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

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.

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.

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

ACTIVE - Static variable in class chemaxon.alchemist.AlchemistProgressLabel

active state of progress label

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

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

Action for perform add molecule to the editor.

AGENTS - Static variable in class chemaxon.struc.RxnMolecule

"Agent" structure type.

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

Deprecated. See predefined colors in AlchemistGraphicsUtilities

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

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.

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.

ALIPHATIC - Static variable in class chemaxon.struc.MolAtom

Aliphatic query atom.

ALL_AVAILABLE_ITEMS - Static variable in class chemaxon.alchemist.configbuilder.ConfigItemList

Deprecated. all items

ALL_H - Static variable in class chemaxon.struc.MolAtom

Include any Hydrogen atom.

ALL_SIDE - Static variable in class chemaxon.reaction.Reaction

Reactant and product sides of the reaction molecule

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

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_TO_RESULT_TABLE - Static variable in class chemaxon.jchem.db.JChemSearch

Constant for the generation of result tables.

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

This method applies performed molecule modification action

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

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.

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.

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.

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

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

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.

ATOM_COUNT_UPPER_BOUND - Static variable in class chemaxon.clustering.LibraryMCS

structures above this size are not searched for pair-wise mcs as it would take to long to calculate the MCS

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.

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.

ATTACHMENT_ATOM - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for attachment point representation in ligands: set attachment points by attaching an "Any" atom.

ATTACHMENT_LABEL - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for attachment point representation in ligands: set attachment points by MolAtom.setExtraLabel(java.lang.String).

ATTACHMENT_MAP - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for attachment point representation in ligands: set attachment points by MolAtom.setAtomMap(int).

ATTACHMENT_NONE - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for attachment point representation in ligands: none (no attachment point data).

ATTACHMENT_POINT - Static variable in class chemaxon.sss.search.RGroupDecomposition

Constant for attachment point representation in ligands: set attachment points by MolAtom.setAttach(int).

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

AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat

Image object (java.awt.Image).

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_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_FONT_BITS - Static variable in class chemaxon.struc.graphics.MTextAttributes

All font bits.

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.

AbbrevGroupRecognizer - class chemaxon.formats.recognizer.AbbrevGroupRecognizer.

AbbrevGroup format recognizer.

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

Creates an AbbrevGroup format recognizer.

AbstractAlchemistMoleculeEditor - class chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor.

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 chemaxon.alchemist.utils.AbstractAlchemistMoleculeEditor.MoleculeIndexArray.

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

AbstractAlchemistMoleculeView - class chemaxon.alchemist.utils.AbstractAlchemistMoleculeView.

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 chemaxon.alchemist.configbuilder.AbstractConfigElementEditor.

A ConfigElementEditor implementation with customizable editor component.

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

AbstractConfigurationReader - class chemaxon.alchemist.configbuilder.AbstractConfigurationReader.

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 chemaxon.alchemist.configbuilder.AbstractConfigurationWriter.

This is an abstract configuration xml file writer for configbuilder

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

AbstractMRecordReader - class chemaxon.marvin.io.formats.AbstractMRecordReader.

Abstract record reader class.

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

Constructs an abstract record reader.

AbstractSketchConfigElement - class chemaxon.alchemist.configbuilder.AbstractSketchConfigElement.

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

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

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

Alchemist - class chemaxon.alchemist.Alchemist.

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

This is the constructor

AlchemistApplication - class chemaxon.alchemist.AlchemistApplication.

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

Constructor.

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

Constructor.

AlchemistApplication.ExitApplicationAction - class chemaxon.alchemist.AlchemistApplication.ExitApplicationAction.

Default Exit Application Action

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

AlchemistApplication.LicenseManagerAction - class chemaxon.alchemist.AlchemistApplication.LicenseManagerAction.

Default License Manager Action

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

AlchemistApplication.NewDocumentAction - class chemaxon.alchemist.AlchemistApplication.NewDocumentAction.

Default New Doucment Action

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

AlchemistApplication.OpenDocumentAction - class chemaxon.alchemist.AlchemistApplication.OpenDocumentAction.

Default Open Document Action

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

AlchemistApplication.SaveDocumentAction - class chemaxon.alchemist.AlchemistApplication.SaveDocumentAction.

Default Save Document Action

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

AlchemistApplication.SaveDocumentAsAction - class chemaxon.alchemist.AlchemistApplication.SaveDocumentAsAction.

Default Save Document As Action

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

AlchemistApplicationInnerDialog - class chemaxon.alchemist.utils.AlchemistApplicationInnerDialog.

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 chemaxon.alchemist.utils.AlchemistApplicationLicenseHandlerInnerDialog.

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

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

AlchemistBanner - class chemaxon.alchemist.AlchemistBanner.

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

Constructor.

AlchemistBrowserLauncher - class chemaxon.alchemist.utils.AlchemistBrowserLauncher.

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

AlchemistComponentSet - class chemaxon.alchemist.utils.AlchemistComponentSet.

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 chemaxon.alchemist.AlchemistController.

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

Creates an AlchemistController instance.

AlchemistDashedBorder - class chemaxon.alchemist.utils.AlchemistDashedBorder.

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 chemaxon.alchemist.AlchemistError.

AlchemistFileChooser - class chemaxon.alchemist.utils.AlchemistFileChooser.

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 chemaxon.alchemist.utils.AlchemistFileTextBox.

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 chemaxon.alchemist.AlchemistGlassPage.

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

AlchemistGraphicsUtilities - class chemaxon.alchemist.utils.AlchemistGraphicsUtilities.

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

AlchemistIconFactory - class chemaxon.alchemist.utils.AlchemistIconFactory.

AlchemistLabel - class chemaxon.alchemist.utils.AlchemistLabel.

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 chemaxon.alchemist.utils.AlchemistLaunchable.

AlchemistLauncher - class chemaxon.alchemist.utils.AlchemistLauncher.

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

This is the default constructor

AlchemistLinearMoleculeView - class chemaxon.alchemist.utils.AlchemistLinearMoleculeView.

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

Creates an AlchemistLinearMoleculeView

AlchemistMViewAccessory - class chemaxon.alchemist.utils.AlchemistMViewAccessory.

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

This is the default constructor.

AlchemistMoleculeEditor - class chemaxon.alchemist.utils.AlchemistMoleculeEditor.

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 chemaxon.alchemist.utils.AlchemistMoleculePainter.

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

AlchemistMoleculeUtilities - class chemaxon.alchemist.utils.AlchemistMoleculeUtilities.

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

AlchemistMoleculeView - class chemaxon.alchemist.utils.AlchemistMoleculeView.

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

AlchemistPage - class chemaxon.alchemist.AlchemistPage.

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

AlchemistProfile - class chemaxon.alchemist.AlchemistProfile.

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 chemaxon.alchemist.configbuilder.AlchemistProfileSupport.

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

AlchemistProgressLabel - class chemaxon.alchemist.AlchemistProgressLabel.

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

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

AlchemistProgressMonitor - class chemaxon.alchemist.utils.AlchemistProgressMonitor.

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

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

AlchemistProgressObject - class chemaxon.alchemist.AlchemistProgressObject.

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 chemaxon.alchemist.utils.AlchemistSpinBox.

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

Constructs an AlchemistSpinBox instance

AlchemistSplashScreen - class chemaxon.alchemist.AlchemistSplashScreen.

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 chemaxon.alchemist.utils.AlchemistSplitPane.

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 chemaxon.alchemist.utils.AlchemistState.

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

AlchemistTableSizeConfigurerComponent - class chemaxon.alchemist.utils.AlchemistTableSizeConfigurerComponent.

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 chemaxon.alchemist.AlchemistTask.

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

Constructor.

AlchemistUtilities - class chemaxon.alchemist.utils.AlchemistUtilities.

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

AngleMonitor - class chemaxon.marvin.space.monitor.AngleMonitor.

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

AtomContext - class chemaxon.jep.context.AtomContext.

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

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

Constructor.

AtomProperty - class chemaxon.marvin.space.AtomProperty.

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 chemaxon.marvin.space.AtomProperty.MoleculeAtomProperty.

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

AtomProperty.StaticMoleculeAtomProperty - class chemaxon.marvin.space.AtomProperty.StaticMoleculeAtomProperty.

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

AutoMapper - class chemaxon.marvin.modules.AutoMapper.

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.

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

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

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.

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

Adds an element.

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.

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).

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

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

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.MObject

Adds the attribute names to the specified vector.

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.

addAuthor(String) - 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.

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

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

Adds the basic MarvinSpace viewer to the container.

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

Adds attribute names to the specified vector.

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

Adds attribute names to the specified vector.

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

Adds a one letter chain identifier to the compond.

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

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.

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

Adds a component to an empty cell.

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

Creates and adds components for mainPanel

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

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.

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

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.

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.

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.Protein

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

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

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

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

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