.canBe3LetterPeptide(String) must be used instead

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

canBeAbbrevgroup(String) - Static method in class chemaxon.formats.MolInputStream

Deprecated. as of Marvin 5.0, AbbrevGroupRecognizer.testLine(String) must be used instead

canBeBase64(String) - Static method in class chemaxon.formats.MFileFormatUtil

Deprecated. as of Marvin 5.0, Base64Recognizer.canBeBase64(String) must be used instead

canBeBase64(String) - Static method in class chemaxon.formats.MolInputStream

Deprecated. as of Marvin 5.0,