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HYDROGENIZE_NO
AtomProperty class provides access to chemical properties of
Molecule atoms by atom index.AutoMapper finds the best mapping from reactant side atoms
to product side atoms of a reaction.Molecule object to the actual cell
of the viewer.
Molecule object to the actual cell
of the viewer and resets the view only if required.
RxnMolecule.addComponent(Molecule, int)
RxnMolecule.addComponent(Molecule, int, boolean)
Component.
ComponentElement of a simple
(not structured) GraphicComponent.
ComponentElement.
- ComponentElement(GraphicComponent, int, int, int) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Creates a new instance of
ComponentElement of a complex (structured) GraphicComponent.
- ComponentElement(GraphicComponent, int, int, Integer) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Creates a new instance of
ComponentElement.
- ComponentElement(ComponentElement) -
Constructor for class chemaxon.marvin.space.ComponentElement
- Copies the given
ComponentElement.
- ConformerPlugin - class chemaxon.marvin.calculations.ConformerPlugin.
- Plugin class for conformer calculation.
- ConformerPlugin() -
Constructor for class chemaxon.marvin.calculations.ConformerPlugin
- Constructor.
- Control - class chemaxon.marvin.space.monitor.Control.
- Transformation on a
GraphicComponent that changes the coordinates, and not just the view. - Control() -
Constructor for class chemaxon.marvin.space.monitor.Control
- Creates a new instance of Control
- cacheMemory -
Variable in class chemaxon.struc.CGraph
-
- 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, CTransform3D) -
Method in class chemaxon.struc.MPoint
- 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.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.
- 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.
- 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
-
- 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.
- calcWidth() -
Method in class chemaxon.struc.MoleculeGraph
- Calculates the molecule width.
- calclogD(double) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Returns the logD value at fixed pH.
- callback(String, Object) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Callback function to make avoiding direct calls easier.
- callback(String, Object) -
Method in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- canBe1LetterPeptide(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether a string can be one-letter-abbreviated
peptide name.
A valid name contains only uppercase letters.
- canBe3LetterPeptide(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether a string can be three-letter-abbreviated
peptide name.
Each peptide's first letter must be
uppercase and the other two are lowercase.
- canBeAbbrevgroup(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether a string can be in abbrevgroup format.
- canBeAbbrevgroup(String) -
Static method in class chemaxon.formats.MolInputStream
- Deprecated. as of Marvin 4.1,
MFileFormatUtil.canBeAbbrevgroup(String)
must be used instead
- canBeBase64(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Deprecated. as of Marvin 4.1,
MFileFormatUtil.canBeBase64(String)
must be used instead
- canBeBase64(String) -
Static method in class chemaxon.formats.MolInputStream
- Deprecated. as of Marvin 4.1,
MFileFormatUtil.canBeBase64(String)
must be used instead
- canBeCT(int, int) -
Method in class chemaxon.struc.MoleculeGraph
- Determines whether the bond between the specified atoms can be a
CIS/TRANS or not.
- canBeCT(int, int, boolean) -
Method in class chemaxon.struc.MoleculeGraph
- Determines whether the bond between the specified atoms can be a
CIS/TRANS or not.
- canBeChime(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether a string can be Chime (MDL compressed mol).
- canBeChime(String) -
Static method in class chemaxon.formats.MolInputStream
- Deprecated. as of Marvin 4.1,
MFileFormatUtil.canBeChime(String)
must be used instead
- canBeJTF(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Determines if a String is valid as the first line of a JTF file.
- canBeJTF(String) -
Static method in class chemaxon.formats.MolInputStream
- Deprecated. as of Marvin 4.1,
MFileFormatUtil.canBeJTF(String)
must be used instead
- canBePDBRecord(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Checks if the given parameter is a PDB record name listed in
PDB_RECORD_TYPES.
- canBeSMARTS(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether a string can be SMARTS.
- canBeSMARTS(String) -
Static method in class chemaxon.formats.MolInputStream
- Deprecated. as of Marvin 4.1,
MFileFormatUtil.canBeSMARTS(String)
must be used instead
- canBeSMILES(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tests whether a string can be SMILES.
- canBeSMILES(String) -
Static method in class chemaxon.formats.MolInputStream
- Deprecated. as of Marvin 4.1,
MFileFormatUtil.canBeSMILES(String)
must be used instead
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.AtomSM
- Can the user point to an atom in this sketching mode?
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.BondSM
- Can the user point to an atom in this sketching mode?
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.MoleculeSM
- Can the user point to an atom in this sketching mode?
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.RubberSM
- Can the user point to an atom in this sketching mode?
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.SelectSM
- Can the user point to an atom in this sketching mode?
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.SgroupSM
- Can the user point to an atom in this sketching mode?
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.SketchMode
- Can the user point to an atom in this sketching mode?
- canPointToAtom() -
Method in class chemaxon.marvin.sketch.modules.LineSM
- Can the user point to an atom in this sketching mode?
- canPointToAtomPair() -
Method in class chemaxon.marvin.sketch.SketchMode
- Can the user point to an atom pair in this sketching mode?
- canPointToAtomPair() -
Method in class chemaxon.marvin.sketch.modules.EFlowSM
- The user can point to an atom pair with the end of the arrow.
- canPointToBond() -
Method in class chemaxon.marvin.sketch.AtomSM
- Can the user point to a bond in this sketching mode?
- canPointToBond() -
Method in class chemaxon.marvin.sketch.BondSM
- Can the user point to a bond in this sketching mode?
- canPointToBond() -
Method in class chemaxon.marvin.sketch.MoleculeSM
- Can the user point to a bond in this sketching mode?
- canPointToBond() -
Method in class chemaxon.marvin.sketch.RubberSM
- Can the user point to a bond in this sketching mode?
- canPointToBond() -
Method in class chemaxon.marvin.sketch.SelectSM
- Can the user point to a bond in this sketching mode?
- canPointToBond() -
Method in class chemaxon.marvin.sketch.SketchMode
- Can the user point to a bond in this sketching mode?
- canPointToBond() -
Method in class chemaxon.marvin.sketch.modules.EFlowSM
- Can the user point to a bond in this sketching mode?
- canPointToBond() -
Method in class chemaxon.marvin.sketch.modules.LineSM
- Can the user point to a bond in this sketching mode?
- canPointToMObject() -
Method in class chemaxon.marvin.sketch.MObjectSM
- Can the user point to a graphics object in this sketching mode?
- canPointToMObject() -
Method in class chemaxon.marvin.sketch.RubberSM
- Can the user point to a graphics object in this sketching mode?
- canPointToMObject() -
Method in class chemaxon.marvin.sketch.SelectSM
- Can the user point to a graphics object in this sketching mode?
- canPointToMObject() -
Method in class chemaxon.marvin.sketch.SketchMode
- Can the user point to a graphics object in this sketching mode?
- canPointToMObject() -
Method in class chemaxon.marvin.sketch.modules.LineSM
- Can the user point to another graphics object in this sketching mode?
- canPointToSgroup() -
Method in class chemaxon.marvin.sketch.AtomSM
- Can the user point to an S-group in this sketching mode?
- canPointToSgroup() -
Method in class chemaxon.marvin.sketch.BondSM
- Can the user point to an S-group in this sketching mode?
- canPointToSgroup() -
Method in class chemaxon.marvin.sketch.RubberSM
- Can the user point to an S-group in this sketching mode?
- canPointToSgroup() -
Method in class chemaxon.marvin.sketch.SelectSM
- Can the user point to an S-group in this sketching mode?
- canPointToSgroup() -
Method in class chemaxon.marvin.sketch.SgroupSM
- Can the user point to an S-group in this sketching mode?
- canPointToSgroup() -
Method in class chemaxon.marvin.sketch.SketchMode
- Can the user point to an S-group in this sketching mode?
- carboRingCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of carbocyclic rings in the molecule (rings
containing carbon atoms only).
- carboaromaticRingCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of aromatic carbocyclic rings in the molecule
(aromatic rings containing carbon atoms only).
- center -
Variable in class chemaxon.marvin.space.monitor.Control
-
- center -
Variable in class chemaxon.marvin.space.monitor.DihedralControl
-
- centerx() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the x coordinate of the center of the box.
- centery() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the y coordinate of the center of the box.
- centerz() -
Method in class chemaxon.marvin.space.BoundingBox
- Returns the z coordinate of the center of the box.
- chainAtomCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of chain atoms in the molecule excluding hydrogens.
- chainBondCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of chain bonds in the molecule excluding bonds of
hydrogen atoms.
- chainId -
Variable in class chemaxon.marvin.modules.MacroMolecule.Component
-
- chainId -
Variable in class chemaxon.marvin.modules.MacroMolecule.Protein.SecondaryStructure
-
- changeColorMapperColors(int) -
Method in class chemaxon.marvin.space.SurfaceColoring
- Switches to another built-in color palette and leaves minimum, maximum
and cutoff values unchanged.
- charAt(int) -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets a character of the document.
- checkLicense() -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Increases the call counter if no valid license exists for this plugin
class.
- checkLicenseKey() -
Method in class chemaxon.marvin.space.GraphicScene
- Checks whether the license ley is set properly.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.ConformerPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.GeometryPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.HBDAPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.IonChargePlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MSAPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MultiformPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.RefractivityPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.TPSAPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.logDPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Checks the input molecule.
- checkMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Checks the input molecule.
- checkRlogicRange(int, String) -
Method in class chemaxon.struc.RgMolecule
- Checks an R-logic occurence range string for syntax errors
and returns a "normalized" string.
- checkType(String, String[]) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Checks result types.
- checkValidity(MDocument, Collection) -
Method in class chemaxon.struc.MObject
- Is it a valid object in the document?
- checkValidity(MDocument, Collection) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Is it a valid object in the document?
- checkValidity(MDocument, Collection) -
Method in class chemaxon.struc.graphics.MPolyline
- Is it a valid object in the document?
- chemaxon.calculations - package chemaxon.calculations
- Contains chemical computations modules.
- chemaxon.formats - package chemaxon.formats
-
Provides miscellaneous utility classes for converting between various
molecule file formats, importing structures, and compressing Molfiles.
- chemaxon.marvin - package chemaxon.marvin
- Contains general purpose classes for marvin including the sketcher, the viewer,
the command line plugin runner and a utility class for printing molecules.
- chemaxon.marvin.calculations - package chemaxon.marvin.calculations
- Provides specific plugin, plugin loader and table form output implementations.
- chemaxon.marvin.modules - package chemaxon.marvin.modules
- Marvin modules.
- chemaxon.marvin.plugin - package chemaxon.marvin.plugin
- Contains the classes responsible for calculator plugin loading, parameter setting,
running and displaying mechanism.
- chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui
- Calculator plugin common GUI classes.
- chemaxon.marvin.sketch - package chemaxon.marvin.sketch
- Contains the sketcher's core classes and various sketching modes.
- chemaxon.marvin.sketch.modules - package chemaxon.marvin.sketch.modules
- Contains sketcher modules.
- chemaxon.marvin.space - package chemaxon.marvin.space
- Contains the core classes of MarvinSpace including the graphic canvas and the
basic visualizer classes.
- chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor
- Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
- chemaxon.marvin.util - package chemaxon.marvin.util
- Contains the fundamental classes for molecule import and export.
- chemaxon.struc - package chemaxon.struc
- Provides classes for implementing and manipulating chemical structures.
- chemaxon.struc.graphics - package chemaxon.struc.graphics
- Contains graphics MDocument elements.
- chemaxon.struc.sgroup - package chemaxon.struc.sgroup
- S-group related classes and interfaces.
- chiralCenterCount() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the number of tetrahedral stereogenic centers.
- chiralCenterCount() -
Method in class chemaxon.marvin.calculations.StereoisomerPlugin
- Calculates the number of tetrahedral stereogenic centers.
- clean(int, String, MProgressMonitor) -
Method in class chemaxon.struc.Molecule
- Calculates atom coordinates.
- clean(int, String) -
Method in class chemaxon.struc.MoleculeGraph
- Calculates atom coordinates.
- clean(int, String, MProgressMonitor) -
Method in class chemaxon.struc.MoleculeGraph
- Calculates atom coordinates.
- cleanSgroups(int, String) -
Method in class chemaxon.struc.Molecule
- Clean S-groups.
- cleanupRemovedRgroupMember(MoleculeGraph, int) -
Method in class chemaxon.struc.RgMolecule
- Clean-up after R-group removal.
- clear() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Clears the display.
- clear() -
Method in class chemaxon.marvin.plugin.CommandPlugger
- Removes all plugins.
- clear() -
Method in class chemaxon.marvin.space.BoundingBox
- Clears all previously set coordinate from the box.
- clear() -
Method in class chemaxon.marvin.space.monitor.Monitor
- Deletes all items from selectedItems.
- clear() -
Method in class chemaxon.struc.MDocument
- Clears the document.
- clear() -
Method in class chemaxon.struc.MPropertyContainer
- Clears properties.
- clear() -
Method in class chemaxon.struc.MSelectionDocument
- Clears the document.
- clear() -
Method in class chemaxon.struc.MolAtom
- Clear query properties, charge, and hcount.
- clear() -
Method in class chemaxon.struc.Molecule
- Clears the molecule.
- clear() -
Method in class chemaxon.struc.MoleculeGraph
- Clears the molecule.
- clearCachedInfo(int) -
Method in class chemaxon.struc.CGraph
- Deletes the cached information depending on the given options.
- clearCachedInfo(int) -
Method in class chemaxon.struc.MoleculeGraph
- Deletes the cached information depending on the given options.
- clearExtraLabel() -
Method in class chemaxon.struc.MolAtom
- Clears the extra label.
- clearExtraLabels() -
Method in class chemaxon.struc.Molecule
- Clears extra atom labels.
- clearForImport(String) -
Method in class chemaxon.struc.Molecule
- Initializes molecule for import.
- clearForImport(String) -
Method in class chemaxon.struc.MoleculeGraph
- Clears the edges vector, the properties, the flags, and sets the
origin coordinates to 0.
- clearForImport(String) -
Method in class chemaxon.struc.RgMolecule
- Clear the edges vector and the properties.
- clearForImport(String) -
Method in class chemaxon.struc.RxnMolecule
- Clear the edges vector and the properties.
- clearMaps(RxnMolecule) -
Static method in class chemaxon.marvin.modules.AutoMapper
- Clears atom maps.
- clearProperties() -
Method in class chemaxon.struc.Molecule
- Clears RDfile/SDfile properties.
- clearQProps() -
Method in class chemaxon.struc.MolAtom
- Clears query props.
- clearSelection(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Sets all components and parts of components to be unselected in the given cell.
- clearSelections() -
Method in class chemaxon.marvin.space.GraphicCell
- Sets all components and parts of components to be unselected.
- clearSets() -
Method in class chemaxon.struc.MDocument
- Clears the atomSets and the bondSets.
- clickPoint -
Variable in class chemaxon.marvin.sketch.modules.RectangleSM
-
- clipSurface(BoundingBox) -
Method in class chemaxon.marvin.space.SurfaceComponent
- The bounding box of the surface can be used to determine 6 clipping planes
and clip (do not draw) parts lying outside of the box.
- clone() -
Method in class chemaxon.marvin.sketch.AtomSM
-
- clone() -
Method in class chemaxon.marvin.sketch.BondSM
-
- clone() -
Method in class chemaxon.marvin.sketch.MObjectSM
- Clones the object.
- clone() -
Method in class chemaxon.marvin.sketch.MoleculeSM
-
- clone() -
Method in class chemaxon.marvin.sketch.RubberSM
- Clones the selection object.
- clone() -
Method in class chemaxon.marvin.sketch.SelectSM
- Clones the selection object.
- clone() -
Method in class chemaxon.marvin.sketch.SgroupSM
- Clones the selection object.
- clone() -
Method in class chemaxon.marvin.sketch.SketchMode
-
- clone() -
Method in class chemaxon.marvin.sketch.modules.ArrowSM
-
- clone() -
Method in class chemaxon.marvin.sketch.modules.EFlow1SM
-
- clone() -
Method in class chemaxon.marvin.sketch.modules.EFlowSM
-
- clone() -
Method in class chemaxon.marvin.sketch.modules.LineSM
-
- clone() -
Method in class chemaxon.marvin.sketch.modules.PolylineSM
-
- clone() -
Method in class chemaxon.marvin.sketch.modules.RectangleSM
- Clones the object.
- clone() -
Method in class chemaxon.marvin.sketch.modules.TextBoxSM
- Clones the object.
- clone() -
Method in class chemaxon.struc.CEdge
- Clones this edge.
- clone() -
Method in class chemaxon.struc.CGraph
- Makes an identical copy of the molecule.
- clone() -
Method in class chemaxon.struc.CNode
- Clones the node.
- clone() -
Method in class chemaxon.struc.DPoint3
- Make an identical copy.
- clone() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- clone() -
Method in class chemaxon.struc.MObject
- Creates a clone.
- clone() -
Method in class chemaxon.struc.MPoint
-
- clone() -
Method in class chemaxon.struc.MPropertyContainer
- Clones this object.
- clone() -
Method in class chemaxon.struc.MolAtom
- Clones the atom.
- clone() -
Method in class chemaxon.struc.MolBond
- Make a copy of this object.
- clone() -
Method in class chemaxon.struc.Molecule
- Makes an identical copy of the molecule.
- clone() -
Method in class chemaxon.struc.MoleculeGraph
- Make an identical copy of the molecule.
- clone() -
Method in class chemaxon.struc.QueryBond
- Make a copy of this object.
- clone() -
Method in class chemaxon.struc.SelectionMolecule
- Create a clone of the selection.
- clone() -
Method in class chemaxon.struc.graphics.MAtomSetPoint
-
- clone() -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Creates a clone.
- clone() -
Method in class chemaxon.struc.graphics.MEFlow
-
- clone() -
Method in class chemaxon.struc.graphics.MFont
- Creates a clone.
- clone() -
Method in class chemaxon.struc.graphics.MMidPoint.Sticky
-
- clone() -
Method in class chemaxon.struc.graphics.MMidPoint
-
- clone() -
Method in class chemaxon.struc.graphics.MPolyline
-
- clone() -
Method in class chemaxon.struc.graphics.MRectangle
-
- clone() -
Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
-
- clone() -
Method in class chemaxon.struc.graphics.MRectanglePoint
-
- clone() -
Method in class chemaxon.struc.graphics.MTextBox
-
- clone() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Clones the S-group superatom.
- cloneArrowSM() -
Method in class chemaxon.marvin.sketch.modules.ArrowSM.Regular
-
- cloneArrowSM() -
Method in class chemaxon.marvin.sketch.modules.ArrowSM.TwoHeaded
-
- cloneArrowSM() -
Method in class chemaxon.marvin.sketch.modules.ArrowSM
-
- cloneBond(MolAtom, MolAtom) -
Method in class chemaxon.struc.MolBond
- Clones this bond.
- cloneBond(MolAtom, MolAtom) -
Method in class chemaxon.struc.QueryBond
- Clones this bond.
- cloneDocument() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- cloneDocument() -
Method in class chemaxon.struc.MSelectionDocument
- Creates a clone.
- cloneEdge(CNode, CNode) -
Method in class chemaxon.struc.CEdge
- Clones this edge.
- cloneEdge(CNode, CNode) -
Method in class chemaxon.struc.MolBond
- Clones this edge.
- cloneFromSgroupCopy() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Clones the S-group superatom partially.
- cloneMFont() -
Method in class chemaxon.struc.graphics.MFont
- Creates a clone.
- cloneMainMolecule() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- cloneMainMoleculeGraph() -
Method in class chemaxon.struc.MDocument
- Creates a clone.
- cloneMol(Molecule) -
Static method in class chemaxon.marvin.sketch.MoleculeSM
-
- cloneMolecule() -
Method in class chemaxon.struc.Molecule
- Makes an identical copy of the molecule.
- cloneMolecule() -
Method in class chemaxon.struc.RgMolecule
- Make an identical copy of the molecule.
- cloneMolecule() -
Method in class chemaxon.struc.RxnMolecule
- Make an identical copy of the molecule.
- cloneMoleculeWithDocument() -
Method in class chemaxon.struc.Molecule
- Makes an identical copy of the molecule and its document.
- cloneProp() -
Method in class chemaxon.struc.MDocument.Prop
- Creates a clone.
- cloneSets(MDocument) -
Method in class chemaxon.struc.MDocument
- Clones the atom/bond sets from doc.
- cloneSgroup(Molecule, Sgroup) -
Method in class chemaxon.struc.Sgroup
- Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup) -
Method in class chemaxon.struc.sgroup.DataSgroup
- Gets a new DataSgroup instance.
- cloneSgroup(Molecule, Sgroup) -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Gets a new Sgroup instance.
- cloneStructure() -
Method in class chemaxon.struc.Sgroup
- Gets the clone of the structure stored.
- clonecopy(CGraph) -
Method in class chemaxon.struc.CGraph
- Copies the clones of nodes and edges of this graph to another one.
- clonecopy(CGraph) -
Method in class chemaxon.struc.Molecule
- Makes another molecule identical to this one.
- clonecopy(CGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Make another molecule identical to this one.
- clonecopy(CGraph) -
Method in class chemaxon.struc.RgMolecule
- Make another molecule identical to this one.
- clonecopy(CGraph) -
Method in class chemaxon.struc.RxnMolecule
- Make another molecule identical to this one.
- clonecopy(CGraph) -
Method in class chemaxon.struc.SelectionMolecule
- Copies the clones of nodes and edges of this graph to another one.
- clonecopyWithoutSgroups(Molecule) -
Method in class chemaxon.struc.Molecule
- Copies the all the contents except the S-groups into another molecule
object.
- clonelesscopy(CGraph) -
Method in class chemaxon.struc.CGraph
- Copy to selection.
- clonelesscopy(CGraph) -
Method in class chemaxon.struc.Molecule
- Copies to selection.
- clonelesscopy(CGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Copy to selection.
- clonelesscopy(CGraph) -
Method in class chemaxon.struc.RgMolecule
- Copy to selection.
- clonelesscopy(CGraph) -
Method in class chemaxon.struc.RxnMolecule
- Copy to selection.
- close() -
Method in class chemaxon.marvin.plugin.CalculatorPluginOutput
- Closes the output.
- close() -
Method in class chemaxon.marvin.util.MolExportModule
- Close the stream.
- color -
Variable in class chemaxon.marvin.space.GraphicComponent
-
- color -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- color -
Variable in class chemaxon.marvin.space.SurfaceComponent
-
- color3 -
Variable in class chemaxon.marvin.space.SurfaceComponent
-
- colorType -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- coloring(boolean) -
Method in class chemaxon.marvin.space.SurfaceComponent
-
- compareTo(Object) -
Method in class chemaxon.marvin.plugin.PluginFactory.PluginRecord
-
- component -
Variable in class chemaxon.marvin.space.monitor.Control
-
- componentBecameSelected() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns true if a component became selected previously.
- componentBecameSelected(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if a component became selected previously in the given cell.
- componentBecameUnselected() -
Method in class chemaxon.marvin.space.GraphicCell
- Returns true if a component became unselected previously.
- componentBecameUnselected(int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if a component became unselected previously in the given cell.
- composition(int) -
Method in class chemaxon.calculations.ElementalAnalyser
- Gets the elemental analysis, the relative percent composition of a pure
chemical substance by element (w/w%).
- computeSurface(MacroMoleculeComponent.MoleculeVisualizer) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Activates the container cell of the
MoleculeVisualizer, and
computes its Connolly surface.
- computeSurface(String) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Computes the given type of surface in the active cell of the viewer.
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.AtomSM
-
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.BondSM
-
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.MObjectSM
-
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.MoleculeSM
-
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.RubberSM
-
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.SelectSM
-
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.SgroupSM
-
- containedObjectEquals(SketchMode) -
Method in class chemaxon.marvin.sketch.SketchMode
-
- containerFrame -
Variable in class chemaxon.marvin.space.MSpaceEasy
-
- contains(float, float, float) -
Method in class chemaxon.marvin.space.BoundingBox
- Tells whether the given location is inside the box.
- contains(Object) -
Method in class chemaxon.struc.CGraph
- Checks if the graph contains the specified node or edge.
- contains(CGraph) -
Method in class chemaxon.struc.CGraph
- Does the graph contain the specified fragment?
- contains(MObject) -
Method in class chemaxon.struc.MDocument
- Searches an object in the document.
- contains(MDocument) -
Method in class chemaxon.struc.MDocument
- Tests whether the document contains all objects of another document.
- contains(CGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Does the graph contain the specified fragment?
- contains(Object) -
Method in class chemaxon.struc.RgMolecule
- Checks if the root structure or an R-group contains the specified node
or edge.
- contains(Object) -
Method in class chemaxon.struc.RxnMolecule
- Checks if a reactant, agent or product structure contains the specified
node or edge.
- containsAllAtomsOf(Sgroup) -
Method in class chemaxon.struc.Sgroup
- Checks if the S-group contains the atoms of another S-group.
- containsAtom(int) -
Method in class chemaxon.marvin.modules.MacroMolecule.Component
- Checks if an atom with the given serial number is found in this
Component.
- containsAtom(int) -
Method in class chemaxon.marvin.modules.MacroMolecule.HeteroComponent
- Checks the atom with the given serial number is part of the
hetero group.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.MObject
- Checks if the object contains the specified atom reference.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MPolyline
- Checks if the atom set contains the specified atom object.
- containsComponent(GraphicComponent) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the component is in the cell.
- containsComponent(GraphicComponent) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if the component exists in the scene.
- containsOnlyOne(Class) -
Method in class chemaxon.struc.MDocument
- Tests whether the document contains only one object of the specified
class.
- containsResidue(int, char) -
Method in class chemaxon.marvin.modules.MacroMolecule.Protein.SecondaryStructure
-
- contract(int) -
Method in class chemaxon.struc.Sgroup
- Sets the state to
Sgroup.XSTATE_C.
- contract(int) -
Method in interface chemaxon.struc.sgroup.Expandable
- Contracts the S-group.
- contract(int) -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Contracts this S-group.
- contract(int) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Contracts this S-group.
- contractSgroups() -
Method in class chemaxon.struc.Molecule
- Contracts all S-groups.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.Control
- Does control on x-y events.
- control(int) -
Method in class chemaxon.marvin.space.monitor.Control
- Does control on z event.
- control(int) -
Method in class chemaxon.marvin.space.monitor.DihedralControl
- One part of the molecule being in one of the end of the torsion bond
will be rotated around the bond.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.DihedralControl
- Does nothing.
- control -
Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
-
- control(int) -
Method in class chemaxon.marvin.space.monitor.DihedralMonitor
- Passes the control event to the control.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
- Changes the location say translates the component of the control
in the global coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
- Changes the location say translates the component of the control
in the global coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Changes the orientation say rotates the component of the control
in the global coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Changes the orientation that is rotates the component of the control
in the global coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.LocalLocationControl
- Changes the location say translates the component of the control
in its local coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.LocalLocationControl
- Changes the location say translates the component of the control
in its local coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
- Changes the orientation say rotates the component of the control
in its local coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
- Changes the orientation say rotates the component of the control
in its local coordinate system.
- control -
Variable in class chemaxon.marvin.space.monitor.Monitor
-
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Causes the monitor's controll to take action with 2 parameters.
- control(int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Causes the monitor's controll to take action with 1 parameter.
- control(int) -
Method in class chemaxon.marvin.space.monitor.ResizeControl
- Resizes the component in z direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.ResizeControl
- Resizes the component in x, y direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- convert() -
Method in class chemaxon.formats.MdlCompressor
- Compression/decompression
- convert(byte[], int) -
Static method in class chemaxon.formats.MdlCompressor
- (Un)compress the specified molfile or SDfile.
- convert(String, int) -
Static method in class chemaxon.formats.MdlCompressor
- (Un)compress the specified molfile or SDfile.
- convert(Molecule) -
Method in class chemaxon.marvin.modules.MolExport
- Creates an MDL mol or compressed mol representation of the molecule.
- convert(MacroMolecule, Molecule) -
Method in class chemaxon.marvin.modules.PDBReader
-
- convert(Molecule) -
Method in class chemaxon.marvin.util.MolExportModule
- Convert a molecule to a string or byte array.
- convertToFrags() -
Method in class chemaxon.struc.Molecule
- Converts this molecule to its disconnected fragments.
- convertToString() -
Method in class chemaxon.struc.MDocument.Prop
- Converts the molecule to text format.
- convertTransform(CTransform3D, boolean) -
Method in class chemaxon.struc.graphics.MRectangle
-
- copyProperties(MPolyline) -
Method in class chemaxon.struc.graphics.MPolyline
- Copies line properties to another line object.
- countAllAtoms() -
Method in class chemaxon.struc.MolAtom
- Counts all atoms represented by this atom.
- countAllAtoms() -
Method in class chemaxon.struc.Sgroup
- Counts the total number of atoms recursively.
- countAllAtoms() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Counts all atoms represented by this atom.
- covalentRadiusOf(int, int) -
Static method in class chemaxon.struc.MolAtom
- Gets the covalent radius in C-C bond length units.
- create(String, String) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
- createBHtab() -
Method in class chemaxon.struc.MoleculeGraph
- Creates the bond table extended with implicit hydrogen atoms.
- createBHtab() -
Method in class chemaxon.struc.RxnMolecule
- Creates the graph union's bond table extended with implicit hydrogen
atoms.
- createBondMol(int) -
Static method in class chemaxon.marvin.sketch.BondSM
-
- createBondMol(int, MolAtom, MolAtom) -
Static method in class chemaxon.marvin.sketch.BondSM
-
- createCHtab() -
Method in class chemaxon.struc.MoleculeGraph
- Creates the connection table extended with implicit hydrogen atoms.
- createCHtab() -
Method in class chemaxon.struc.RxnMolecule
- Creates the graph union's connection table extended with implicit
hydrogen atoms.
- createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) -
Method in class chemaxon.struc.graphics.MTextAttributes
-
- createDefaultParameterPanel(String, Component) -
Static method in class chemaxon.marvin.plugin.PluginFactory
- Creates default parameter panel based on XML config.
- createDehydrogenizedReadOnlyGraph() -
Method in class chemaxon.struc.MoleculeGraph
- Creates a dehydrogenized version of the molecule.
- createImage(Buffer, int, int) -
Method in class chemaxon.marvin.space.GraphicScene
-
- createLine(MPoint, MPoint) -
Method in class chemaxon.marvin.sketch.modules.EFlowSM
- Creates a line object.
- createLine(MPoint, MPoint) -
Method in class chemaxon.marvin.sketch.modules.LineSM
- Creates a line object.
- createMol() -
Method in class chemaxon.marvin.modules.MolImport
- Creates a new target molecule object.
- createMol() -
Method in interface chemaxon.marvin.util.MolImportIface
- Creates a new target molecule object for the import.
- createMol(String) -
Static method in class chemaxon.struc.RgMolecule
- Deprecated. As of Marvin 3.4,
MolImportIface.createMol() must be used.
- createMolecule() -
Method in class chemaxon.struc.Sgroup
- Creates a molecule object that contains only this group.
- createMolecule() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Creates a molecule object that contains only this group.
- createNewCell() -
Method in class chemaxon.marvin.space.GraphicScene
- Sets an empty cell to be the active cell.
- createNext() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Creates identical attributes for the next section.
- createParameterPanel() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates the parameter panel.
- createPolyline(MPolyline, MPoint) -
Method in class chemaxon.marvin.sketch.modules.LineSM
- Creates a polyline object.
- createReaction(Molecule, DPoint3[], int) -
Static method in class chemaxon.struc.RxnMolecule
- Creates a reaction.
- createSpaceFrame(Molecule[]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates space panel with given molecules,
creates colored surface to each molecule.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Creates standardized molecule, the original input molecule is cloned.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.calculations.MultiformPlugin
- Creates standardized molecule, the original input molecule is cloned
only if the original molecule should not be modified.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Creates standardized molecule, the original input molecule is cloned.
- createViewPanel(Molecule[]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates view panel with given molecules,
places molecule properties in formatted texts.
- createViewPanel(Molecule[], int, int, int, int) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates view panel with given molecules,
places molecule properties in formatted texts.
- ctab -
Variable in class chemaxon.struc.CGraph
- Connection table.
- current() -
Method in class chemaxon.marvin.modules.MacroMolecule.ComponentIterator
-
- current() -
Method in class chemaxon.marvin.modules.MacroMolecule.NucleicAcid.BackboneAtomIterator
- Gets the current atom index without enumerating the next one.
- current() -
Method in class chemaxon.marvin.modules.MacroMolecule.Polymer.AtomIterator
- Gets the index of the current atom without moving to the next atoms.
- current() -
Method in class chemaxon.marvin.modules.MacroMolecule.Protein.CAlphaAtomIterator
- Gets the current atom index without enumerating the next one.
- current() -
Method in interface chemaxon.marvin.modules.MoleculeIterators.AtomIteratorInterface
- Gets the index of the current atom.
- current() -
Method in class chemaxon.marvin.modules.MoleculeIterators.MoleculeAtomIterator
-
- current -
Variable in class chemaxon.marvin.modules.MoleculeIterators.MoleculeBondIterator
-
- currentAtom -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer.AtomIterator
-
- currentAtom -
Variable in class chemaxon.marvin.modules.MoleculeIterators.MoleculeAtomIterator
-
- currentBackBoneAtomIndex -
Variable in class chemaxon.marvin.modules.MacroMolecule.NucleicAcid
-
- currentICode -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer.AtomIterator
-
- currentICode -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer
-
- currentModelSerial -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer
- these are used in build-up phase
- currentResidue -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer.AtomIterator
-
- currentResidue -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer.BondIterator
-
- currentResidueIndex -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer
-
- currentResidueType -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer
-
- currentSeqNo -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer
-
- currentSequenceIndex -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer
-
- cursorDown(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
- Move the cursor down.
- cursorUp(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
- Moves the cursor up.
- customPaletteColors -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- cyclomaticNumber() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the smallest number of graph edges which must be removed such
that no circuit remains.
refresh()
or redraw() instead.
SurfaceColoring object in case of custom properties.
SurfaceColoring object in case of built-in properties.
GraphicCell from the Jogl rendering thread and draws the molecule.
DOTTED_TYPE or FILLED_TYPE.
three quality modes.
MESH_TYPE or TRANSPARENT_TYPE.
Sgroup.XSTATE_X or Sgroup.XSTATE_XC.
double[][] 2xN table
to a 2-column tab-separated string representation of the table.
GraphicComponent
in the global coordinate system.GraphicComponent
in the global coordinate system.GraphicCell is a rectangular part of the OpenGL canvas containing GraphicComponents.GraphicCell.
GraphicCell.
GraphicScene is the main "entry point" to MarvinSpace.GraphicScene.
Iterator that can enumerate the components
associated to (depending on) this component.
Component.
AtomPropertyInterface that can retrieve
various atom related properties.
MoleculeIterators.AtomPropertyInterface for details.
geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
-1 if the two atoms are not connected by bond.
Component.
BoundingBox that is the smallest container box of the component.
GraphicCell which has the given index.
ComponentElement.
ComponentElement.
ComponentElement or the whole
component as a ComponentElement, if no picking happened.
GraphicComponents of the cell.
componentPartId identifies
a part of the component.
ComponentElement.
MacroMolecule.Polymer.AtomIterator.current().
Component.
ComponentElement,
for example type of the atom.
Double.NaN for no value.
-1 for no value.
ComponentElement
in the GraphicComponent.
ComponentElement.
ChargePlugin.run()
returned false (calculation error): hydrogen valence error.
HBDAPlugin.run()
returned false (calculation error): hydrogen valence error.
HuckelAnalysisPlugin.run()
returned false (calculation error): hydrogen valence error.
IonChargePlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
IsoelectricPointPlugin.run()
returned false (calculation error): hydrogen valence error.
MSAPlugin.run()
returned false (calculation error).
PolarizabilityPlugin.run()
returned false (calculation error): hydrogen valence error.
RefractivityPlugin.run()
returned false (calculation error): hydrogen valence error.
TPSAPlugin.run()
returned false (calculation error): hydrogen valence error.
logDPlugin.run()
returned false (calculation error): hydrogen valence error.
logPPlugin.run()
returned false (calculation error): hydrogen valence error.
pKaPlugin.run()
returned false (calculation error): the number of ionizable atoms
exceeds the specified limit (given in the "ions" parameter) or
hydrogen valence error.
CalculatorPlugin.run()
returned false (calculation error).
GraphicComponent having the given index in the active cell.
GraphicComponent of the given cell.
GraphicComponent with the given id.
GraphicComponents in the cells.
GraphicScene of MarvinSpace to be able to explicitly
set more advanced features.
Component.
UOID.
InputStream from the given String.
MFileFormatUtil.getJTFFields(String)
must be used instead
null if there is no license field
to be managed by the central mechanism.
null if there is no license field for the plugin.
null if there is no license field
to be managed by the central mechanism.
MacroMolecule this component visualizes.
MoleculeComponent visualizes
a ligand in a complex.
MajorMicrospeciesAccessorPlugin.setpH(double).
getCurrentAtomId().
MolInputStream from the given String to
be able to manually add molecules to the event handler.
Molecule that represent the hetero group.
Molecule representation of the MacroMolecule.
Molecule of the MoleculeComponent.
Component.
Double.NaN for no value.
-1 for no value.
Double.NaN for no value.
CalculatorPlugin.PLUGIN_DIR.
a(xx), a(yy), a(zz)
of polarizability tensor
(for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
CalculatorPlugin.setProgressMonitor(chemaxon.marvin.util.MProgressMonitor).
properties().getKeys()
null.
null otherwise.
null.
type of the residue
of the current bond's atoms.
type of the residue
of the current bond's atoms.
Double.NaN, otherwise returns the input molecule itself.
1.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.MOLECULE
or CalculatorPlugin.MOLECULE in case of increments .
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or CalculatorPlugin.MOLECULE.
A for acceptor, D for donor.
pKaPlugin.setpH(double).
RxnMolecule.getComponent(int, int)
RxnMolecule.getComponentCount(int)
MSAPlugin.setSurfaceAreaType(int).
TPSAPlugin.getSurfaceArea()
Double.NaN for no value.
null
otherwise.
null otherwise.
null
otherwise.
logDPlugin.setpH(double).
pKaPlugin.ACIDIC, pKaPlugin.BASIC or 0
if there is no pKa value for the given atom.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment
molecules, false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if the plugin handles multifragment molecules,
false otherwise.
true if plugin has parameter panel,
false otherwise.
ComponentElement
in the active cell.
MESH_TYPE or TRANSPARENT_TYPE.
DRAW_TYPE_WIRE or
DRAW_TYPE_BALL_AND_WIRE mode.
GraphicComponent.hasTransparentPart().
MESH_TYPE or TRANSPARENT_TYPE.
PharmacophorePoint.ACCEPTOR_TYPE.
cellIndex is the active cell of the scene.
true if aliphatic atom.
PharmacophorePoint.ANIONIC_TYPE.
PharmacophorePoint.AROMATIC_TYPE.
true if aromatic atom.
true if asymmetric atom.
true if atom is selected.
PharmacophorePoint.CATIONIC_TYPE.
true if chain atom.
true if pH-Charge calculation.
true if two atoms are in the same connected component,
false for atoms of disconnected structures.
PharmacophorePoint.DONOR_TYPE.
true sketcher canvas is empty.
true if molecule cell is empty.
PharmacophorePoint.EXCLUDED_TYPE.
PharmacophorePoint.HYDROPHOBIC_TYPE.
true if the input molecule has aromatic bond.
true if the original molecule should be modified
(e.g.
MoleculeComponent is a visualizer of a ligand in a complex
or an independent small molecule.
true if molecule output.
true if microspecies calculation.
true if microspecies calculation.
true if microspecies calculation.
true if results for more molecules can be displayed
in a single component, false if each molecule should be displayed
in a separate component.
true if no calculation error,
false on error.
true if the calculation has run without error.
true is options pane is loaded for plugin,
false otherwise.
true if overflow calculation:
maximum number of ionizable atoms exceeded and protein ionization invoked.
true if molecule with R-groups.
true if ring atom.
true if stream output.
ComponentElement is visible in the component.
GraphicComponent
in its local coordinate system.- LocalLocationControl(Monitor) -
Constructor for class chemaxon.marvin.space.monitor.LocalLocationControl
- Creates a new instance of LocalLocationControl
- LocalOrientationControl - class chemaxon.marvin.space.monitor.LocalOrientationControl.
- This control is to change the orientation say rotate a
GraphicComponent
in its local coordinate system. - LocalOrientationControl(Monitor) -
Constructor for class chemaxon.marvin.space.monitor.LocalOrientationControl
- Creates a new instance of LocalOrientationControl
- label -
Variable in class chemaxon.marvin.space.monitor.MeasurementMonitor
-
- labelScale -
Variable in class chemaxon.marvin.space.monitor.Label
-
- labelSize -
Variable in class chemaxon.marvin.space.monitor.Label
- Size of drawn labels.
- largestRingSize() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the size of the largest ring in the molecule (SSSR based).
- largestRingSizeOfAtom(int) -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the size of the largest ring an atom is a member of (SSSR based).
- last -
Variable in class chemaxon.marvin.modules.MoleculeIterators.MoleculeBondIterator
-
- lastModelSerial -
Variable in class chemaxon.marvin.modules.MacroMolecule.NucleicAcid
-
- lastResidue -
Variable in class chemaxon.marvin.modules.MacroMolecule.Polymer.AtomIterator
-
- length() -
Method in class chemaxon.struc.graphics.MTextDocument.Portion
- Gets the number of characters.
- length() -
Method in class chemaxon.struc.graphics.MTextDocument.Section
- Gets text length.
- length() -
Method in class chemaxon.struc.graphics.MTextDocument
- Gets the length of the document.
- lineWidth -
Variable in class chemaxon.marvin.space.MoleculeComponent
-
- load() -
Method in class chemaxon.marvin.plugin.PluginFactory
- Loads default property file.
- load(String) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Loads plugin data from property file.
- load(Properties) -
Method in class chemaxon.marvin.plugin.PluginFactory
- Loads plugin data from properties.
- loadClass(String) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Loads a class, first tries from original CALSSPATH, then from the
class loader used to load this plugin class.
- loadMarvinModule(String) -
Static method in class chemaxon.marvin.util.MolExportModule
- Loads a molecule export module for the specified format.
- locateCell(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the internal index of the cell under x,y position.
- locateCellId(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the id of the cell under x, y position.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the internal id of the component under x, y location,
or the id of the cell itself if there is no component in that location.
- locateObject(int, int, Class) -
Method in class chemaxon.marvin.space.GraphicCell
- Returns the internal id of the given class component under x, y location,
or the id of the cell itself if there is no component in that location.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.GraphicComponent
- Picking action at x, y coordinates, returns the z coordinate of the nearest
picked item, or -1.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the identifire of the object under x,y position.
- locateObject(int, int, Class) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns the identifire of the given class object under x,y position.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.monitor.Label
- Pickes the label in x, y position.
- locateObject(int, int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Pickes the control in x, y position.
- locationNearEdge(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Tells whether the given location is near to any edges of any cell.
- locationNearEdgeX(int, int) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the given location is near the vertical edges of the cell.
- locationNearEdgeX(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Tells whether the given location is near the vertical edges of any cell.
- locationNearEdgeY(int, int) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the given location is near the horizontal edges of the cell.
- locationNearEdgeY(int, int) -
Method in class chemaxon.marvin.space.GraphicScene
- Tells whether the given location is near the horizontal edges of any cell.
- logDPlugin - class chemaxon.marvin.calculations.logDPlugin.
- Plugin class for logD calculation.
- logDPlugin() -
Constructor for class chemaxon.marvin.calculations.logDPlugin
- Constructor.
- logPPlugin - class chemaxon.marvin.calculations.logPPlugin.
- Plugin class for logP calculation.
- logPPlugin() -
Constructor for class chemaxon.marvin.calculations.logPPlugin
- Constructor.
- lowPrecisions -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
MacroMolecule class provides the internal representation
of biochemical data stored in PDB files.MacroMoleculeobject.
MacroMolecule
class.Component class represents any kind of molecular structure
connected by covalent bonds.Component with the given name.
Component with the given name and chain
id.
MacroMolecule.Compound class partially represents the COMPND record
in the PDB file.Compound with the given id and name.
Component class to represent
ligands, ions and water molecules.HeteroComponent to represent a ligand
with a given identification code,
chain code, sequence number, insertion code.
Polymer class represents nucleic acid and amino acid
chains.Protein with the given name and chain
identifier.
Monitor that measures something on its elements.MoleculeComponent is the basic visualizer of simple molecules in MarvinSpace.MoleculeComponent from the given molecule.
MoleculeComponent from the given
HeteroComponent and MacroMoleculeComponent;
this class can be used as a visualizer of a ligand.
MoleculeIterators is a collection of iterators that
enumerate atoms and bonds of molecules.AtomIteratorInterface interface
enumerate atoms of a molecule.BondIteratorInterface interface
enumerate bonds of a molecule.Molecule.Molecule.AtomIteratorInterface interface that enumerates atoms,
and BondIteratorInterface interface that enumerates bonds.Monitor is for "watching" something in the scene.Monitor.
setReaction() and
setMap() in one method.
setReaction() and
setMap() in one method.
HeteroComponent.
Double.NaN.
PdbImport.PharmacophoreArrow provides an extension of
PharmacophorePoint to represent pharmacophores by introducing
directionality.PharmacophoreArrow.
PharmacophoreArrow at the position of the given
ComponentElement getting the coordinates by getCoordinates().
PharmacophoreArrow at the given position.
PharmacophorePoint.
PharmacophorePoint at the position of the given ComponentElement
getting the coordinates by getCoordinates().
GraphicComponent.pickedItem to be the picked part of the component.
GraphicComponent.pickedItem to the
pharmacophore point.
GraphicComponent by changing the coordinates.null if not a reaction.
Sgroup.removeAtom(MolAtom, int) of
sg.
RxnMolecule.removeComponent(int, int)
FILLED_TYPE.
FILLED_TYPE.
FILLED_TYPE.
$HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or
$HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux).
20).
-10).
setModel(int)
Cl- concentration (default: 0.1).
Cl- concentration (default: 0.1).
ComponentElement that will
be returned by {#getDescription()}.
draw property.
draw property.
draw property.
PharmacophoreSphere.
draw property.
DropTarget of the graphic canvas.
SurfaceComponent.setExclusiveColor(byte[]).
SurfaceComponent.setExclusiveColor(byte[]).
MacroMoleculeComponent can be set and in this case this will be a
visualizer of a ligand in the macromolecule.
RxnMolecule passed in
setReaction( final
RxnMolecule rm )mapId map.
MolAtom.setForSpecIsotopeSymbol(String)
pKaPlugin.MODEL_SMALL model, it
sets the maximum number of ionizable atoms to be considered
and uses simple calculation method to compute pKa values.
Molecule of the MoleculeComponent to mol,
sets proper atomIterators, and computes the bounding box.
Na+, K+ concentration (default: 0.1).
Na+, K+ concentration (default: 0.1).
Component.
PharmacophoreArrow.
ConformerPlugin.run() to display progress
status.
IsoelectricPointPlugin.run() to display progress status.
MolecularDynamicsPlugin.run() to display progress
status.
MultiformPlugin.run() to display progress status.
StereoisomerPlugin.run() to display
progress status.
pKaPlugin.run() to display progress status.
CalculatorPlugin.run() to display progress status.
PharmacophoreArrow.setRenderingQuality(int).
RENDERING_* constants.
PharmacophorePoint.setRenderingQuality(int).
GraphicComponent.RENDERING_QUALITY_HIGH constants.
Palette.smoothColorToCutoffValues(boolean).
MSAPlugin.VAN_DER_WAALS or MSAPlugin.SOLVENT.
true then symmetrical structures
are filtered out, otherwise symmetrical structures are returned as duplicates.
true then take dominant structures.
298 Kelvin).
CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
Double.NaN then the input molecule is taken as it is.
0.0).
1.0).
14.0).
[O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
sulphynil groups: [#6][S+:1]([#6])[#8-:2]>>[#6][S:1]([#6])=[O:2]
[O:1]=[N:2] >> [O-:1][N+:2], [H:3][O:2][N:1] >> [NH1+:1][O-:2]
sulphynil group transformation: [#6][S:1]([#6])=[O:2] >> [#6][S+:1]([#6])[#8-:2]
MolBond.UP or UP to MolBond.DOWN.
CompnentElement.
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