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Smolecule.A_PARITY|Smolecule.A_CHIRALITY"abbrevgroups".
"abbrevgroupsAllowed".
AbstractStructureChecker detecting abbreviations
("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in
abbreviated group form."absLabelVisible" or "absLabel".
StructureFixer implementation which removes absolute stereo property from the molecule.StructureFixer interfacetrue if molecule is accepted by the filter.
"addRemoveHatomsEnabled".
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)
Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[])
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.
PropertyChangeListener that will receive all the PropertyChangeEvent fired by this class
PropertyChangeListener that will receive the PropertyChangeEvent fired when the property with
the given name is changed
PropertyChangeListener for a specific property.
PropertyChangeListener for a specific property.
RxnMolecule.addComponent(Molecule, int)
RxnMolecule.addComponent(Molecule, int, boolean)
TransferableDescriptor to the MTransferable
Registry.
ClipboardHandler.addTransferable(String, String, Integer, Integer, boolean, boolean, boolean)
instead.
TransferableDescriptor to the registry, and constructing it
by the given parameters.
CheckerRunner implementation with advanced fixing capabilities.CheckerRunner with more advanced fixing capabilities.
AbstractStructureChecker detecting atoms with alias
labels.HitColoringAndAlignmentOptions.setAlignmentMode(int)
and HitColoringAndAlignmentOptions.getAlignmentMode() to access this field.
AlignmentMolecule form a Molecule
based on the settings.AlignmentAPIRing.aliphaticAtomCount()
Ring.aliphaticBondCount()
Ring.aliphaticRingCount()
Ring.aliphaticRingCount(int)
Ring.aliphaticRings()
Ring.aliphaticRings(int)
"animate".
"animDelay".
"animFPS".
"animSync".
DispOptConsts.AUTOMATIC_FOG
Ring.aromaticAtomCount()
Ring.aromaticBondCount()
DefaultStructureCheckerResult for identifying aromaticity problems,
thus errorType property is StructureCheckerErrorType.AROMATICITYStructureCheckerErrorType.AROMATICITY by default.
AbstractStructureChecker detecting aromatization problems.Ring.aromaticRingCount()
Ring.aromaticRingCount(int)
Ring.aromaticRings()
Ring.aromaticRings(int)
CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean)
To keep the same functionality use with TRUE boolean parameters.
MoleculeGraph#setBond(int, MolBond)
MDocSource implementation for an array of documents or molecules.Stereochemistry.asymmetricAtomCount()
Stereochemistry.asymmetricAtoms()
"atomFont".
"atomMappingVisible".
"atomNumbersVisible".
"atomPropertiesVisible".
"atomSet".
"atomSetColor".
"atomsize".
"atomStrings".
"atomSymbolsVisible".
AtomChecker detecting atom maps.AtomProperty class provides access to chemical properties of
Molecule atoms by atom index.AtomChecker detecting atoms having an query property
set.AtomChecker detecting atoms with atom value.AbstractStructureChecker detecting attached data in the molecule."autoscale".
"autoTabScale".
AutoMapper finds the best mapping from reactant side atoms
to product side atoms of a reaction."automaticFogEnabled".
"background".
"bgloadEnabled".
"bgload".
"ballRadius".
CheckerRunner interface/BasicCheckerRunner instance which will can execute StructureChecker instances read from
configurationReader
BasicCheckerRunner instance which will can execute StructureChecker instances read from
configurationReader
BasicCheckerRunner instance with specified StructureChecker list.
"bondDraggedAlong".
"bondLengthVisible".
"bondSet".
"bondSetColor".
"bondSpacing".
BondChecker for the detection of unpreferred bond angles in 2D
molecule layouts.BondChecker detecting bonds with unpreferred lengths in 2D molecule
layouts."border".
"buttonmenubar".
"cacheMols".
PluginWorkUnit.getResult().
getResult().
CallbackIface.
CallbackIface.callback(String, Object)
to the context.
CallbackIface.
CallbackIface.
CallbackIface.
CallbackIface.
AbbrevGroupRecognizer.testLine(String)
must be used instead
JTFRecognizer.canBeJTFHeader(String)
must be used instead
PDBRecognizer.testRecord(String)
must be used instead
true if repeatedly running the same plugin object
while getting the results on the GUI is allowed, false otherwise.
Ring.carboaliphaticRingCount()
Ring.carboaromaticRingCount()
Ring.carboRingCount()
Ring.carboRingCount(int)
Ring.carboRings()
Ring.carboRings(int)
MolBond instead"cell".
MoleculeGraph insteadRing.chainAtomCount()
Ring.chainBondCount()
"chargeWithCircle".
true if molecule should be processed,
false otherwise.
List of StructureCheckerResult
which contains all the identified problems
UserSettings.getPropertiesDescriptionChangedByOtherApp() method
to retreive the return value of this method. If you really
need it.
StructureChecker instances automaticallyStructureFixer instances.CheckerRunnerImpl instance which will can execute StructureChecker instances read from
configurationReader
Stereochemistry.chiralCenterCount()
Stereochemistry.chiralCenters()
"chiralitySupport".
String
Cleaner.clean(MoleculeGraph, int, String)
Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor)
AbstractStructureFixer which cleans the molecule in
2d"clean2dOpts".
"clean3dOpts".
"cleanDim".
"cleanOpts".
ConcurrentProcessor instance, awaits termination of associated
worker threads and releases any resource this processor has reserved.
ConcurrentProcessor.cleanup(long) with Long.MAX_VALUE.
ClipboardHandler the
functionalities in this class will be unsupported after Marvin
5.4
The class will be removed in 5.5MolBond.cloneBond(MolAtom a1, MolAtom a2).
MolExportModule and the underlying stream.
MolExportModule and, optionally, the underlying stream.
MolAtom insteadCodeAssistFactory to set up CodeAssist"colorScheme".
HitColoringAndAlignmentOptions.setColoringEnabled(boolean)
and HitColoringAndAlignmentOptions.isColoringEnabled() to access this field.
"cols".
ChemJEP object.
ChemJEP object.
ChemJEP object.
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.
- componentHidden(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Hides windows if the parent frame is hidden.
- componentMoved(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Does nothing.
- componentResized(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Does nothing.
- componentShown(ComponentEvent) -
Method in class chemaxon.marvin.beans.MarvinPane
- Shows windows if the parent frame is hidden.
- CompositeInputProducer - Class in chemaxon.util.concurrent.marvin
- Input producer composed of an array of input producers.
- CompositeInputProducer() -
Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
- Constructor.
- CompositeInputProducer(InputProducer[]) -
Constructor for class chemaxon.util.concurrent.marvin.CompositeInputProducer
- Constructor.
- CompositeWorkUnit - Class in chemaxon.util.concurrent.marvin
- Work unit composed of an array of work units, to be called in a linear fashion
in a single thread, one after the other in the specified order.
- CompositeWorkUnit() -
Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
- Constructor.
- CompositeWorkUnit(WorkUnit[]) -
Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnit
- Constructor.
- CompositeWorkUnitFactory - Class in chemaxon.util.concurrent.marvin
- Work unit factory composed of an aray of work unit factories.
- CompositeWorkUnitFactory(WorkUnitFactory[]) -
Constructor for class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
- Constructor.
- composition(int) -
Method in class chemaxon.calculations.ElementalAnalyser
- Gets the elemental analysis, the relative percent composition of a pure
chemical substance by element (w/w%).
- COMPRESS -
Static variable in class chemaxon.formats.MdlCompressor
- Compression flag.
- computeFunctionScale() -
Method in class chemaxon.calculations.nmr.NMRSpectrum
- Computes the scaling factor for the unscaled NMR spectrum function.
- computeFunctionScale(double, double[]) -
Method in class chemaxon.calculations.nmr.NMRSpectrum
-
- computeSurface(MacroMoleculeComponent.MoleculeVisualizer) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Activates the container cell of the
MoleculeVisualizer, and
computes its Connolly surface.
- computeSurface(String) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Computes the given type of surface in the active cell of the viewer.
- ConcurrentProcessor - Interface in chemaxon.util.concurrent
- Executes jobs in parallel and returns their results iterator-style.
- ConcurrentProcessors - Class in chemaxon.util.concurrent.processors
- Creates
ConcurrentProcessor instances. - CONFIDENCE -
Static variable in class chemaxon.naming.DocumentToStructure
- The confidence that the structure is correct.
0 or less means very little confidence.
1 or more means high confidence.
- CONFIG_DIR -
Static variable in class chemaxon.jep.Evaluator
- Default directory for storing configuration files.
- ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader
- This interface is provided for classes which can read the configuration of
CheckerRunner. - CONFIRM_TRANSFER -
Static variable in class chemaxon.marvin.view.ViewParameterConstants
- Identifier of parameter:
"confirmTransfer".
- CONFORMATION_PLUGIN_GROUP -
Static variable in class chemaxon.license.LicenseManager
- Identifier of plugin: Conformation Plugin Group
- ConformerPlugin - Class in chemaxon.marvin.calculations
- Plugin class for conformer calculation.
- ConformerPlugin() -
Constructor for class chemaxon.marvin.calculations.ConformerPlugin
- Constructor.
- CONJUGATED -
Static variable in class chemaxon.struc.MolBond
- Conjugation state of the bond.
- constant -
Variable in class chemaxon.marvin.services.ServiceArgument
- field indicates constant argument
- containerFrame -
Variable in class chemaxon.marvin.space.MSpaceEasy
-
- contains(float, float, float) -
Method in class chemaxon.marvin.space.BoundingBox
- Tells whether the given location is inside the box.
- contains(MObject) -
Method in class chemaxon.struc.MDocument
- Searches an object in the document.
- contains(MDocument) -
Method in class chemaxon.struc.MDocument
- Tests whether the document contains all objects of another document.
- contains(MolAtom) -
Method in class chemaxon.struc.Molecule
- Checks if the molecule graph contains the specified atom.
- contains(MolAtom) -
Method in class chemaxon.struc.MoleculeGraph
- Checks if the molecule graph contains the specified atom.
- contains(MolBond) -
Method in class chemaxon.struc.MoleculeGraph
- Checks if the molecule graph contains the specified bond.
- contains(MoleculeGraph) -
Method in class chemaxon.struc.MoleculeGraph
- Does the molecule graph contain the specified fragment?
- contains(MProp) -
Method in class chemaxon.struc.MPropertyContainer
- Tests whether the container contains the specified property object.
- contains(MProp) -
Method in class chemaxon.struc.prop.MCollectionProp
- Tests whether the collection contains the specified property.
- contains(MolAtom) -
Method in class chemaxon.struc.RgMolecule
- Checks if the root structure or an R-group contains the specified node.
- contains(MolBond) -
Method in class chemaxon.struc.RgMolecule
- Checks if the root structure or an R-group contains the specified edge.
- contains(MolAtom) -
Method in class chemaxon.struc.RxnMolecule
- Checks if a reactant, agent or product structure contains the specified
node.
- contains(MolBond) -
Method in class chemaxon.struc.RxnMolecule
- Checks if a reactant, agent or product structure contains the specified
edge.
- containsAllAtomsOf(Sgroup) -
Method in class chemaxon.struc.Sgroup
- Checks if the S-group contains the atoms of another S-group.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MAtomSetPoint
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MChemicalStruct
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MEFlowBasePoint
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.graphics.MPolyline
- Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) -
Method in class chemaxon.struc.MObject
- Checks if the object contains the specified atom reference.
- containsComponent(GraphicComponent) -
Method in class chemaxon.marvin.space.GraphicCell
- Tells whether the component is in the cell.
- containsComponent(GraphicComponent) -
Method in class chemaxon.marvin.space.GraphicScene
- Returns true if the component exists in the scene.
- containsCoordinateBond(MoleculeGraph) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Decides whether a molecule graph contains coordinate bonds.
- containsLadderTypePolymer() -
Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
- Decides whether the structure of this sgroup contains a
ladder-type repeating unit.
- containsMulticenterSgroup(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Decides whether a molecule contains Multicenter S-groups.
- containsOnlyOne(Class) -
Method in class chemaxon.struc.MDocument
- Tests whether the document contains only one object of the specified
class.
- containsPoint(DPoint3, CTransform3D) -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- containsPoint(DPoint3, CTransform3D) -
Method in class chemaxon.struc.MObject
-
- containsPropertyKey(String) -
Method in class chemaxon.struc.MolAtom
- Returns true if this atom has a mapping for the specified property key.
- containsPropertyKey(String) -
Method in class chemaxon.struc.MolBond
- Returns true if this bond has a mapping for the specified property key.
- containsPseudoAtom(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns
true if molecule contains pseudo atom.
- containsSRUSgroup(Molecule) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Decides whether a molecule contains SRU S-groups.
- contract(int) -
Method in class chemaxon.struc.Sgroup
- Sets the state to
Sgroup.XSTATE_C.
- contract(int) -
Method in interface chemaxon.struc.sgroup.Expandable
- Contracts the S-group.
- contract(int) -
Method in class chemaxon.struc.sgroup.MultipleSgroup
- Contracts this S-group.
- contract(int) -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Contracts this S-group.
- ContractGroupFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which contracts the abbreviated groups in the molecule - ContractGroupFixer() -
Constructor for class chemaxon.fixers.ContractGroupFixer
-
- contractOrExpandSgroups(int, String, boolean) -
Method in class chemaxon.marvin.view.MDocStorage
- Contract or expand S-groups in the specified cell.
- contractOrExpandSgroupsAll(boolean) -
Method in class chemaxon.marvin.view.MDocStorage
- Contract or expand S-groups in all molecules.
- contractSgroups() -
Method in class chemaxon.struc.Molecule
- Contracts all S-groups.
- Control - Class in chemaxon.marvin.space.monitor
- Transformation on a
GraphicComponent that changes the coordinates, and not just the view. - Control() -
Constructor for class chemaxon.marvin.space.monitor.Control
- Creates a new instance of Control
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.Control
- Does control on x-y events.
- control(int) -
Method in class chemaxon.marvin.space.monitor.Control
- Does control on z event.
- control(int) -
Method in class chemaxon.marvin.space.monitor.DihedralControl
- One part of the molecule being in one of the end of the torsion bond
will be rotated around the bond.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.DihedralControl
- Does nothing.
- control -
Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
-
- control(int) -
Method in class chemaxon.marvin.space.monitor.DihedralMonitor
- Passes the control event to the control.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
- Changes the location say translates the component of the control
in the global coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
- Changes the location say translates the component of the control
in the global coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Changes the orientation say rotates the component of the control
in the global coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
- Changes the orientation that is rotates the component of the control
in the global coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.LocalLocationControl
- Changes the location say translates the component of the control
in its local coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.LocalLocationControl
- Changes the location say translates the component of the control
in its local coordinate system.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
- Changes the orientation say rotates the component of the control
in its local coordinate system.
- control(int) -
Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
- Changes the orientation say rotates the component of the control
in its local coordinate system.
- control -
Variable in class chemaxon.marvin.space.monitor.Monitor
-
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Causes the monitor's controll to take action with 2 parameters.
- control(int) -
Method in class chemaxon.marvin.space.monitor.PositionMonitor
- Causes the monitor's controll to take action with 1 parameter.
- control(int) -
Method in class chemaxon.marvin.space.monitor.ResizeControl
- Resizes the component in z direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- control(int, int) -
Method in class chemaxon.marvin.space.monitor.ResizeControl
- Resizes the component in x, y direction uniformly which means that it will
either increase or decrease its size with one unit or do nothing
if the given value was positive, negative or zero.
- CONV_SELFREF -
Static variable in class chemaxon.struc.MProp
- Conversion of self referring property.
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) -
Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) -
Method in class chemaxon.checkers.result.SgroupCheckerResult
-
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) -
Method in interface chemaxon.checkers.result.StructureCheckerResult
- This method converts the entities contained in this result according to the convertData.
- convert() -
Method in class chemaxon.formats.MdlCompressor
- Compression/decompression
- convert(byte[], int) -
Static method in class chemaxon.formats.MdlCompressor
- (Un)compress the specified molfile or SDfile.
- convert(String, int) -
Static method in class chemaxon.formats.MdlCompressor
- (Un)compress the specified molfile or SDfile.
- convert() -
Method in class chemaxon.formats.MolConverter
- Convert the next molecule.
- convert(double[][]) -
Static method in class chemaxon.marvin.alignment.AlignRigidEasy
-
- convert(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Creates an MDL mol or compressed mol representation of the molecule.
- convert(Molecule) -
Method in class chemaxon.marvin.io.MolExportModule
- Convert a molecule to a string or byte array.
- convert(String) -
Method in interface chemaxon.naming.NameConverter
- Convert a name into the corresponding structure.
- ConvertAliasToGroupFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts the aliases to
contracted abbreviated groups in the molecule - ConvertAliasToGroupFixer() -
Constructor for class chemaxon.fixers.ConvertAliasToGroupFixer
-
- convertBase64Gzip2Text(String) -
Static method in class chemaxon.util.HTMLUtil
- Converts gzip compressed data with base64 encoding to text.
- convertCoordinateBondsToData(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Converts coordinate bonds to data sgroups (attached data)
with field name MRV_COORDINATE_BOND.
- convertExplicitHToImplicit(MoleculeGraph, int) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.
- convertExplicitLonePairsToImplicit(MoleculeGraph) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Converts explicit lone pairs from a molecule to implicit.
- convertForJavaScript(String) -
Static method in class chemaxon.util.HTMLUtil
- Converts a string to a format that can be used as a
value of JavaScript variable in an HTML page.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert implicit Hydrogen atoms of the specified atoms in a molecule
to explicit.
- convertImplicitHToExplicit(MoleculeGraph) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert implicit Hydrogen atoms of the molecule to explicit.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
- convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) -
Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
- Convert implicit lone pairs of the atoms of a molecule to explicit.
- convertMultiCenterSgroupsToData(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Converts the multicenter sgroups to data sgroups in the molecule.
- convertPageSettingsToData(Molecule) -
Method in class chemaxon.marvin.io.formats.mdl.MolExport
- Converts page setting of multipage molecular document to data sgroups (attached data)
with field name MRV_PAGE_XXX.
- ConvertPseudoToGroupFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts the pseudo
informations to contracted abbreviated groups in the molecule - ConvertPseudoToGroupFixer() -
Constructor for class chemaxon.fixers.ConvertPseudoToGroupFixer
-
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) -
Method in class chemaxon.checkers.AbbreviatedGroupChecker
- This implementation does nothing.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) -
Method in class chemaxon.checkers.AbstractStructureChecker
- Handles the mapping of a cloned and expanded molecule result to the original molecule.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) -
Method in class chemaxon.checkers.RgroupReferenceErrorChecker
- Deprecated. This implementation does nothing.
- convertResult(StructureCheckerResult) -
Method in class chemaxon.checkers.runner.BasicCheckerRunner
- This method provides the possibility to convert back the affected properties of the result
if there was any convert in the molecule structure before check.
- convertResult(StructureCheckerResult) -
Method in class chemaxon.checkers.runner.SketchCheckerRunner
- This method converts the result by changing the atoms and bonds back to the original
instead of the cloned ones
- ConvertToAtomFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts the aliases to
atom with atom number contained in the alias information - ConvertToAtomFixer() -
Constructor for class chemaxon.fixers.ConvertToAtomFixer
-
- ConvertToCarbonFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts pseudo atoms to
carbon atoms - ConvertToCarbonFixer() -
Constructor for class chemaxon.fixers.ConvertToCarbonFixer
-
- convertToFrags() -
Method in class chemaxon.struc.Molecule
- Converts this molecule to its disconnected fragments, expanding all
S-groups and keeping disconnected Multicenter S-groups in the same fragment,
but ungroupping and separating fragments in all other types of S-groups.
- convertToSmilingFormat(Molecule) -
Static method in class chemaxon.formats.MFileFormatUtil
- Tries to convert a molecule to a SMILES related format.
- convertToSmilingFormat(MProp) -
Static method in class chemaxon.formats.MFileFormatUtil
- Try to convert a property to text with a SMILES related format argument.
- convertToString(MDocument, String, int) -
Static method in class chemaxon.formats.MolExporter
- Converts the document to text format.
- convertToString(MProp, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Converts the property to text format.
- convertToString(MPropertyContainer, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Convert key of MPropertyContainer to string.
- convertToString(String, int) -
Method in class chemaxon.struc.MDocument.Prop
- Deprecated. As of release 5.7, replaced by
MolExporter.convertToString(MDocument, String, int)
- convertToString(String, int) -
Method in class chemaxon.struc.MProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String).
Instead MProp.CONV_SELFREF flag use fmt + ":-selfrefprops" string in fmt.
- convertToString(String) -
Method in class chemaxon.struc.MProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MBooleanProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MDoubleArrayProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MDoubleProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MHashProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MHCoords3DProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MIntegerArrayProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MIntegerProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MListProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MMoleculeProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
Instead MProp.CONV_SELFREF flag use fmt + ":-selfrefprops" string in fmt.
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MObjectProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) -
Method in class chemaxon.struc.prop.MStringProp
- Deprecated. As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertTransform(CTransform3D, boolean) -
Method in class chemaxon.struc.graphics.MRectangle
-
- COORDDEP -
Static variable in class chemaxon.struc.MProp
- Coordinate dependent property.
- COORDINATE -
Static variable in class chemaxon.struc.MolBond
- Coordinate bond flag.
- COORDINATE_BOND_ARROW_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_OFFSET -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_AT_MULTICENTER_STYLES -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_HASHED_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_SOLID_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLE -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"coordinateBondStyle".
- COORDINATE_BOND_STYLE_AT_MULTICENTER -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"coordinateBondStyleAtMulticenter".
- COORDINATE_BOND_STYLE_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLE_OFFSET -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- COORDINATE_BOND_STYLES -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- CoordinationSystemErrorChecker - Class in chemaxon.checkers
- Detects errors of multicenter coordination systems.
- CoordinationSystemErrorChecker() -
Constructor for class chemaxon.checkers.CoordinationSystemErrorChecker
- Default constructor
- COORDS_UPDATE -
Static variable in interface chemaxon.struc.sgroup.Expandable
- Performs coordinate update during the unbinding of atoms.
- COPY_AS_FORMAT -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Default format to be selected on Copy as dialog.
- COPY_AS_IMAGE_BITMAP -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_AS_IMAGE_EMF -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_AS_OLE -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_AS_TEXT -
Static variable in interface chemaxon.marvin.util.CopyOptConstants
- Deprecated.
- COPY_OPTIONS -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Deprecated. since 5.3.3 has no sense
- CopyOptConstants - Interface in chemaxon.marvin.util
- Deprecated. since 5.2.1 the whole copy-paste engine was refactored. The
constants defined in this interface either non exists in the new
implementation or its value has changed. See the constants own
description for details.
- copyProperties(MBracket) -
Method in class chemaxon.struc.graphics.MBracket
- Copies line properties to another line object.
- copyProperties(MPolyline) -
Method in class chemaxon.struc.graphics.MPolyline
- Copies line properties to another line object.
- correctCornersRadius(double, double) -
Method in class chemaxon.struc.graphics.MRoundedRectangle
-
- countAllAtoms() -
Method in class chemaxon.struc.MolAtom
- Counts all atoms represented by this atom.
- countAllAtoms() -
Method in class chemaxon.struc.Sgroup
- Counts the total number of atoms recursively.
- countAllAtoms() -
Method in class chemaxon.struc.sgroup.SgroupAtom
- Counts all atoms represented by this atom.
- countEnumerations() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the number of all enumerated structures,
no arithmetic overflow because counts in
BigInteger.
- countEnumerationsMagnitude() -
Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
- Returns the magnitude (the number of decimal "digits")
of the number of all enumerated structures.
- countExpandableContractableSgroups() -
Method in class chemaxon.struc.Molecule
- Counts the expandable and contractable S-groups.
- countOrderedComponentSgroups() -
Method in class chemaxon.struc.Molecule
- Counts the ordered component S-groups.
- countRecords(MProgressMonitor, int, Runnable, int) -
Method in class chemaxon.marvin.view.MDocStorage
- Counts the total number of records and sets the size of the document
storage.
- countRecordsInFraction(double, int, MProgressMonitor) -
Method in class chemaxon.marvin.view.MDocStorage
- Deprecated.
- COVALENT_HYDRATION_ERROR_REMARK -
Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
- Covalent hydration error remark.
- covalentRadiusOf(int, int) -
Static method in class chemaxon.struc.MolAtom
- Gets the covalent radius in C-C bond length units.
- CPK_SCHEME -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- CPK color scheme in display option flags.
- CPK_SCHEME_S -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- CPK color scheme.
- Cr -
Static variable in class chemaxon.struc.PeriodicSystem
-
- crdMolRefresh() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- crdSafeRefresh() -
Method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- create(byte[]) -
Static method in class chemaxon.marvin.alignment.AlignmentMolecule
-
- create(String, String) -
Static method in class chemaxon.marvin.plugin.CalculatorPlugin
- Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
- create(int, InputProducer) -
Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- create(int, InputProducer, WorkUnitFactory) -
Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
-
- create(String) -
Static method in class chemaxon.util.DotfileUtil
- Opens a dotfile for writing.
- createArgument(T) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value
- createArgument(String, T) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value
- createArgumentAs(T, Class<T>) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value and type
- createArgumentAs(String, T, Class<T>) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Returns a service argument based on value and type
- createArray(String, String, int, int) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates an array property.
- createArrayXSD(String, String, int, int) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates an array property from the XSD type.
- createAtomIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an atom iterator for the specified molecule of the factory
according to the atom related behavior set in the factory.
- createAtomNeighbourIterator(MolAtom) -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an iterator to get the atom neighbours of the specified
atom.
- createBHtab() -
Method in class chemaxon.struc.MoleculeGraph
- Creates the bond table extended with implicit hydrogen atoms.
- createBHtab() -
Method in class chemaxon.struc.RxnMolecule
- Creates the graph union's bond table extended with implicit hydrogen
atoms.
- createBondIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs a bond iterator for the specified molecule of the factory
according to bond related behavior set in the factory.
- createBondNeighbourIterator(MolAtom) -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an iterator to get the bonds connecting to the specified
atom.
- createBracket(Sgroup, DPoint3[], int) -
Static method in class chemaxon.marvin.util.CleanUtil
-
- createChemicalTermsTextPane() -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
- createChemicalTermsTextPane(boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
- createChemicalTermsTextPane(boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(boolean, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
- createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane.
- createChemicalTermsTextPane(String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
- createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
- createChemicalTermsTextPane(String, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, boolean, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space
- createChemicalTermsTextPane(String, String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String, boolean, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
- createChemicalTermsTextPane(String, String, boolean, String) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Deprecated. use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates a JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) -
Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
- Creates a
JTextPane instance with code assist capabilities.
- createCHtab() -
Method in class chemaxon.struc.MoleculeGraph
- Creates the connection table extended with implicit hydrogen atoms.
- createCHtab() -
Method in class chemaxon.struc.RxnMolecule
- Creates the graph union's connection table extended with implicit
hydrogen atoms.
- createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) -
Method in class chemaxon.struc.graphics.MTextAttributes
-
- createConstantFromString(String, Class<?>) -
Static method in class chemaxon.marvin.services.ServiceArgument
- Creates a
ServiceArgument constant based on string value and argument type.
- createDefaultParameterPanel(String, Component) -
Static method in class chemaxon.marvin.plugin.PluginFactory
- Creates default parameter panel based on XML config.
- createDefaultParameterPanel(Class, String, Component) -
Static method in class chemaxon.marvin.plugin.PluginFactory
-
- createDehydrogenizedReadOnlyGraph() -
Method in class chemaxon.struc.MoleculeGraph
- Creates a dehydrogenized version of the molecule.
- createEMF(String, String) -
Static method in class chemaxon.util.ImageExportUtil
- Creates a .NET based EMF picture.
- createExportModule() -
Method in class chemaxon.formats.MFileFormat
- Creates the export module.
- createExportModule(String) -
Method in class chemaxon.formats.MFileFormat
- Creates the export module.
- createExportModule(String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Creates an export module for the specified format.
- createExportModule(String, String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Creates an export module for the specified format with the specified encoding.
- createGearch() -
Method in class chemaxon.struc.Molecule
-
- createGearch() -
Method in class chemaxon.struc.MoleculeGraph
-
- createGearch() -
Method in class chemaxon.struc.RgMolecule
-
- createGearch() -
Method in class chemaxon.struc.RxnMolecule
-
- createGearch() -
Method in class chemaxon.struc.SelectionMolecule
-
- createImage(Buffer, int, int) -
Method in class chemaxon.marvin.space.GraphicScene
-
- createImageExporterParameter(Properties, String, MDocument) -
Static method in class chemaxon.util.ImageExportUtil
- Creates the Image Exporter parameter String based on the values in the
Properties object.
- createImportMod(MolInputStream) -
Static method in class chemaxon.marvin.io.MRecordImporter
- Creates an importer for the specified molecule input stream.
- createImportMod(String) -
Static method in class chemaxon.marvin.io.MRecordImporter
- Creates an importer for the specified molecule format.
- createImportModule() -
Method in class chemaxon.formats.MFileFormat
- Creates the molecule import module.
- createInput() -
Method in class chemaxon.util.concurrent.marvin.ReusableInputProducer
-
- createLicenseManagerPanel() -
Static method in class chemaxon.license.LicenseManager
- Creates the main panel which is used for end-user license managing.
- createMenu(ResourceBundle, String) -
Static method in class chemaxon.marvin.beans.MarvinPane
- Deprecated. as of Marvin 3.3.1, replaced by SwingUtil.createMenu
- createMenu(ResourceBundle, String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Utility method to create a menu with a label specified as a resource.
- createMenu(ResourceBundle, String, boolean) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu with a label specified as a resource.
- createMenuItem(ResourceBundle, String, Class, boolean) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu item with a label specified as a resource.
- createMenuItem(ResourceBundle, String, boolean) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu with a label specified as a resource.
- createMenuItem(ResourceBundle, String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a menu with a label specified as a resource.
- createMessagePane(String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a message pane with HTML text content.
- createMMoleculeProp(String) -
Static method in class chemaxon.marvin.io.MPropHandler
-
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.logPPlugin
- Returns the major tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
- Returns the molecule form with largest distribution.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
- Returns the major tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.pKaPlugin
- Returns the canonical tautomeric form of the molecule.
- createModifiedInputMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Returns the modified input molecule (e.g. microspecies, major tautomeric form).
- createMol() -
Method in class chemaxon.formats.MolImporter
- Creates a target molecule object for import.
- createMol() -
Method in class chemaxon.marvin.io.formats.mdl.MolImport
- Creates a new target molecule object.
- createMol() -
Method in class chemaxon.marvin.io.MolImportModule
- Creates a new target molecule object for the import.
- createMol() -
Method in class chemaxon.marvin.io.MRecordImporter
- Creates an empty target molecule for import.
- createMol(String) -
Static method in class chemaxon.struc.RgMolecule
- Deprecated. As of Marvin 3.4,
MolImportModule.createMol() must be used.
- createMolConverter(InputStream, OutputStream, String[], int[]) -
Static method in class chemaxon.formats.MolConverter
- Creates a MolConverter instance with the attributes specified in the
parameters.
- createMolecule() -
Method in class chemaxon.struc.Sgroup
- Creates a molecule object that contains only this group.
- createMolecule(Molecule) -
Method in class chemaxon.struc.Sgroup
- Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
- createMolecule() -
Method in class chemaxon.struc.sgroup.SuperatomSgroup
- Creates a molecule object that contains only this group.
- createMoleculeFromInputStream(InputStream) -
Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Helper function to get Molecule or MacroMolecule from the given
InputStream with MolImporter.
- createMoleculeIterator(Collection<Molecule>) -
Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
- Creates a
MoleculeIterator object for iterating through collection of
molecules (Molecule objects).
- createMoleculeIterator(Molecule[]) -
Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
- Creates a
MoleculeIterator object for iterating through a molecule
array (Molecule[]).
- createMolIfNeeded() -
Method in class chemaxon.marvin.io.MRecordImporter
- Creates an empty target molecule for import if non-concurrent mode,
returns
null if concurrent mode.
- createMolsFrame() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- createNewCell() -
Method in class chemaxon.marvin.space.GraphicScene
- Sets an empty cell to be the active cell.
- createNext() -
Method in class chemaxon.struc.graphics.MTextAttributes
- Creates identical attributes for the next section.
- createParameterPanel() -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates the parameter panel.
- createPooledWu(int, InputProducer, WorkUnitFactory) -
Static method in class chemaxon.util.concurrent.processors.ConcurrentProcessors
- For test only
- createReaction(Molecule, DPoint3[], int) -
Static method in class chemaxon.struc.RxnMolecule
- Creates a reaction.
- createReaction(MoleculeGraph, DPoint3[]) -
Static method in class chemaxon.struc.RxnMolecule
- Creates a reaction.
- createRecognizer(String) -
Method in class chemaxon.formats.MFileFormat
- Creates a recognizer module.
- createRecordReader(MolInputStream, String) -
Method in class chemaxon.formats.MFileFormat
- Creates the record reader.
- createRecordReader(InputStream, String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Creates a record reader for an input stream.
- createRecordReader(InputStream, String, String, String) -
Static method in class chemaxon.formats.MFileFormatUtil
- Creates a record reader for an input stream.
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AliasChecker
-
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AtomChecker
-
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.AtomQueryPropertyChecker
-
- createResult(Molecule, List<MolBond>) -
Method in class chemaxon.checkers.BondChecker
-
- createResult(Molecule, List<E>) -
Method in class chemaxon.checkers.ComponentChecker
- Creates a
StructureCheckerResult from a List containing the components.
- createResult(Molecule, List<MolAtom>) -
Method in class chemaxon.checkers.PseudoAtomChecker
-
- createResult(Molecule, List<StructureCheckerResult>) -
Method in class chemaxon.checkers.ReactionChecker
- This method a merged StructureCheckerResult from the
List
of StructureCheckerResult which contains the problems of the components in
the reaction
- createResultView(String, MolPanel) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
- createRgComponentIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs an rgroup definition component iterator for the specified molecule of the factory
if the molecule is an RgMolecule, an empty iterator otherwise.
- createRotationAboutBond(MolBond, double) -
Static method in class chemaxon.marvin.util.CleanUtil
- Creates a rotation transformation about a bond.
- createRxnComponentIterator() -
Method in class chemaxon.util.iterator.IteratorFactory
- Constructs a reaction component iterator for the specified molecule of the factory
if the molecule is an RxnMolecule, an empty iterator otherwise.
- createSavedCoordsArray(MoleculeGraph) -
Static method in class chemaxon.marvin.util.CleanUtil
- Creates an empty array for the atomic coordinates of a structure.
- createScalar(String, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates a scalar property.
- createScalar(String, String, MProgressMonitor) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates a scalar property.
- createScalarXSD(String, String) -
Static method in class chemaxon.marvin.io.MPropHandler
- Creates a scalar property from the XSD type.
- createSelectionPanel(int) -
Method in class chemaxon.marvin.space.MSpaceEasy
- Adds the basic MarvinSpace selection panel to the container.
- createSelectionPanelAndProgressBar() -
Method in class chemaxon.marvin.space.MSpaceEasy
- Adds the basic MarvinSpace selection panel to the container.
- createSmolecule() -
Method in class chemaxon.struc.MoleculeGraph
- Creates a
Smolecule represenation of this molecule.
- createSpacePanel(Molecule[]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates space panel with given molecules,
creates colored surface to each molecule.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Deprecated. Use
ResonancePlugin.createStandardizedMolecule(Molecule) instead
- createStandardizedMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.ResonancePlugin
- Creates standardized molecule, the original input molecule is cloned
only if the original molecule should not be modified.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Deprecated.
- createStandardizedMolecule(Molecule) -
Method in class chemaxon.marvin.calculations.TautomerizationPlugin
- Creates standardized molecule, the original input molecule is cloned
only if the original molecule should not be modified.
- createStandardizedMolecule(Molecule, boolean) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Deprecated. Use
CalculatorPlugin.createStandardizedMolecule(Molecule) instead
- createStandardizedMolecule(Molecule) -
Method in class chemaxon.marvin.plugin.CalculatorPlugin
- Creates standardized molecule, the original input molecule is cloned.
- createSubPanel(String) -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates a sub-panel with a title.
- createTopLeftConstraints() -
Static method in class chemaxon.marvin.util.SwingUtil
- Creates GridBagConstraints for the top left component.
- createViewPanel(Molecule[]) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates view panel with given molecules,
places molecule properties in formatted texts.
- createViewPanel(Molecule[], int, int, int, int) -
Method in class chemaxon.marvin.plugin.CalculatorPluginDisplay
- Creates view panel with given molecules,
places molecule properties in formatted texts.
- createWorkUnit() -
Method in class chemaxon.util.concurrent.marvin.CompositeWorkUnitFactory
- Creates a
CompositeWorkUnit object composed of work units created by the factories.
- createWorkUnit() -
Method in interface chemaxon.util.concurrent.WorkUnitFactory
-
- CRITICAL_ERROR_MSG -
Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
- Critical error message.
- cross(DPoint3, DPoint3) -
Static method in class chemaxon.struc.DPoint3
- Calculates the cross product of the two vectors
- CrossedDoubleBondChecker - Class in chemaxon.checkers
- A descendant of
BondChecker for the detection of unspecified double bonds
represented by crossed bond type. - CrossedDoubleBondChecker() -
Constructor for class chemaxon.checkers.CrossedDoubleBondChecker
- Default constructor
- CrossedDoubleBondFixer - Class in chemaxon.fixers
- A descendant of
AbstractStructureFixer which converts crossed double
bond to wiggly - CrossedDoubleBondFixer() -
Constructor for class chemaxon.fixers.CrossedDoubleBondFixer
-
- Cs -
Static variable in class chemaxon.struc.PeriodicSystem
-
- CSMDL_IN -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed Molfiles, RGfiles, Rgfiles, SDfiles or RDfiles.
- CSMOL_OUT -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed Molfiles and Rgfiles.
- CSRDF -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed RDfiles.
- CSRXN_OUT -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed Rxnfiles.
- CSSDF_OUT -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Compressed SDfiles.
- ctab -
Variable in class chemaxon.struc.MoleculeGraph
- Connection table.
- CTransform3D - Class in chemaxon.struc
- 3D transformation matrix.
- CTransform3D(CTransform3D) -
Constructor for class chemaxon.struc.CTransform3D
- Copy constructor.
- CTransform3D() -
Constructor for class chemaxon.struc.CTransform3D
- Constructs an identity transformation.
- CTSPECIFIC_H -
Static variable in class chemaxon.struc.MolAtom
- Deprecated. graph invariants are checked by default when calculating CIS/TRANS stereo, so this
option is out of use
- CTUMASK -
Static variable in interface chemaxon.struc.StereoConstants
- Double bond stereo mask.
- CTUNKNOWN -
Static variable in interface chemaxon.struc.StereoConstants
- CIS/TRANS cannot be determined because bond angle is close to
180 degrees.
- CTUNSPEC -
Static variable in interface chemaxon.struc.StereoConstants
- Unspecified double bond.
- Cu -
Static variable in class chemaxon.struc.PeriodicSystem
-
- CubeRecognizer - Class in chemaxon.formats.recognizer
- Gaussian Cube format recognizer.
- CubeRecognizer(String) -
Constructor for class chemaxon.formats.recognizer.CubeRecognizer
- Creates a Gaussian Cube format recognizer.
- currentBond -
Variable in class chemaxon.util.iterator.IteratorFactory.BondIterator
- Current bond index pointer of the iterator.
- currentBond -
Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
- Current bond pointer of the iterator.
- cursorDown(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
- Move the cursor down.
- cursorToRowEnd(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
-
- cursorToRowStart(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
-
- cursorUp(boolean) -
Method in class chemaxon.struc.graphics.MTextBox
- Moves the cursor up.
- CUSTOMIZATION_ENABLED -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"customizationEnabled".
- customPaletteColors -
Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- CXSMARTS -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Extended SMARTS.
- CXSMILES -
Static variable in class chemaxon.formats.MFileFormat
- ChemAxon Extended SMILES.
- cyclomaticNumber() -
Method in class chemaxon.calculations.TopologyAnalyser
- Calculates the smallest number of graph edges which must be removed such
that no circuit remains.
"debug".
"defaultSaveFormat".
MPolyline.DEFAULT_ARROW_HEAD_LENGTH instead.
MPolyline.DEFAULT_ARROW_HEAD_WIDTH instead.
"defaultTool".
StructureCheckerResultMoleculeGraph.implicitizeHydrogens(int)
with parameter MolAtom.ALL_H does the same.
String
"detach".
"detachable".
"disableSpecialNodes".
refresh()
or redraw() instead.
"dispQuality".
SurfaceColoring object in case of custom properties.
SurfaceColoring object in case of built-in properties.
RingStrainErrorChecker instead."downWedge".
"draggable".
GraphicCell from the Jogl rendering thread and draws the molecule.
DOTTED_TYPE or FILLED_TYPE.
three quality modes.
MESH_TYPE or TRANSPARENT_TYPE.
ServiceArguments implementing this interface
should support automatic evaluation of arguments before service call
based on context."editable".
"elements".
"2dviewerEnabled".
"3dviewerEnabled".
HitColoringAndAlignmentOptions.setMarkushDisplayMode(int)
and HitColoringAndAlignmentOptions.getMarkushDisplayMode() to access this field.
MarkushEnumerationPlugin"escapeChar".
boolean.
boolean[].
double.
double[].
Sgroup.XSTATE_X or Sgroup.XSTATE_XC.
AbstractStructureFixer which expands all abbreviated groups in the moleculeDefaultStructureCheckerResult for identifying explicit hydrogen
problems, thus errorType property is StructureCheckerErrorType.EXPLICIT_H by default.StructureCheckerErrorType.EXPLICIT_H by default.
MolExporter.exportToBinFormat(MDocument, String)
MolExporter.exportToBinFormat(Molecule, String)
MolExporter.exportToFormat(MDocument, String)
MolExporter.exportToFormat(Molecule, String)
MolExporter.exportToObject(MDocument, String)
MolExporter.exportToObject(Molecule, String)
StructureCheckerResult that supports external
StructureChecker development."extraBonds".
"xtmpls".
"ezVisible".
MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie().
0D molecules only.
MoleculeGraph.findFrag(int, int, MoleculeGraph),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
MoleculeGraph.findFragById(int, int, MoleculeGraph),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFragById(fragId, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
MoleculeGraph.findFrags(Class, int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
StructureChecker on the given molecule and after that fixes all
identified problems with the first StructureFixer which is associated with the current problem.
StructureFixer which
is associated with the StructureCheckerErrorType of the result.
StructureFixer implementations which
StructureCheckerErrorType can be fixed by the current fixerStructureFixer implementations which
error codes (identified by a unqie String) can be fixed by the current fixer"fogFactor".
double[][] 2xN table
to a 2-column tab-separated string representation of the table.
Ring.fusedAliphaticRingCount()
Ring.fusedAliphaticRingCount(int)
Ring.fusedAliphaticRings()
Ring.fusedAliphaticRings(int)
Ring.fusedAromaticRingCount()
Ring.fusedAromaticRingCount(int)
Ring.fusedAromaticRings()
Ring.fusedAromaticRings(int)
Ring.fusedRingCount()
Collection of the base colors.
Collection of the base Molecule RGB colors and base
colors.
Collection of the base Molecule RGB colors.
Collection of black and white colorAlignmentMolecule form a Molecule
based
on the values of the setters.
Colors, which are
different enough from the specified forbidden colors.
Colors, with no
forbidden colors.
AlignmentMolecule form a Molecule
based
on the values of the setters.
UserSettings.getProperty(String) instead.
TopologyAnalyserPlugin.getAliphaticRingCount(int)
TopologyAnalyserPlugin.getAromaticRingCount(int)
Iterator that can enumerate the components
associated to (depending on) this component.
PeriodicSystem.findAtomicNumber(String).
PeriodicSystem.findAtomicNumber(String).
logPPlugin.getAtomlogPIncrement(int)
MoleculeIterators.AtomPropertyInterface for details.
MolPrinter.getAtomSize().
geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
-1 if the two atoms are not connected by bond.
MarvinPane.getBondSpacing()
MolPrinter.getBondSpacing()
BoundingBox that is the smallest container box of the component.
MoleculeGraph.getBondTable() instead
RgMolecule.getBondTable() instead
RxnMolecule.getBondTable() instead
GraphicCell which has the given index.
Molecule instance.
Double.NaN for no value.
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.
Transferable object.
Molecule.
TemplateHandler.DEFAULT_MY_TEMPLATES_VALUE instead.
ServiceDescriptorEditorProvider instance
ServiceDescriptorReader instance
ServiceDescriptorWriter instance
ServiceDialogProvider instance
ComponentElement,
for example type of the atom.
StructureCheckerDescriptor instance which represents the user interface
related informations of the checker
ServiceDescriptor represented by editor state or null
if the editor is in not valid state
MolBond.desiredLength(int, int, int, int) instead
MolBond.desiredLength(int, int, int, int) instead
MolBond.desiredLength(int, int, int, int) instead.
MolBond.desiredLength(int, int, int, int) instead.
MolAtom.getBond(int).
MoleculeGraph.getBond(int).
MoleculeGraph.getBondArray().
MolAtom.getBondCount().
MoleculeGraph.getBondCount().
MolAtom.getBondTo(MolAtom).
Arrays.asList(getAtomArray()).
ServiceDescriptor
ServiceDescriptorEditor instance for specified ServiceDescriptor class
HuckelAnalysisPlugin.getHMOEigenVector()
Double.NaN for no value.
Double.NaN for no value.
HuckelAnalysisPlugin.getHMOElectrophilicOrder(int)
ComponentElement
in the GraphicComponent.
ComponentElement.
String which identifies the problems thus this
must be unique for each class that implements this interface
String represented error code of the checker (this error code
should be used for external implementation support instead of StructureChecker.getErrorType())
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.
logDPlugin.run()
returned false (calculation error): hydrogen valence error.
logPPlugin.run()
returned false (calculation error): hydrogen valence error.
MSAPlugin.run()
returned false (calculation error).
OrbitalElectronegativityPlugin.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.
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.
CalculatorPlugin.run()
returned false (calculation error).
null otherwise.
StructureFixer instances which associated with the
StructureCheckerErrorType of the result
MoleculeGraph.getFragCount(int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
MoleculeGraph.getFragIds(int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.getFragIds(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
Evaluator.getFunctionData()
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.
Double.NaN for no value.
Double.NaN for no value.
Double.NaN for no value.
-1 for no value.
Double.NaN for no value.
-1 for no value.
HuckelAnalysisPlugin.getHMOHuckelOrbitalCoefficients()
UOID.
MTransferable object when importing from
clipboard.
InputStream from the given String.
logDPlugin.setpH(double).
ChemJEP.TRUE, ChemJEP.FALSE or ChemJEP.UNDECIDED.
MacroMolecule this component visualizes.
MoleculeComponent visualizes
a ligand in a complex.
CalculatorPlugin.createModifiedInputMolecule(Molecule) instead
MajorMicrospeciesPlugin.setpH(double).
Molecule representation of the MacroMolecule.
Molecule of the MoleculeComponent.
MolInputStream from the given String to
be able to manually add molecules to the event handler.
TemplateHandler.MYTEMPLATES_KEY
instead.
MTransferable.
Molecule.setName(String).
null if no more structures.
MoleculeGraph.getAtom(int).
MolBond.getAtom1().
MolBond.getAtom2().
MoleculeGraph.getAtomCount().
Arrays.asList(getAtomArray()).
Double.NaN for no value.
HuckelAnalysisPlugin.getHMONucleophilicOrder(int)
MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie().
MolBond.getOtherAtom(MolAtom).
pKaPlugin.getpKaValues(int, int)
pKaPlugin.ACIDIC, pKaPlugin.BASIC or 0
if there is no pKa value for the given atom.
Evaluator.getFunctionData()
a(xx), a(yy), a(zz)
of polarizability tensor
(for geom3D=true, see PolarizabilityPlugin.setGeom3D(boolean)).
MFileFormat.getPriority(java.lang.String) instead
MTransferable object by exporting to
clipboard.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
LicenseManager.
CalculatorPlugin.setProgressMonitor(chemaxon.common.util.MProgressMonitor).
MPropHandler.convertToString(MProp, String),
the following usage will give the same results:
String property = MPropHandler.convertToString(mol.properties(), key);
PropertyChangeSupport associated with this editor
properties().getKeys()
null otherwise.
MolAtom.getQueryString()
MarvinPane.getSaveGlobalGUIProperties() function
have been merged.
UserSettings.getSaveGUIPropertiesInMRV(). It will be removed in a
future version of Marvin.
HuckelAnalysisPlugin.getHMORealEigenValue()
AlignRigidEasy.align() method must be called
null.
Long.MAX_VALUE),
null otherwise.
null otherwise.
null otherwise.
null.
MTransferable.
Double.NaN, otherwise returns the input molecule itself.
CalculatorPlugin.run().
StructuralFrameworksPlugin.getResultMolecule() after a
StructuralFrameworksPlugin.run() call in the given format StructuralFrameworksPlugin.setFormat(String)
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.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.ATOM or
CalculatorPlugin.MOLECULE.
CalculatorPlugin.MOLECULE.
CalculatorPlugin.MOLECULE
or CalculatorPlugin.MOLECULE in case of increments .
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.
CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
A for acceptor, D for donor.
TopologyAnalyserPlugin.getRingCount(int)
MolBond
instance represented by bond parameter
TopologyAnalyserPlugin.getRingSystemCount(int)
AlignRigidEasy.align() method must be called
AlignRigidEasy.align() method must be called
InputStream with service configuration
InputStream with service configuration
null.
ServiceDescriptorEditorProvider instance if
available, or null
ServiceDescriptorReader instance if available, or
null
ServiceDescriptorWriter instance if available, or
null
ServiceDialogProvider instance if available, or
null
List which contains the affected groups of the problem
MSketchPane.isBondDraggedAlong()
pKaPlugin.setpH(double).
pKaPlugin.getMacropKaValues(int,double[],int[]) instead
MPropHandler.convertToString(MPropertyContainer, String)
DataFlavor.stringFlavor
RxnMolecule.getComponent(int, int)
-1 in case of arithmetical overflow
(if the number would exceed Long.MAX_VALUE).
RxnMolecule.getComponentCount(int)
Molecule[] array.
TautomerizationPlugin.getStructure(int)
ServiceDescriptor classes.
MSAPlugin.setSurfaceAreaType(int).
MoleculeIterator.next() throws NoSuchElementException in case of error.
HuckelAnalysisPlugin.getHMOTotalPiEnergy()
TPSAPlugin.getSurfaceArea()
MTransferable object to the given Molecule with
the given properties.
MTransferable to the given Molecule with the
given properties in the given format.
JLabel instance, dinamically showing validation result of textPane
NOTE: will validate against Molecular Context.
JLabel instance, dinamically showing validation result of textPane
NOTE: textPane have to be created with this factory
JLabel instance, dinamically showing validation result of textPane
NOTE: will validate against Reaction Context.
null
otherwise.
null otherwise.
null
otherwise.
GraphicComponent
in the global coordinate system.GraphicComponent
in the global coordinate system."grinv".
"grinvVisible".
GraphicCell is a rectangular part of the OpenGL2 canvas containing GraphicComponents.GraphicCell.
GraphicCell.
GraphicScene is the main "entry point" to MarvinSpace.GraphicScene.
PeptideRecognizer.guessPeptideFormat(String)
must be used instead
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 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 there are more structures.
true if all input producers have next input.
true if there are more molecules,
false if end has been reached.
true.
true if plugin has parameter panel,
false otherwise.
ComponentElement
in the active cell.
SmartsAtomQuerifier.hasSMARTSProps(MolAtom atom)
SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude)
MESH_TYPE or TRANSPARENT_TYPE.
DRAW_TYPE_WIRE or
DRAW_TYPE_BALL_AND_WIRE mode.
GraphicComponent.hasTransparentPart().
MESH_TYPE or TRANSPARENT_TYPE.
MolAtom.haveSimilarBonds(MolAtom).
Ring.heteroaliphaticRingCount()
Ring.heteroaliphaticRingCount(int)
Ring.heteroaliphaticRings()
Ring.heteroaliphaticRings(int)
Ring.heteroaromaticRingCount()
Ring.heteroaromaticRingCount(int)
Ring.heteroaromaticRings()
Ring.heteroaromaticRings(int)
Ring.heteroRingCount()
Ring.heteroRingCount(int)
Ring.heteroRings()
Ring.heteroRings(int)
MListProp and
MHashProp objects.
HitColoringAndAlignmentOptions.setHitColor(Color)
and HitColoringAndAlignmentOptions.getHitColor() to access this field.
HitColoringAndAlignmentOptions.setHitHomologyColor(Color)
and HitColoringAndAlignmentOptions.getHitHomologyColor() to access this field.
ServiceDescriptor implementation
for HTTP POST/GET based servicesHTTPServiceDescriptor
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph) and
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph)
"imageSaveFormat".
"imageSaveURL".
"imageShowURL".
"implicitH".
chemaxon.calculations.hydrogenize.Hydrogenize#convertExplicitHToImplicit(MoleculeGraph)(MoleculeGraph, int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(mol, f);
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int),
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)
the following usage will give the same results:
chemaxon.calculations.hydrogenize.Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)
"importConv".
"importEnabled".
MolImporter.importMol(String,String);
if you have a byte array, call MolImporter.importMol(byte[], String, String).
MolImporter.importMol(String, String);
if you have a byte array, call MolImporter.importMol(byte[], String, String, Molecule).
IteratorFactory.INCLUDE_CHEMICAL_ATOMS_ONLY.
AlignmentMolecule.create(byte[] bytes)
initialize variables.
MoleculeGraph.insertBond(int, MolBond).
MoleculeGraph.insertBondInOrder(MolBond, MolBond[]).
MoleculeGraph.insertAtom(int, MolAtom).
PharmacophorePoint.ACCEPTOR_TYPE.
cellIndex is the active cell of the scene.
true if services are displayed in the popup list
Ring.isAliphaticAtom(int)
true if aliphatic atom.
PharmacophorePoint.ANIONIC_TYPE.
true if count is approximate due to multiple position bonds with
multicenters of variable size, false otherwise.
PharmacophorePoint.AROMATIC_TYPE.
Ring.isAromaticAtom(int)
true if aromatic atom.
Stereochemistry.isAsymmetricAtom(int)
true if asymmetric atom.
TopologyUtil.isBridgeHeadAtom(MoleculeGraph, int)
PharmacophorePoint.CATIONIC_TYPE.
Ring.isChainAtom(int)
true if chain atom.
Ring.isChainBond(int)
true if pH-Charge calculation.
Stereochemistry.isChiral()
Stereochemistry.isChiralCenter(int)
true if clean is needed for GUI display.
true if two atoms are in the same connected component,
false for atoms of disconnected structures.
MolBond.isCoordinate()
MTransferable is appearing as an option in
the Copy As dialog.
CubeRecognizer.isCubeLine(String, int)
must be used instead
MarvinTransferable.flavor equals with the given parameter.
MTransferable instance should be used by
the default copy operation.
PharmacophorePoint.DONOR_TYPE.
true if the context is empty.
PharmacophorePoint.EXCLUDED_TYPE.
MolPrinter.isEZLabelsVisible()
true if molecule filter is set.
MListProp and MHashProp.
PharmacophorePoint.HYDROPHOBIC_TYPE.
true if structures are returned in 3D.
true if the input molecule has aromatic bond.
true if large molecule
(number of atoms exceeds 1000).
true if the plugin is licensed.
true if the plugin is licensed.
true if the plugin is licensed.
true if the plugin is licensed.
true if the plugin is licensed.
true if the plugin is licensed.
true if the plugin is licensed.
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.
PeriodicSystem.isNobleGas(int z).
true if no calculation error,
false on error.
true if the calculation has run without error.
true if "OK" button is enabled.
MoleculeGraph.removeAtom(chemaxon.struc.MolAtom), especially for large molecule graphs.
MoleculeGraph.removeBond(chemaxon.struc.MolBond), especially for large molecule graphs.
true is options pane is loaded for plugin,
false otherwise.
AbstractStructureFixer which converts the isotopes to non isotope atomstrue if overflow calculation:
maximum number of ionizable atoms exceeded and protein ionization invoked.
true if random enumeration is requested.
Are reaction errors highlighted?
Are reaction errors visible?
true if molecule with R-groups.
Ring.isRingAtom(int)
true if ring atom.
Ring.isRingBond(int)
true if stream output.
MoleculeGraph.getValenceCheckState() instead
true if service argument is valid
true if editor represents a valid descriptor in current state
ComponentElement is visible in the component.
IteratorFactory class provides implementations of Iterator
to ease the handling of atoms and bonds used in Molecule objects and its
descendants.AtomIterator class provides
an iterator for the atoms of the specified molecule of the factory
according to the atom related behavior set in the factory.AtomNeighbourIterator class provides an iterator to process
the atoms connecting to a specified atom according to the atom and bond related
behavior of this factory.BondIterator class provides an iterator to process
the bonds of the specified molecule in this factory
according to the bond related behavior of this factory.BondNeighbourIterator class provides an iterator to
process the bonds connecting to the specified atom according to the atom
and bond related behavior of this factory.NeighbourIterator class provides an iterator to process the bonds connecting to the
specified atom according to the atom and bond related behavior of this factory.RgComponentIterator class provides an iterator to process
the rgroup definition components in the specified molecule of
the factory.RxnComponentIterator class provides an iterator to process
the components (reactant, product and agent components) in the reaction molecule of
the factory.UserSettings.getPropertyMap() instead.
Ring.largestRing()
Ring.largestRingSize()
Ring.largestRingSizeOfAtom(int)
Ring.largestRingSystem()
Ring.largestRingSystemSize()
"layout".
"layoutH".
"license".
"licenseFile".
"ligandErrorVisible".
LIGAND_ORDER_OFF
LIGAND_ORDER_ON
LIGAND_ORDER_ONLY_WITH_DEFINITION
"listenmouseevent".
"listenpropertychange".
"loadMols".
GraphicComponent
in its local coordinate system.- LocalLocationControl(Monitor) -
Constructor for class chemaxon.marvin.space.monitor.LocalLocationControl
- Creates a new instance of LocalLocationControl
- LocalOrientationControl - Class in chemaxon.marvin.space.monitor
- 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
- LocalServiceDescriptor - Class in chemaxon.marvin.services.localservice
- Service Descriptor for java based local services.
- LocalServiceDescriptor() -
Constructor for class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
- 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 in chemaxon.marvin.calculations
- Plugin class for logD calculation.
- logDPlugin() -
Constructor for class chemaxon.marvin.calculations.logDPlugin
- Constructor.
- logger -
Variable in class chemaxon.checkers.runner.AdvancedCheckerRunner
-
- logPPlugin - Class in chemaxon.marvin.calculations
- Plugin class for logP calculation.
- logPPlugin() -
Constructor for class chemaxon.marvin.calculations.logPPlugin
- Constructor.
- LONE_PAIR_TYPE -
Static variable in class chemaxon.marvin.space.MoleculeComponent
-
- LONE_PAIRS_AS_LINE -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"lonePairsAsLine".
- LONE_PAIRS_AS_LINE_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- LONE_PAIRS_AS_LINE_OFFSET -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
- LONE_PAIRS_AUTO_CALCULATION -
Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- Identifier of parameter:
"lonePairsAutoCalc".
- LONE_PAIRS_VISIBLE -
Static variable in class chemaxon.marvin.common.ParameterConstants
- Identifier of parameter:
"lonePairsVisible".
- LONELY_H -
Static variable in class chemaxon.struc.MolAtom
- Include lonely Hydrogen atom(s).
- lowPrecisions -
Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
-
- LP -
Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
-
- LP -
Static variable in class chemaxon.struc.MolAtom
- "Atomic number" of the lone pair.
- LP_AUTO_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Lone pair automatic calculation visible flag.
- LP_FLAG -
Static variable in interface chemaxon.marvin.paint.DispOptConsts
- Lone pair visibility flag.
- Lr -
Static variable in class chemaxon.struc.PeriodicSystem
-
- Lu -
Static variable in class chemaxon.struc.PeriodicSystem
-
MarvinPane.addHelpMenu(java.awt.Container) should be used.
MarvinPane.addToolsMenu(java.awt.Container) should be used.
setReaction() and
setMap() in one method.
setReaction() and
setMap() in one method.
AbstractStructureFixer which maps the atoms of the molecule incrementallysetReaction() and
setMap() in one method.
AbstractStructureFixer which maps the reaction with AutoMapperHitColoringAndAlignmentOptions.setMarkushDisplayMode(int)
and HitColoringAndAlignmentOptions.getMarkushDisplayMode() to access this field.
"maxscale".
Monitor that measures something on its elements."menuconfig".
"menubar".
"mergedst".
MoleculeGraph.mergeFrags(int, int, int),
to keep the same functionality, use value MoleculeGraph.FRAG_KEEPING_MULTICENTERS
for parameter fragmentationType, e.g.:
mol.mergeFrags(id1, id2, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
MoleculeGraph.mergeAtoms(MolAtom, MolAtom).
AbstractStructureFixer which converts a single incorrectly drawn
metallocene into multicenter based coordinate bond representation.MPropHandler.createMMoleculeProp(String)
"molLoaderFinishedEvent".
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.Builder.build()
instead.
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.MolConverter(Builder)
MolConverter.Builder instead.Molecule instance to check
"mol".
Molecule which will be transferred to the clipboard.
"molbg".
"molChanged".
"molFormat".
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.
chemaxon.core.util.MoleculeUtilMolExportExceptionMolExportModuleMolImporter object.Monitor is for "watching" something in the scene.Monitor.
"moreEnabled".
TemplateHandler.MYTEMPLATES_GROUP_INDEX instead.
NameConverter
to indicate that even though a name cannot be converted to a structure,
it is the prefix of a valid name.String
Double.NaN.
"navmode".
IteratorFactory.AtomIterator.next() instead.
IteratorFactory.AtomNeighbourIterator.next() instead.
IteratorFactory.BondIterator.next() instead.
IteratorFactory.BondNeighbourIterator.next() instead.
IteratorFactory.RgComponentIterator.next() instead.
IteratorFactory.RxnComponentIterator.next() instead.
HitColoringAndAlignmentOptions.setNonHitColor(Color)
and HitColoringAndAlignmentOptions.getNonHitColor() to access this field.
HitColoringAndAlignmentOptions.setNonHitColor3D(Color)
and HitColoringAndAlignmentOptions.getNonHitColor3D() to access this field.
MolAtom.getAtomicNumber(String).
AlignmentSimilarity3D"param".
"paramH".
MolImporter.parseMRV(String)
Cleaner.partialClean(Molecule, Molecule[], String)
Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String)
Cleaner.partialClean(MoleculeGraph, int, int[], String)
"peptideDisplayType"
See
Parameters and Events documentation
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.
Throwable and the plugin object which
has thrown the Throwable.String
"preload".
String represents the name of the property which represents
the arom type String property
String represents the name of the
configuration file property which is responsible for searching contracted
abbreviated groups
String represents the name of the property which is
responsible for searching too long bonds in the molecule
String represents the name of the property which is
responsible for searching too short bonds in the molecule
String represents the name of the
configuration file property which is responsible for searching expanded
abbreviated groups
String represents the name of the configuration file property which is
responsible for searching too long bonds in the molecule
String represents the name of the property which is
responsible for searching all ratoms in the molecule
String represents the name of the property
which is responsible for searching self references in the molecule
String represents the name of the property
which is responsible for searching contracted abbreviated groups
String represents the name of the property which is
responsible for searching disconnected ratoms in the molecule
String represents the name of the property
which is responsible for searching expanded abbreviated groups
String represents the name of the property which is
responsible for searching generic ratoms in the molecule
String represents the name of the property which is
responsible for searching linker ratoms in the molecule
String represents the name of the property
which is responsible for searching missing rgroups in the molecule
String represents the name of the property which is
responsible for searching nested ratoms in the molecule
String represents the name of the property
which is responsible for searching unused rgroups in the molecule
String represents the name of the configuration file property which is
responsible for searching too short bonds in the molecule
String represents the name of the property which is
responsible for using the given aromatization type during the check mechanism.
Boolean
UserSettings.getPropertyMap(String)
method to get all properties that are stored.
UserSettings.getPropertyMap(String)
method to get the default properties.
UserSettings.getPropertyMap(String)
method to get the properties set by UserSettings.setProperty(String, String)
method or by the setter methods.
UserSettings.getPropertyMap(String)
method to get the properties that are being stored temporary, and will
not be saved to the properties file.
AtomChecker detecting pseudo atoms.UserSettings.setProperty(String, String) or
UserSettings.setProperty(String, String, boolean) instead.
StringSelection.
"queryAtoms".
AtomChecker detecting generic atoms or ones having query properties.BondChecker detecting query bonds."rgroupsVisible".
AtomChecker detecting radical atoms.AbstractStructureChecker detecting R-atoms."reactionSupport".
null if not a reaction.
ReactionChecker detecting reactions with invalid mapping.Molecule object.
ServiceDescriptor objects from specified InputStream
AbstractStructureFixer which rearomatize the moleculeMoleculeGraph.regenBonds().
CodeAssist instances created with this factory to reload the code completion data.
MoleculeGraph.removeAllBonds().
Sgroup.removeAtom(MolAtom, int) of
sg.
AbstractStructureFixer which removes the atoms of the
molecule signed in the resultAbstractStructureFixer which removes the atom maps from the moleculeAbstractStructureFixer which removes the atom value from the moleculeAbstractStructureFixer which removes the attached data from the moleculeAbstractStructureFixer which removes the bonds of the molecule
signed by the resultMoleculeGraph.removeBond(MolBond).
MoleculeGraph.removeBond(int).
Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph)
null atom entries in the atoms array
and sets the index fields appropriately.
null bond entries in the bonds array
and sets the index fields appropriately.
MoleculeGraph.removeAtom(MolAtom).
MoleculeGraph.removeAtom(int).
MoleculeGraph.removeAtom(MolAtom, int).
MoleculeGraph.removeAtom(int, int).
AbstractStructureFixer which removes the radicals from the
atoms of the moleculeRxnMolecule.removeComponent(int, int)
TransferableDescriptor to the MTransferable
Registry.
TransferableDescriptor to the MTransferable
Registry by name.
"rendering".
MoleculeGraph.replaceBond(MolBond, MolBond).
mark method was last called on this input stream.
GraphicComponent by changing the coordinates.CalculatorPlugin.setMolecule(Molecule, boolean, boolean, boolean)
The parameter should be topologically equal to the input molecule
for a successfull restore.
AbstractStructureChecker detecting invalid
attachments in R-group definitions.Ring.ringAtomCount()
Ring.ringBondCount()
Ring.ringCount()
Ring.ringCount(int)
Ring.ringCountOfAtom(int)
Ring.rings(int)
Ring.rings(int)
Ring.ringSystemCount()
Ring.ringSystemCount(int)
Ring.ringSystems()
Ring.ringSystems(int)
"RLogicVisible" or "RLogic".
"rows".
UserSettings.save(String).
$HOME/chemaxon/<plugin class name>Parameters.properties (Windows), or
$HOME/.chemaxon/<plugin class name>Parameters.properties (UNIX / Linux).
"scale".
"script".
"selectable".
"selectedIndex".
"selection".
String
ServiceDescriptorServiceDescriptorEditor instances based on ServiceDescriptor classes.ServiceDescriptorsServiceDescriptorReader,
ServiceDescriptorWriter and ServiceDialogProvider
implementations and various configuration data for services.ServiceDescriptorsDialog instances to provide argument editor and result view for ServiceDescriptorException for failure indication for services.ServiceException with specified message and cause
ServiceException with specified message
ServiceException with specified cause
"setColoringEnabled".
MoleculeGraph.setAbsStereo(boolean) for the
component
20).
MolPrinter.setAtomSize(double).
-10).
MarvinPane.setBondSpacing(double)
MolPrinter.setBondSpacing(double)
setModel(int)
UserSettings.setCleanHOptionEnabled(boolean)
true then resonants returned
by ResonancePlugin.getStructure(int) and ResonancePlugin.getStructures() methods are cleaned in 2D.
true then tautomers returned
by TautomerizationPlugin.getStructure(int) and TautomerizationPlugin.getStructures() methods are cleaned in 2D.
Cl- concentration (default: 0.1).
Cl- concentration (default: 0.1).
ComponentElement that will
be returned by {#getDescription()}.
ServiceDescriptorEditor.getDescriptor() may NOT return same instance
MolPrinter.setDispopts(int), but affects only limited
display options using a mask.
MolPrinter.setDispoptsExt(int), but affects only limited
display options using a mask.
true then dominant tautomer
distribution is calculated.
draw property.
draw property.
draw property.
draw property.
PharmacophoreSphere.
DropTarget of the graphic canvas.
MoleculeGraph.setBond(int, MolBond).
SurfaceComponent.setExclusiveColor(byte[]).
SurfaceComponent.setExclusiveColor(byte[]).
MolPrinter.setEZLabelsVisible(boolean)
CalculatorPlugin.getResultAsString(int, Object)
MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes.
MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes.
MolImporter, then set the
cell synchronously using MViewPane.setM(int, Molecule). The
reason is to simplify the public API and minimize the risk
of related concurrency problems in user codes.
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.
Multiplet array of the spectrum.
Na+, K+ concentration (default: 0.1).
Na+, K+ concentration (default: 0.1).
MoleculeGraph.setAtom(int, MolAtom).
MFileFormatUtil.MOLMOVIE,
MFileFormatUtil.NOMOLMOVIE, MolImporter.isMolMovie().
Double.NaN then the input molecule is taken as it is.
Double.NaN then the input molecule is taken as it is.
0.0).
0.0).
1.0).
14.0).
14.0).
pKaPlugin.STATICpKaPREFIX)
STATIC pKa prefix: pKa's prefix does not depend on the submitted micro state
DYNAMIC pKa prefix: pKa's prefix does depend on the submitted micro state
PharmacophoreArrow.
AlignmentPlugin.run() to display progress status.
ConformerPlugin.run() to display progress
status.
IsoelectricPointPlugin.run() to display progress status.
MolecularDynamicsPlugin.run() to display progress
status.
pKaPlugin.run() to display progress status.
ResonancePlugin.run() to display progress status.
StereoisomerPlugin.run() to display
progress status.
TautomerizationPlugin.run() to display progress status.
CalculatorPlugin.run() to display progress status.
true then all tetrahedral stereo
information is preserved by the tautomer generator.
true then aromatic bonds are not modified by the tautomer
generator.
true then the charge of charged atoms are not modified by the tautomer
generator.
true then the stereo configuration of double bonds
with preset stereo information will not be changed.
true then double bonds stereo information is preserved by
the tautomer generator.
true then ester groups are excluded from the tautomerization.
true then labeled tetrahedral stereo
centers are protected by the tautomer generator.
true then stereo configuration of
tetrahedral stereo centers with preset stereo information will not be changed.
SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s)
and MolAtom.setQueryString(String)
SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options)
and MolAtom.setQueryString(String)
UserSettings.setSaveGUIPropertiesInMRV(boolean). It will be
removed in a future version of Marvin.
AlignRigidEasy.getReferenceAndRotatedFused() cannot be applied
PharmacophoreArrow.setRenderingQuality(int).
RENDERING_* constants.
PharmacophorePoint.setRenderingQuality(int).
GraphicComponent.RENDERING_QUALITY_HIGH constants.
AlignRigidEasy.getReferenceAndRotatedFused() and AlignRigidEasy.getRotatedMolecule() cannot be applied
MSketchPane.setBondDraggedAlong(boolean)
UserSettings.MAX_RECENT_FILE_LIST_SIZE then the size will be the value of
UserSettings.MAX_RECENT_FILE_LIST_SIZE
SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)
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 symmetrical structures
are filtered out, otherwise symmetrical structures are returned as duplicates.
logPPlugin.setConsiderTautomerization(boolean)
pKaPlugin.setConsiderTautomerization(boolean)
298 Kelvin).
CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
CTransform3D.m03, CTransform3D.m13 and CTransform3D.m23).
DipoleResult.Unit.
MoleculeGraph.setValenceCheckState(ValenceCheckState) instead
DefaultStructureCheckerResult for identifying Sgroup problems."shortcuts".
"showSets".
HitColoringAndAlignmentOptions.setSimilarityScoreDisplay(int)
and HitColoringAndAlignmentOptions.getSimilarityScoreDisplay() to access this field.
"simpView".
"sketchAnyBond".
"sketchArrowHeadLength".
"sketchArrowHeadWidth".
"sketchArrowTailLength".
"sketchArrowTailWidth".
"sketchCarbonVisibility".
"sketchHelp".
"sketchLigandOrderVisibility".
"sketchQuickHelp".
SketchCheckerRunner instance which will can execute StructureChecker instances read from
configurationReader
"skin".
Ring.smallestRing()
Ring.smallestRingSize()
Ring.smallestRingSizeOfAtom(int)
Ring.smallestRingSystem()
Ring.smallestRingSystemSize()
Smolecule representation of this molecule.
MoleculeGraph.sortBondsAccordingTo(MolBond[]).
"spin".
"splashScreenImage".
[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]
InputProducer instance using WorkUnit instances returned
by the WorkUnitFactory instance.
"statusBar".
MolBond.UP or UP to MolBond.DOWN.
Stereochemistry.stereo(int)
Stereochemistry.stereo(int, int)
Stereochemistry.stereoDoubleBondCount()
"stickdst".
"stickThickness".
modfunc()
StructureCheckerResult identifies a molecule problemStructureFixer can fix a Molecule problem identified by a
StructureCheckerResultStructureToJC4XL
Adds molecule/structure data to a JChemExcel workbook.FILLED_TYPE.
FILLED_TYPE.
FILLED_TYPE.
"tabScale".
"templateToolbarCustomizable".
"tmpls".
AtomChecker detecting atoms having non-zero Z coordinates.MolExporter.exportToBinFormat(Molecule, String)
MolExporter.exportToFormat(Molecule, String)
MolExporter.exportToObject(Molecule, String)
"toolbarFloatable".
"ttmpls".
CompnentElement.
HitColoringAndAlignmentOptions.setOptions(HitColoringAndAlignmentOptions, String)
to fill another HitColoringAndAlignmentOptions object with parameters.
HitColoringAndAlignmentOptions.setOptions(HitColoringAndAlignmentOptions, String)
to fill another HitColoringAndAlignmentOptions object with parameters.
Transferable which represents the clipboard data.
"transferButtonIcon".
"transferButtonText".
"transferButtonVisible".
TransferableDescriptor object.
AtomChecker detecting reaction schemes having more atoms
on one side of the reaction arrow than on the other."undetachByX".
"undo".
AbstractStructureFixer which ungroups all abbreviated groups
in the moleculepKaPlugin.setCorrectionLibrary(String)
"usedJars".
"valenceCheckEnabled".
"valenceErrorVisible".
"valenceErrorVisibleInView".
"valencePropertyVisible".
MolAtom.valenceCheck().
AtomChecker detecting atoms with invalid valences.AbstractStructureFixer which fixes valence problem in the
molecule if it is possible with removing explicit hydrogens or by adding chargeAtomChecker detecting atoms having an
explicitly set valence property."viewAnyBond".
"viewCarbonVisibility".
"viewHelp".
"viewLigandOrderVisibility".
"viewonly".
"viewQuickHelp".
"visibleCols".
"visibleRows".
BondChecker detecting double bonds havong wiggly bond ligands representing
unspecified double bond stereo configuration.AbstractStructureFixer which sets wiggly bond to
crossed double bond"winScale".
"wireThickness".
Callable which returns a result in function of an input.WorkUnit instances.String
ConfigurationReader which can read CheckerRunner
configuration described ChemAxon's own
checker configuration XML format (schema in jar:
chemaxon/checkers/runner/configuration/reader/resoruce/checkerconfiguation.xsd)XMLBasedConfigurationReader instance with the given inputSteam with the configuration
ServiceDescriptor implementation for XML-RPC services.
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