Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- A_ALL - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
All identifiers.
- A_ALL - Static variable in interface chemaxon.struc.Smolecule
-
Use all atom and bond property arrays.
- A_ASTEREO - Static variable in interface chemaxon.struc.Smolecule
-
Use atom stereo properties arrays, equals
.Smolecule.A_PARITY
|Smolecule.A_CHIRALITY
- A_ATOMMAP - Static variable in interface chemaxon.struc.Smolecule
-
Use atom type array.
- A_BOLD - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the font's bold subattribute.
- A_BOND - Static variable in interface chemaxon.struc.Smolecule
-
Use arrays to store bonds.
- A_CHARGE - Static variable in interface chemaxon.struc.Smolecule
-
Use charge array.
- A_CHIRALITY - Static variable in interface chemaxon.struc.Smolecule
-
Chirality.
- A_DX - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the x shift attribute.
- A_DY - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the y shift attribute.
- A_EXPLH - Static variable in interface chemaxon.struc.Smolecule
-
Use explicit Hydrogen count array.
- A_FONT - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the font attribute.
- A_FONT_BITS - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
All font bits.
- A_FONTFAMILY - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the font family subattribute.
- A_FONTSIZE - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the font size subattribute.
- A_FOREGROUND - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the color attribute.
- A_HYBRIDIZATION - Static variable in interface chemaxon.struc.Smolecule
-
Use hybridization state array.
- A_IMPLH - Static variable in interface chemaxon.struc.Smolecule
-
Use implicit Hydrogen count array.
- A_ITALIC - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the font's italic subattribute.
- A_MASSNO - Static variable in interface chemaxon.struc.Smolecule
-
Use mass number array.
- A_PARITY - Static variable in interface chemaxon.struc.Smolecule
-
Atom parity.
- A_RADICAL - Static variable in interface chemaxon.struc.Smolecule
-
Use radical array.
- A_RGROUP - Static variable in interface chemaxon.struc.Smolecule
-
Use R-group ID array.
- A_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the font scale attribute.
- A_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Identifier of the subscript/superscript level attribute.
- A_VALENCE - Static variable in interface chemaxon.struc.Smolecule
-
Use valence array.
- AAMAP_MASK - Static variable in class chemaxon.struc.MolAtom
-
Atom map mask in flags.
- AAMAP_MAX - Static variable in class chemaxon.struc.MolAtom
-
Maximum atom-atom mapping number.
- AAMAP_OFF - Static variable in class chemaxon.struc.MolAtom
-
Atom map offset in flags.
- AATOM - Static variable in class chemaxon.jep.context.ReactionContext
- ABBREV_GROUPS_KEY - Static variable in class chemaxon.standardizer.actions.AliasToGroupAction
-
Property Key of the abbreviated group modification
- ABBREVGROUP - Static variable in class chemaxon.formats.MFileFormat
-
Chemaxon SMILES Abbreviated Groups.
- AbbrevGroupRecognizer - Class in chemaxon.formats.recognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.No longer used, will be removed.
- AbbrevGroupRecognizer() - Constructor for class chemaxon.formats.recognizer.AbbrevGroupRecognizer
-
Deprecated.
- ABBREVIATED_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that abbreviated groups had found in the molecule
- ABBREVIATED_GROUP_WITH_ONLY_CONTRACTED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that only contracted abbreviated groups had found in the molecule
- ABBREVIATED_GROUP_WITH_ONLY_EXPANDED - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that only expanded abbreviated groups had found in the molecule
- ABBREVIATED_GROUPS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"abbrevgroups"
. - ABBREVIATED_GROUPS_ALLOWED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"abbrevgroupsAllowed"
. - AbbreviatedGroupChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting abbreviations ("COOH", "Ala", "NO2", etc.) in a Molecule instance represented in abbreviated group form. - AbbreviatedGroupChecker() - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker
-
Default constructor.
- AbbreviatedGroupChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AbbreviatedGroupChecker
-
Parameterized constructor.
- ABS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
-
Stereogenic centers belonging to ABS represent absolute stereochemistry, i.e.
- ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.sss.SearchConstants
-
Option for absolute stereo matching.
- ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.sss.SearchConstants
-
Option for absolute stereo matching.
- ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.sss.SearchConstants
-
Option for absolute stereo matching.
- ABSENT_CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that molecule is chiral, but flag is not added to the molecule
- AbsentChiralFlagChecker - Class in chemaxon.checkers
-
Detects chiral molecules with no chiral flag defined
- AbsentChiralFlagChecker() - Constructor for class chemaxon.checkers.AbsentChiralFlagChecker
-
Initializes the absent chiral flag error checker
- AbsentChiralFlagFixer - Class in chemaxon.fixers
-
Deprecated, for removal: This API element is subject to removal in a future version.
- AbsentChiralFlagFixer() - Constructor for class chemaxon.fixers.AbsentChiralFlagFixer
-
Deprecated.
- ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"absLabelVisible"
or"absLabel"
. - ABSOLUTE_STEREO_CONFIGURATION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents molecules in which all asymmetric centers have absolute stereo configuration
- AbsoluteStereoAction - Class in chemaxon.standardizer.actions
-
Deprecated, for removal: This API element is subject to removal in a future version.use
SetAbsoluteStereoAction
orRemoveAbsoluteStereoAction
instead - AbsoluteStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AbsoluteStereoAction
-
Deprecated.Initializes the action with parameters
- AbsoluteStereoAction.Type - Enum Class in chemaxon.standardizer.actions
-
Deprecated.Type of absolute stereo action
- AbsoluteStereoConfigurationChecker - Class in chemaxon.checkers
-
Detects molecules in which all asymmetric centers have absolute stereo configuration
- AbsoluteStereoConfigurationChecker() - Constructor for class chemaxon.checkers.AbsoluteStereoConfigurationChecker
-
Initializes the absolute stereo configuration checker
- AbsoluteStereoFixer - Class in chemaxon.fixers
-
Deprecated, for removal: This API element is subject to removal in a future version.
- AbsoluteStereoFixer() - Constructor for class chemaxon.fixers.AbsoluteStereoFixer
-
Deprecated.
- AbstractMRecordReader - Class in chemaxon.marvin.io.formats
-
Abstract record reader class.
- AbstractMRecordReader(InputStream, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Constructs an abstract record reader.
- AbstractMRecordReader(InputStream, String, String) - Constructor for class chemaxon.marvin.io.formats.AbstractMRecordReader
- AbstractSgroupAction - Class in chemaxon.standardizer.actions
-
Abstract class for standardizer actions modifying S-groups.
- AbstractSgroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AbstractSgroupAction
-
Initializes an abstract s-group action with the exclude list
- AbstractStandardizerAction - Class in chemaxon.standardizer
-
Abstract implementation of the
StandardizerAction
. - AbstractStandardizerAction(Map<String, String>) - Constructor for class chemaxon.standardizer.AbstractStandardizerAction
-
Initializes the functionality of the abstract implementation.
- AbstractStereoFilter<T extends StereoCenter> - Class in com.chemaxon.calculations.stereoanal.filters
-
Abstract class for Filter interface.
- AbstractStereoFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
- AbstractStructureChecker - Class in chemaxon.checkers
-
Abstract base class of all functions checking and repairing chemical structures.
- AbstractStructureChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AbstractStructureChecker
-
Constructor to create a Structure checker instance with the given errorType
- AbstractStructureFixer - Class in chemaxon.fixers
-
This class is the default abstract implementation of
StructureFixer
interface - AbstractStructureFixer() - Constructor for class chemaxon.fixers.AbstractStructureFixer
-
Constructor to create a Structure fixer
- Ac - Static variable in class chemaxon.core.ChemConst
- accept(Molecule) - Method in interface chemaxon.util.MolFilter
-
Returns
true
if molecule is accepted by the filter. - accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
- accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
- accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
- accept(StereoCenterVisitor) - Method in interface com.chemaxon.calculations.stereoanal.stereocenters.StereoCenter
-
Accepts visitors.
- accept(StereoCenterVisitor) - Method in class com.chemaxon.calculations.stereoanal.stereocenters.TetrahedralStereoCenter
- ACCEPT - Enum constant in enum class chemaxon.marvin.collecting.Consent
- ACCEPT_ONLY_SAME - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
- Accepted - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type
-
Indicates, that the structure checker puts valid or fixed structures to the output file.
- ACCEPTOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
-
Acceptor sign displayed in GUI.
- ACCORD - Static variable in class chemaxon.formats.MFileFormat
-
ACCORD file format
- ACCP - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
- ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentAccuracyMode
-
Atomic contribution with correction terms.
- ACCURATE - Enum constant in enum class chemaxon.marvin.alignment.AtropIsomerDetector.Accuracy
- ACIDIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
Constant denoting acidic pKa.
- ACT_KEY - Static variable in class chemaxon.standardizer.actions.AbsoluteStereoAction
-
Deprecated.Key of type for parsing and property change
- actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.OptionsPane
-
Action handler.
- actionPerformed(ActionEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView
-
Handles window closing and format choice events.
- actionPerformed(ActionEvent) - Method in class chemaxon.marvin.swing.MAction
-
Sets the action state, performs a custom action, then propagates the event.
- ACTIONSTRING_TOKEN - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
action string token of the checker
- ACTIONSTRING_TOKEN - Static variable in class chemaxon.fixers.StructureFixerDescriptor
-
action string tokens of the fixer
- ACTIONSTRING_TOKEN - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
-
action string token of the action
- ActionStringBasedConfigurationReader - Class in chemaxon.checkers.runner.configuration.reader
-
An implementation of
ConfigurationReader
for parsing action strings - ActionStringBasedConfigurationReader(String) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
-
Default constructor
- ActionStringBasedConfigurationReader(String, StructureCheckerFactory, StructureFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
-
Deprecated.
- ActionStringBasedConfigurationReader(String, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.configuration.reader.ActionStringBasedConfigurationReader
-
Constructor with custom checker factory
- actionStringToken() - Element in annotation interface chemaxon.checkers.CheckerInfo
-
Returns the action string token of the checker
- actionStringToken() - Element in annotation interface chemaxon.fixers.FixerInfo
-
Returns the action string token of the fixer.
- actionStringToken() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
-
Returns the action string tokens of the action as a string, divided by comma characters
- add(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
-
Add a name to structure converter.
- add(StandardizerActionFactory.StandardizerClassDescriptor) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
-
Adds a standardizer action class descriptor to the factory
- add(DPoint3) - Method in class chemaxon.struc.DPoint3
-
Add the given point to this one.
- add(DPoint3, DPoint3) - Static method in class chemaxon.struc.DPoint3
-
Calculates the sum of the two vectors
- add(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Adds an atom to the molecule.
- add(MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Adds an atom to the root structure.
- add(MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
Adds an atom to a reactant, product or agent structure.
- add(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
-
Adds an atom to the molecule.
- add(MolAtom) - Method in class chemaxon.struc.Sgroup
-
Adds a new atom to the S-group.
- add(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Adds a new atom to the S-group.
- add(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Adds a new atom to the S-group.
- add(MolAtom, boolean) - Method in class chemaxon.struc.SelectionMolecule
-
Adds an atom to the molecule.
- add(MolBond) - Method in class chemaxon.struc.MolAtom
-
Add a bond if it had not been already added.
- add(MolBond) - Method in class chemaxon.struc.Molecule
- add(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Adds a bond to the molecule.
- add(MolBond) - Method in class chemaxon.struc.RgMolecule
-
Adds a bond to the root structure.
- add(MolBond) - Method in class chemaxon.struc.RxnMolecule
-
Adds a bond to a reactant, product, agent.
- add(MolBond) - Method in class chemaxon.struc.SelectionMolecule
-
Adds a bond to the graph.
- add(MolBond) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Add an edge if it had not been already added.
- add(MolBond, boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Add a bond to the molecule.
- add(MolBond, boolean) - Method in class chemaxon.struc.SelectionMolecule
-
Add a bond to the molecule.
- add(MolBond, MolAtom) - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Add an edge to the given atom of the sgroup, if it had not been already added.
- add(MProp) - Method in class chemaxon.struc.prop.MListProp
-
Adds an element.
- add(CheckerFixerFactory.CheckerClassDescriptor) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
-
Adds a checker class descriptor to the factory
- add(CheckerFixerFactory.FixerClassDescriptor) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
-
Adds a fixer class descriptor to the factory
- add(InputStream) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
-
Adds an input stream containing standardizer specifications to be stored by the output factory
- add(InputStream) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
-
Adds an input stream containing checker and fixer specifications to be stored by the output factory
- add(String) - Method in class chemaxon.checkers.util.AtomLabels
-
Adds an atom label to the atom labels
- add(String, double) - Method in class chemaxon.jep.ConstantTableBuilder
-
Adds a double constant to this builder.
- add(String, Molecule) - Method in class chemaxon.jep.ConstantTableBuilder
-
Adds a molecule constant to this builder.
- add(String, Molecule[]) - Method in class chemaxon.jep.ConstantTableBuilder
-
Adds a molecule array constant to this builder.
- add(String, String) - Method in class chemaxon.jep.ConstantTableBuilder
-
Adds a string constant to this builder.
- add(URL) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
-
Adds an input stream containing standardizer specifications to be stored by the output factory
- add(URL) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
-
Adds an input stream containing checker and fixer specifications to be stored by the output factory
- add(Properties) - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
-
Adds a property map containing properties of standardizer actions to be stored by the output factory
- add(Properties) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
-
Adds a property map containing properties of checkers and fixers to be stored by the output factory
- ADD - Enum constant in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
-
Deprecated.Add absolute stereo
- ADD_REMOVE_H_ATOMS_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"addRemoveHatomsEnabled"
. - addAction(StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
-
Adds an action to the configuration
- addActionListener(ActionListener) - Method in class chemaxon.marvin.beans.MarvinPane
-
Adds an action listener.
- addActionListener(ActionListener) - Method in class chemaxon.marvin.view.swing.TableOptions
-
Adds an action listener.
- addActions(List<StandardizerAction>) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
-
Adds actions to the configuration
- addActionToGroup(String, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
-
Adds an action to the group
- addActionToGroups(Collection<String>, StandardizerAction) - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
-
Adds an action to a list of groups
- addAll(ConstantTable) - Method in class chemaxon.jep.ConstantTableBuilder
-
Adds all constants in the given table to this builder.
- addAllAtoms(Collection<MolAtom>) - Method in class chemaxon.standardizer.Changes
-
Adds atoms to the "added atom" list.
- addAllAtoms(Collection<MolAtom>, boolean) - Method in class chemaxon.standardizer.Changes
-
Adds atoms to the "added atom" list.
- addArgument(ServiceArgument<?>) - Method in class chemaxon.marvin.services.ServiceDescriptor
-
Adds a new argument to the end of the argument list
- addAtom(int) - Method in class chemaxon.calculations.nmr.Multiplet
-
Adds a new atom to this multiplet.
- addAtom(MolAtom) - Method in class chemaxon.standardizer.Changes
-
Adds an atom to the "added atom" list.
- addAtom(MolAtom, boolean) - Method in class chemaxon.standardizer.Changes
-
Adds an atom to the "added atom" list.
- addAtom0(MolAtom) - Method in class chemaxon.struc.Molecule
-
Adds an atom.
- addAtom0(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Adds an atom.
- addAtom0(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
-
Adds an atom.
- addAtomPair(int, int) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
Adds an alignment constraint between the reference and aligned molecule.
- addAtomPair(int, int, double) - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
-
Adds an alignment constraint between the reference and aligned molecule.
- addAtomsAndBondsTo(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Adds all atoms and bonds to the specified molecule.
- addAtomToFragment(MolAtom) - Method in class chemaxon.struc.Molecule
-
Adds an atom to a fragment.
- addAtomToFragment(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Adds an atom to a fragment.
- addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RgMolecule
- addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RxnMolecule
- addAtomWithBonds(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
-
Adds an atom to the molecule.
- addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Adds an atom without setting its parentGraph and index fields.
- addAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.SelectionMolecule
-
Adds an atom without setting its parentGraph and index fields.
- addAttachmentPoint(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Adds a new free attachment point for an atom.
- addAttachmentPoint(MolAtom, int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Adds a new free attachment point of the given attachment atom and order.
- addAttachmentPoint(MolAtom, int, MolBond) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Adds a new free attachment point.
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MAnalysisBox
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MBracket
-
Adds the attribute names to the specified list.
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MEFlow
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MElectron
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MElectronContainer
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MNameTextBox
-
Adds the attribute names to the specified list.
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MPolyline
-
Adds the attribute names to the specified vector.
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRectangle
-
Adds the attribute names to the specified list.
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MRoundedRectangle
-
Adds the attribute names to the specified vector.
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
-
Adds the attribute names to the specified list.
- addAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
-
Adds the attribute names to the specified list.
- addBond0(MolBond) - Method in class chemaxon.struc.Molecule
-
Adds a bond.
- addBond0(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Adds a bond.
- addBond0(MolBond) - Method in class chemaxon.struc.SelectionMolecule
-
Adds a bond.
- addBondWithoutChangingIt(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Adds a bond without setting its parentGraph and index fields.
- addBracket(MBracket) - Method in class chemaxon.struc.Sgroup
-
Adds a bracket to this S-group.
- addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MAnalysisBox
- addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.graphics.MTextBox
-
Adds attribute names to the specified list.
- addCdataAttributeKeys(List<String>) - Method in class chemaxon.struc.MObject
-
Adds attribute names to the specified list.
- addCentralAtom() - Method in class chemaxon.struc.sgroup.MulticenterSgroup
-
Adds a central atom to this sgroup.
- addChar(char) - Method in class chemaxon.struc.graphics.MTextBox
-
Adds a character to the text.
- addCheckerMark(MDocument.CheckerMark) - Method in class chemaxon.struc.MDocument
-
Adds a checker mark to the document.
- addChildSgroup(Sgroup) - Method in class chemaxon.struc.Sgroup
-
Adds a child S-group.
- AddChiralFlagFixer - Class in chemaxon.fixers
-
Absent chiral flag fixer.
- AddChiralFlagFixer() - Constructor for class chemaxon.fixers.AddChiralFlagFixer
- addComparator(MolComparator) - Method in class chemaxon.sss.search.MolSearch
-
Add a comparator to the search object.
- addComplex() - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.Complex number support will be removed without replacement.
- addComplexVariable(String, double, double) - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.Complex number support will be removed without replacement.
- addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule
-
Adds a reactant, product or agent.
- addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule
-
Adds a reactant, product or agent.
- addConstraintsFromUserMappedAtoms() - Method in class chemaxon.marvin.alignment.Alignment
-
An atomMap can be added to some of the atoms in MarvinSketch using the single reaction arrow.
- addCouplingConstants(double[]) - Method in class chemaxon.calculations.nmr.Multiplet
-
Adds a new coupling constant array.
- addCrossingBonds(List<MolBond>, List<MolBond>) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Sets the crossing bonds (head and tail) of a ladder-type polymer.
- addData(Molecule, MolAtom, String, String) - Method in class chemaxon.marvin.io.MolExportModule
-
Adds a data sgroup to the given atom in the given molecule with fieldName and value.
- addDataLine(String) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Adds a line to the data stored in the field.
- addDihedralStep(DihedralScanStep) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
-
Add a new step.
- addError(Exception) - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
- addExplicitHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)
.
Usage:Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
- addExplicitHydrogens(int, MolAtom[]) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)
.
Usage:Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
- AddExplicitHydrogensAction - Class in chemaxon.standardizer.actions
-
Hydrogenization standardizer action
- AddExplicitHydrogensAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AddExplicitHydrogensAction
-
Initializes the action
- addExplicitLonePairs() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[])
.
Usage:Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
- addFunction(String, PostfixMathCommandI) - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.The function table will not be modifiable anymore. No replacement.
- addGroup(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
-
Adds a group definition to the group list of the action
- addGroup(String) - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
-
Adds a group to the list defined by its abbreviation
- addHAtoms(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated, for removal: This API element is subject to removal in a future version.since Marvin 5.11, use
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph)
instead - addHAtoms(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated, for removal: This API element is subject to removal in a future version.since Marvin 5.11, use
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[])
instead - addHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated, for removal: This API element is subject to removal in a future version.since Marvin 5.11, use
Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)
instead - addHeavyAtomLimitChecker(int) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Creates an input checker by calling
CalculatorInputChecker.heavyAtomLimit(int)
and adds it to this plugin. - addHelpMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane
-
Adds the help menu to a parent menu.
- addHyperlinkListener(JEditorPane) - Static method in class chemaxon.marvin.util.SwingUtil
-
Adds HTML link handling to an editor pane.
- addInactiveTasks(Standardizer, String) - Static method in class chemaxon.standardizer.StandardizerUtil
-
Adds the Standardizer tasks specified in the
configuration
parameter to the inactive tasks list. - addInput(File, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Adds an input file.
- addInput(File, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Adds an input stream.
- addInput(InputStream, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- addInput(String, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Adds an input file.
- addInput(String, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- addInputChecker(TaggedCalculatorInputChecker) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Adds the specified input checker to this plugin.
- addItemListener(ItemListener) - Method in class com.chemaxon.calculations.gui.MChart
- addLabel(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
-
Defines a label component inside the MarvinView table.
- addLabel(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
-
Defines a label component inside the MarvinView table.
- addLine(MTextDocument.Portion) - Method in class chemaxon.struc.graphics.MTextBox
- addListener(MDocStorage.Listener) - Method in class chemaxon.marvin.view.MDocStorage
-
Adds a listener if it is not yet added.
- addLonePairs(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated, for removal: This API element is subject to removal in a future version.since Marvin 5.11, use
Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[])
instead - addMatch(int[], int[], int) - Method in class chemaxon.sss.search.MolSearch
- addMatch(int[], int[], int) - Method in class chemaxon.sss.search.Search
-
Specifies extra prerequisites of the structure search that queryAtoms[0] must match to targetAtoms[0] only AND queryAtoms[1] must match to targetAtoms[1], etc.
- addMatch(int, int) - Method in class chemaxon.sss.search.MolSearch
-
Adds a fixed matching between the given query and target atoms.
- addMatch(int, int) - Method in interface com.chemaxon.search.SimpleSearcher
-
Adds a fixed matching between the given query and target atoms.
- addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane
-
Adds a menubar change listener.
- addMolecule(int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
-
Defines a molecule viewer component inside the MarvinView table.
- addMolecule(int, int, int, int, int, int, int, int) - Method in class chemaxon.marvin.beans.MViewParams
-
Defines a molecule viewer component inside the MarvinView table.
- addMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.Alignment
-
Add molecule to align
- addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.Alignment
-
User may define extra weights between colors defined at setColoringScheme.
- addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseAlignment
- addNodeColorWeight(int, int, double) - Method in interface chemaxon.marvin.alignment.PairwiseComparison
- addNodeColorWeight(int, int, double) - Method in class chemaxon.marvin.alignment.PairwiseSimilarity3D
- addNotify(MDocument) - Method in class chemaxon.struc.graphics.MElectronContainer
- addNotify(MDocument) - Method in class chemaxon.struc.graphics.MMidPoint
-
Point added to a document.
- addNotify(MDocument) - Method in class chemaxon.struc.graphics.MRectanglePoint
-
Point added to a document.
- addNotify(MDocument) - Method in class chemaxon.struc.MObject
-
Called when the object is added to a document.
- addNumbering - Variable in class chemaxon.marvin.io.MolExportModule
-
Add numbers to atoms corresponding to the (IUPAC) naming of the molecule.
- addObject(MObject) - Method in class chemaxon.struc.MDocument
-
Adds an object to the document.
- addObject(MObject) - Method in class chemaxon.struc.MSelectionDocument
-
Adds an object to the document.
- addOwner(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
-
Adds an owner, that should be notified about the changes in the properties.
- addParameters(File) - Method in class chemaxon.descriptors.MDParameters
-
Sets parameters from an XML config file keeping all previous settings.
- addParameters(String) - Method in class chemaxon.descriptors.MDParameters
-
Sets parameters from an XML string representation keeping all previous settings.
- addParametrizedMetric(String, String, String) - Method in class chemaxon.descriptors.MDParameters
-
Expands the set of parametrized metrics with a new item.
- addParametrizedMetricNode(String, String, String) - Method in class chemaxon.descriptors.MDParameters
-
Adds a
ParametrizedMetric
node to the DOM tree. - addParametrizedMetricsNode() - Method in class chemaxon.descriptors.MDParameters
-
Adds the
ParametrizedMetrics
node to the DOM tree. - addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
- addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Adds a
PropertyChangeListener
that will receive all thePropertyChangeEvent
fired by this class - addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
-
Add a PropertyChangeListener to the listener list.
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Add a PropertyChangeListener to the listener list.
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Add a PropertyChangeListener to the listener list.
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.marvin.common.UserSettings
-
Add a property change listener
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
- addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
-
Adds a
PropertyChangeListener
that will receive all thePropertyChangeEvent
fired by this class - addPropertyChangeListener(PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction
-
Add a PropertyChangeListener to the listener list.
- addPropertyChangeListener(PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
-
Add a PropertyChangeListener to the listener list.
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.AbstractStructureChecker
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.InvalidChecker
- addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Adds a
PropertyChangeListener
that will receive thePropertyChangeEvent
fired when the property with the given name is changed - addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.checkers.StructureChecker
-
Add a PropertyChangeListener for a specific property.
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.checkers.StructureCheckerDescriptor
-
Add a PropertyChangeListener for a specific property.
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.fixers.StructureFixerDescriptor
-
Add a PropertyChangeListener for a specific property.
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MSketchPane
-
Adds a
PropertyChangeListener
for a specific property. - addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.marvin.beans.MViewPane
-
Adds a
PropertyChangeListener
for a specific property. - addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.AbstractStandardizerAction
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
- addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
-
Adds a
PropertyChangeListener
that will receive thePropertyChangeEvent
fired when the property with the given name is changed - addPropertyChangeListener(String, PropertyChangeListener) - Method in interface chemaxon.standardizer.StandardizerAction
-
Add a PropertyChangeListener for a specific property.
- addPropertyChangeListener(String, PropertyChangeListener) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
-
Add a PropertyChangeListener for a specific property.
- addRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Adds an atom to the list of paradigmatic repeating unit atoms.
- addRgroup(int, Molecule) - Method in class chemaxon.struc.RgMolecule
-
Adds an R-group member.
- addRgroupAttachmentPoint(int, int) - Method in class chemaxon.struc.MolAtom
-
Attaches a new R-group attachment point to this atom by a bond of a specified type.
- addRgroupBridgeMember(RgroupBridgeId, Molecule) - Method in class chemaxon.struc.RgMolecule
-
Adds a definition member to an R-group bridge.
- addRGroupsInPlaceOfImplHs(Molecule) - Static method in class chemaxon.sss.search.RGroupDecomposition
-
Adds different rgroup atoms connected by any-bonds to query molecule in place of all implicit H-s.
- addRGroupsInPlaceOfImplHs(Molecule, int) - Static method in class chemaxon.sss.search.RGroupDecomposition
-
Adds different rgroup atoms connected by the specified bond type to query molecule in place of all implicit H-s.
- addRgroupsTo(Molecule) - Method in class chemaxon.struc.RgMolecule
-
Creates an RgMolecule containing R-groups of this object from the 'simplified molecule' object made of 'm'.
- addSalt(String, Molecule) - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
-
Adds a salt to the salt list of the action
- addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.Molecule
-
Adds an S-group to this object.
- addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RgMolecule
-
Adds an S-group to this object.
- addSgroup(Sgroup, boolean) - Method in class chemaxon.struc.RxnMolecule
-
Adds an S-group to this object.
- addSgroupClones(Molecule, Molecule, Molecule) - Method in class chemaxon.struc.Molecule
-
Adds the S-groups of a child molecule clone to the new parent molecule clone.
- addSgroupsOf(Molecule) - Method in class chemaxon.struc.Molecule
-
Adds S-groups to this object and its parent.
- addSimpleAtomWithoutChangingIt(MolAtom) - Method in class chemaxon.struc.MoleculeGraph
-
Adds a non-SgroupAtom atom without setting its parentGraph and index fields.
- addSolvent(String, Molecule) - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
-
Adds a solvent to the solvent list of the action
- addStandardConstants() - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.The symbol table has been replaced with the constant table, and it will become unmodifiable. Use
Evaluator.compile(String, Class, ConstantTable)
instead. - addStandardFunctions() - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.These functions will be removed without replacement.
- addStarAtoms() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Changes terminal carbon atoms to star atoms (*).
- addString(String) - Method in class chemaxon.struc.graphics.MTextBox
-
Adds a string to the text.
- addThreadLocal(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
-
Add a thread-local name to structure converter.
- addTo(Container) - Method in class chemaxon.marvin.swing.MAction
-
Add menu item to the specified menu.
- addTo(Container, int) - Method in class chemaxon.marvin.swing.MAction
-
Add menu item to the specified menu.
- addTo(Container, int, Object) - Method in class chemaxon.marvin.swing.MAction
-
Add menu item to the specified menu.
- addToolsMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated, for removal: This API element is subject to removal in a future version.Not used.
- addToSelection(MDocument, MSelectionDocument) - Static method in class chemaxon.struc.NoStructure
-
Adds the selected NoStrutures from the document to the selectionDocument
- addToSketchRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
-
Add an element to marvinsketch's recent file list
- addToViewRecentFileList(File) - Method in class chemaxon.marvin.common.UserSettings
-
Add an element to marvinview's recent file list
- addUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions
-
Adds the given user-defined comparator to the search.
- addUserConstraint(int, int, int, int) - Method in class chemaxon.marvin.alignment.Alignment
-
Adds user constraint between two atoms of two different molecules The addMol method calls must precede this method.
- addVariable(String, double) - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.The symbol table has been replaced with the constant table, and it will become unmodifiable. Use
Evaluator.compile(String, Class, ConstantTable)
instead. - addVariableAsObject(String, Object) - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.The symbol table has been replaced with the constant table, and it will become unmodifiable. Use
Evaluator.compile(String, Class, ConstantTable)
instead. - adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph
-
Checks whether the molecule has multiple chiral centres
- adjustTautomerizationPlugin(TautomerizationPlugin) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode
- AdvancedCheckerRunner - Class in chemaxon.checkers.runner
-
CheckerRunner
implementation with advanced fixing capabilities.
StructureFixer
selection is based on provided fixer class if available, or falls back toStructureCheckerResult
based selection.
Supports multiple iterations of checking and fixing for the best fixing efforts. - AdvancedCheckerRunner(ConfigurationReader) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
-
Constructs
CheckerRunner
with more advanced fixing capabilities. - affectsPerformance() - Method in enum class chemaxon.calculator.CalculatorTag
-
Returns whether the presence of this tag affects the performance of the calculator.
- Ag - Static variable in class chemaxon.core.ChemConst
- AGENT - Static variable in class chemaxon.jep.context.ReactionContext
- AGENTS - Static variable in class chemaxon.struc.RxnMolecule
-
"Agent" structure type.
- Al - Static variable in class chemaxon.core.ChemConst
- alias - Variable in class chemaxon.marvin.services.ServiceArgument
-
the alias of the argument
- alias() - Element in annotation interface chemaxon.checkers.Persistent
-
Returns the alias name of the annotated property
- ALIAS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that alias values had found in the molecule
- ALIAS - Static variable in class chemaxon.marvin.services.ServiceDescriptor
-
Property key for Service alias as
String
- ALIAS_ATOM - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that alias value that could be converted to an element had found in the molecule
- ALIAS_GROUP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that alias value that could be converted to an abbreviated group had found in the molecule
- ALIAS_NONE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that alias value had found in the molecule
- AliasChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting atoms with alias labels. - AliasChecker() - Constructor for class chemaxon.checkers.AliasChecker
-
Default constructor.
- AliasToAtomAction - Class in chemaxon.standardizer.actions
-
Alias to Atom standardizer action.
- AliasToAtomAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToAtomAction
-
Initializes the action
- AliasToGroupAction - Class in chemaxon.standardizer.actions
-
Alias to Group standardizer action
- AliasToGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AliasToGroupAction
-
Initializes the action with parameters
- align() - Method in class chemaxon.marvin.alignment.Alignment
-
3D alignment on two or more molecules.
- align() - Method in class chemaxon.marvin.alignment.AlignOnPairedAtoms
- align() - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
does a simple one-to-one atom mappin and aligns.
- align() - Method in class chemaxon.marvin.alignment.MolAligner
-
Executes the best alignment based on hit map provided earlier
- align(int[]) - Method in class chemaxon.marvin.alignment.MolAligner
-
Calculates and performs the best alignment possible specified by the hit map array.
- align(int[][]) - Method in class chemaxon.marvin.alignment.AlignRigidEasy
-
Rigid alignment on the user defined atom index
- align(Molecule) - Method in interface chemaxon.marvin.alignment.MCSAlignment
-
Align the given molecule to the reference.
- align(Molecule, Molecule, int[]) - Static method in class chemaxon.marvin.alignment.MolAligner
-
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
- align(Molecule, Molecule, int[][]) - Static method in class chemaxon.marvin.alignment.MolAligner
-
Returns an aligned (rotated) version of the given target molecule with respect to the given pattern molecule and search hit mapping.
- ALIGN_AS_IS - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
- ALIGN_BOTTOM - Static variable in class chemaxon.struc.graphics.MTextBox
-
Align text to bottom of box.
- ALIGN_CENTER - Static variable in class chemaxon.struc.graphics.MTextBox
-
Align text to center of box.
- ALIGN_LEFT - Static variable in class chemaxon.struc.graphics.MTextBox
-
Align text to left edge of box.
- ALIGN_RIGHT - Static variable in class chemaxon.struc.graphics.MTextBox
-
Align text to right edge of box.
- ALIGN_TOP - Static variable in class chemaxon.struc.graphics.MTextBox
-
Align text to top of box.
- Alignment - Class in chemaxon.marvin.alignment
-
3D Alignment aligns two or more 3D molecules onto each other.
- Alignment() - Constructor for class chemaxon.marvin.alignment.Alignment
- Alignment(AlignmentProperties) - Constructor for class chemaxon.marvin.alignment.Alignment
- ALIGNMENT - Enum constant in enum class chemaxon.descriptors.SimilarityCalculatorFactory.Representation
- AlignmentAccuracyMode - Enum Class in chemaxon.marvin.alignment
-
Settings for the representation of a molecular shape.
- AlignmentException - Exception in chemaxon.marvin.alignment
- AlignmentException() - Constructor for exception chemaxon.marvin.alignment.AlignmentException
- AlignmentException(String) - Constructor for exception chemaxon.marvin.alignment.AlignmentException
- AlignmentException(Throwable) - Constructor for exception chemaxon.marvin.alignment.AlignmentException
- AlignmentMolecule - Class in chemaxon.marvin.alignment
- AlignmentMoleculeFactory - Class in chemaxon.marvin.alignment
-
Creates an
AlignmentMolecule
form aMolecule
based on the settings. - AlignmentMoleculeFactory() - Constructor for class chemaxon.marvin.alignment.AlignmentMoleculeFactory
- AlignmentMoleculeFactory.ProgressBarInterface - Interface in chemaxon.marvin.alignment
- AlignmentPlugin - Class in chemaxon.marvin.calculations
-
Plugin layer for the
AlignmentAPI
- AlignmentPlugin() - Constructor for class chemaxon.marvin.calculations.AlignmentPlugin
- AlignmentProperties - Enum Class in chemaxon.marvin.alignment
- AlignmentProperties.ColoringScheme - Enum Class in chemaxon.marvin.alignment
- AlignmentProperties.ColorNotSpecifiedCase - Enum Class in chemaxon.marvin.alignment
- AlignmentProperties.DegreeOfFreedomType - Enum Class in chemaxon.marvin.alignment
- AlignmentProperties.FlexibilityMode - Enum Class in chemaxon.marvin.alignment
-
Conformational flexibility treatment during the alignment for a pair of a molecule.
- AlignmentProperties.NodeType - Enum Class in chemaxon.marvin.alignment
- AlignmentProperties.OrientationType - Enum Class in chemaxon.marvin.alignment
- AlignOnPairedAtoms - Class in chemaxon.marvin.alignment
-
Overlays two molecules using the user defined atom pairs
Example: - AlignOnPairedAtoms() - Constructor for class chemaxon.marvin.alignment.AlignOnPairedAtoms
- AlignRigidEasy - Class in chemaxon.marvin.alignment
-
Aligns pairs of molecules by translating and rotating one of them and leave the one called the reference molecule intact.
- AlignRigidEasy() - Constructor for class chemaxon.marvin.alignment.AlignRigidEasy
- ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
-
Aliphatic query atom.
- ALIPHATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
- aliphaticAtomCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of all aliphatic atoms in the molecule excluding hydrogens.
- aliphaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aliphaticAtomCount()
- aliphaticBondCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of all aliphatic bonds in the molecule excluding bonds connected to hydrogens.
- aliphaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aliphaticBondCount()
- aliphaticRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of aliphatic ring systems of the molecule.
- aliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aliphaticRingCount()
- aliphaticRingCount(int) - Method in class chemaxon.calculations.Ring
-
Calculates the number of aliphatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
- aliphaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aliphaticRingCount(int)
- aliphaticRings() - Method in class chemaxon.calculations.Ring
-
Identifies the aliphatic rings in the molecule.
- aliphaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aliphaticRings()
- aliphaticRings(int) - Method in class chemaxon.calculations.Ring
-
Identifies aliphatic rings in the molecule having a given size (number of atoms).
- aliphaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aliphaticRings(int)
- ALL - Enum constant in enum class chemaxon.sss.search.options.HomologyTranslationOption
-
All atoms can have translation.
- ALL - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
- ALL_H - Static variable in class chemaxon.struc.MolAtom
-
Include any Hydrogen atom.
- ALL_MATCH_AMBIG - Enum constant in enum class chemaxon.sss.search.options.MarkushAromaticityHandlingOption
-
Ambiguous aromatic parts of the target Markush structure can be matched by aliphatic and aromatic forms as well.
- ALL_PERM - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.OrientationType
- allringsystems - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
- allStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
All stereo centers of molecule.
- allStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
All stereo centers with attached data.
- Am - Static variable in class chemaxon.core.ChemConst
- AMBIGUOUS - Enum constant in enum class com.chemaxon.search.AromatizationMethod
-
Aromatization for ambiguous 5-membered rings.
- AMBIGUOUS - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
- AMBIGUOUS_AROMATIC_ATOMS_IGNORED - Enum constant in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
-
Deprecated.As of Marvin 6.0, replaced by
MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions)
andValenceCheckOptions.DEFAULT
.
Usage:molecule.setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
- AMINOACID - Enum constant in enum class chemaxon.struc.SgroupType
- AMINOACID_BOND_COLORING_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"aminoAcidBondColoringEnabled"
. - ANCHOR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
- AND - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.EnhancedStereoType
-
Stereogenic centers belonging to an ANDn group (e.g.
- AND - Static variable in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
- AND_OR - Static variable in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
-
Set of enhanced stereo flags.
- ANGLE_STEP - Static variable in class chemaxon.struc.MolAtom
- angle2D(double, double) - Method in class chemaxon.struc.DPoint3
-
Calculates the absolute angle in the XY plane of the vector pointing from this point to the other point.
- angle3D(DPoint3) - Method in class chemaxon.struc.DPoint3
-
Calculate the angle of two vectors (this and p) in the range 0.0 through pi.
- ANIMATE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"animate"
. - ANIMATION_DELAY - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"animDelay"
. - ANIMATION_FPS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"animFPS"
. - ANIMATION_SYNCHRONIZATION - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"animSync"
. - ANTI - Static variable in interface chemaxon.struc.StereoConstants
-
Non-CIP stereodescriptor, anti (relative configuration).
- ANY - Enum constant in enum class chemaxon.struc.BondType
-
Any bond type.
- ANY - Enum constant in enum class chemaxon.struc.SgroupType
- ANY - Static variable in class chemaxon.struc.MolAtom
-
"Atomic number" of the any atom A.
- ANY - Static variable in class chemaxon.struc.MolBond
-
Any bond type.
- ANY_BOND - Static variable in class chemaxon.marvin.common.ParameterConstants
- anyBooleanPropertyTrue(Map<String, String>, String...) - Method in class chemaxon.standardizer.AbstractStandardizerAction
-
Check the given map, whether there is a String 'true' (case in-sensitive) value for any of the given keys
- append(Changes) - Method in class chemaxon.standardizer.Changes
-
Appends a set of changes to the already existing changes.
- append(String, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextDocument
-
Append text to end of document.
- appendChars(int, char) - Method in class chemaxon.marvin.io.MolExportModule
-
Append a character n times to the string buffer.
- appendLeft(String, int) - Method in class chemaxon.marvin.io.MolExportModule
-
Append a string to the buffer in %-ns format.
- appendLine(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Appends line to string buffer with closing '\n' character.
- appendLines(StringBuffer, String) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Appends lines to string buffer with closing '\n' character if it is not yet present.
- appendMEnd() - Method in class chemaxon.marvin.io.formats.mdl.MolExport
-
Appends the "M END" line to the string buffer.
- appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.MDParameters
-
Extends internal data with a new parametrized metric.
- appendParametrizedMetric(String, String) - Method in class chemaxon.descriptors.PFParameters
- appendpHText(String) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Appends the pH text.
- appendRight(int, int, char) - Method in class chemaxon.marvin.io.MolExportModule
-
Append an integer to the buffer in the right hand side of an n-characters wide field.
- appendRight(String, int, char) - Method in class chemaxon.marvin.io.MolExportModule
-
Append a string to the buffer in the right hand side of an n-characters wide field.
- apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker
- apply(TaggedCalculator, Molecule) - Method in interface chemaxon.calculator.TaggedCalculatorInputChecker
-
Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.
- apply(Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker
-
Checks the given molecule and returns the found errors, or an empty list if the molecule is valid.
- applyRotationMatrices() - Method in class chemaxon.marvin.beans.MViewPane
-
Applies the rotation part of the viewing transformation matrix on the atom coordinates in all molecule cells.
- applyRotationMatrix(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Applies the rotation part of the viewing transformation matrix on the atom coordinates in the specified molecule cell.
- Ar - Static variable in class chemaxon.core.ChemConst
- ARC_BRACES - Static variable in class chemaxon.struc.graphics.MBracket
-
The default arc angle of the Braces Rectangle in degrees.
- ARC_ROUND - Static variable in class chemaxon.struc.graphics.MBracket
-
The default arc angle of the Rounded Rectangle in degrees.
- areAttachmentPointsVisible() - Method in class chemaxon.marvin.MolPrinter
-
Gets the attachment points visibility.
- areChildSgroupsVisible() - Method in class chemaxon.struc.Sgroup
-
Checks whether the child S-groups are visible.
- areChildSgroupsVisible() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Checks whether the child S-groups are visible.
- areMonomersTransformed() - Method in class chemaxon.sss.search.SearchOptions
-
Obtain monomer transformation information.
- areNeighbors(int, int) - Method in interface chemaxon.struc.Smolecule
-
Tests whether two atoms are connected.
- arePopupMenusEnabled() - Method in class chemaxon.marvin.beans.MarvinPane
-
Are popup menus enabled?
- ArgumentException - Exception in chemaxon.common.util
-
Checked exception to indicate that a tool has been passed an illegal argument, typically used for CLI.
- ArgumentException() - Constructor for exception chemaxon.common.util.ArgumentException
-
Creates a new instance of
ArgumentException
without detail message. - ArgumentException(String) - Constructor for exception chemaxon.common.util.ArgumentException
-
Constructs an instance of
ArgumentException
with the specified detail message. - ARGUMENTS - Static variable in class chemaxon.marvin.services.ServiceDescriptor
-
Property key for Arguments as an Unmodifiable
List
- ARO_R - Enum constant in enum class chemaxon.calculations.bbb.BBBFunction
-
Number of aromatic rings.
- AROM_AMBIGUOUS - Static variable in class chemaxon.struc.MoleculeGraph
-
Aromatization type for ambiguous 5-membered rings.
- AROM_BASIC - Static variable in class chemaxon.struc.MoleculeGraph
-
Basic aromatization.
- AROM_CHUCKEL - Static variable in class chemaxon.struc.MoleculeGraph
-
Huckel aromatization.
- AROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph
-
General (Daylight conform) aromatization.
- AROM_LOOSE - Static variable in class chemaxon.struc.MoleculeGraph
-
Loose aromatization.
- AROM_SUBSTRUCTURE - Static variable in class chemaxon.struc.MoleculeGraph
-
Substructure aromatization.
- AROMATIC - Enum constant in enum class chemaxon.struc.BondType
-
Aromatic bond type.
- AROMATIC - Static variable in class chemaxon.struc.MolAtom
-
Aromatic query atom.
- AROMATIC - Static variable in class chemaxon.struc.MolBond
-
Aromatic bond type.
- AROMATIC_ATOM - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
- AROMATIC_OR_ALIPHATIC - Static variable in class chemaxon.struc.MolAtom
-
Aromatic or aliphatic query atom.
- AROMATIC_RINGCENTER - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
- aromaticAtomCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of all aromatic atoms in the molecule.
- aromaticAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aromaticAtomCount()
- aromaticBondCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of all aromatic bonds in the molecule.
- aromaticBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aromaticBondCount()
- AROMATICITY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that aromaticity problem had found in the molecule
- AromaticityCheckerResult - Class in chemaxon.checkers.result
-
A descendant of
DefaultStructureCheckerResult
for identifying aromaticity problems, thus errorType property isStructureCheckerErrorType.AROMATICITY
- AromaticityCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, int, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AromaticityCheckerResult
-
Constructor which initialize all the properties.
- AromaticityErrorChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting aromatization problems. - AromaticityErrorChecker() - Constructor for class chemaxon.checkers.AromaticityErrorChecker
-
Default constructor.
- AromaticityErrorChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AromaticityErrorChecker
-
Parameterized constructor.
- aromaticRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of all aromatic ring systems in the molecule (SSSR).
- aromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aromaticRingCount()
- aromaticRingCount(int) - Method in class chemaxon.calculations.Ring
-
Calculates the number of aromatic rings (SSSR smallest set of smallest rings) of a given size in the molecule.
- aromaticRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aromaticRingCount(int)
- aromaticRings() - Method in class chemaxon.calculations.Ring
-
Identifies the aromatic rings in the molecule.
- aromaticRings() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aromaticRings()
- aromaticRings(int) - Method in class chemaxon.calculations.Ring
-
Indentifies aromatic rings in the molecule having a given size (number of rings).
- aromaticRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.aromaticRings(int)
- aromatization(GeneralExportOptions.AromatizationMethod) - Method in class chemaxon.formats.GeneralExportOptions.Builder
-
Sets the aromatization method.
- AROMATIZATION_AMBIG - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
Ambiguous aromatizatization.
- AROMATIZATION_BASIC - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
Aromatization using the basic method.
- AROMATIZATION_GENERAL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
Aromatization using the general method.
- AROMATIZATION_LOOSE - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
Aromatization using the loose method.
- AromatizationMethod - Enum Class in com.chemaxon.search
-
Enum for aromatization methods used during the search process.
- aromatize - Variable in class chemaxon.marvin.io.MolExportModule
-
Aromatize molecule according to basic aromatization if MoleculeGraph.AROM_BASIC + 1, according to general aromatization if MoleculeGraph.AROM_GENERAL + 1, etc, dearomatize if -1, do nothing if 0.
- aromatize() - Method in class chemaxon.struc.MoleculeGraph
-
Aromatize molecule using the default general aromatization method.
- aromatize(boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Aromatize (using the default general aromatization method) or dearomatize molecule.
- aromatize(int) - Method in class chemaxon.struc.Molecule
-
Aromatizes molecule.
- aromatize(int) - Method in class chemaxon.struc.MoleculeGraph
-
Aromatizes molecule.
- aromatize(int) - Method in class chemaxon.struc.RgMolecule
-
Aromatizes molecule.
- aromatize(int, boolean) - Method in class chemaxon.struc.Molecule
-
Aromatizes molecule.
- aromatize(int, boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Aromatizes molecule.
- aromatize(int, boolean) - Method in class chemaxon.struc.RgMolecule
-
Aromatizes molecule.
- aromatize(int, String, boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Aromatize or dearomatize molecule in the specified cell.
- AromatizeAction - Class in chemaxon.standardizer.actions
-
Aromatization standardizer action
- AromatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.AromatizeAction
-
Initializes the action with parameters
- AromatizeAction.Type - Enum Class in chemaxon.standardizer.actions
-
Type of aromatization
- aromatizeAll(boolean, int, String[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Aromatize or dearomatize molecules in all cells.
- Aromatizer - Enum Class in com.chemaxon.search.transformation.transformers
-
Aromatizer transformer.
- arrangeComponents() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean)
.
Usage:CleanUtil.arrangeComponents(molecule, true, true);
- arrangeComponents(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arranges molecule components (reactants, agents, products, R-group definitions) nicely.
- arrangeComponents(MoleculeGraph, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
- arrangeComponents(MoleculeGraph, boolean, boolean) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
- arrangeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arrange data attached to DataSgroup.
- arrangeHydrogenIncerments(Molecule, int, String, double) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
- arrangeMolecules(MoleculeGraph[], int, int) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice.
- arrangeReaction(RxnMolecule) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arranges reaction components nicely
- arrangeRelativeDataSgroupData(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arrange data attached to DataSgroup.
- arrangeSgBrackets(MoleculeGraph) - Static method in class chemaxon.marvin.util.CleanUtil
-
Arrange sgroup brackets in the molecule.
- ArrayMDocSource - Class in chemaxon.marvin.io
-
MDocSource
implementation for an array of documents or molecules. - ArrayMDocSource(MDocument[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
-
Creates a document source for an array of documents.
- ArrayMDocSource(Molecule[]) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
-
Creates a document source for an array of molecules.
- ArrayMDocSource(List<?>) - Constructor for class chemaxon.marvin.io.ArrayMDocSource
-
Creates a document source for a list of documents or molecules.
- ARROW_BACK_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Arrow points back.
- ARROW_CROSSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Crossed arrow flag.
- ARROW_CURVED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Curved arrow flag.
- ARROW_DASHED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Dashed arrow flag.
- ARROW_EQUILIBRIUM_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Equilibrium arrow flag.
- ARROW_GROUP1_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
-
Mask for the equilibrium and retrosynthetic arrow flags.
- ARROW_GROUP2_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
-
Mask for the curved, dashed and crosed arrow flags.
- ARROW_HALF_LEFT - Static variable in class chemaxon.struc.graphics.MPolyline
-
Only the left half of the arrow head is drawn.
- ARROW_HALF_MASK - Static variable in class chemaxon.struc.graphics.MPolyline
-
Unshifted mask of the half arrow option bits in flags.
- ARROW_HALF_RIGHT - Static variable in class chemaxon.struc.graphics.MPolyline
-
Only the right half of the arrow head is drawn.
- ARROW_RETROSYNTHETIC_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Retrosynthetic arrow flag.
- arrowFlags - Variable in class chemaxon.struc.graphics.MPolyline
-
Arrow flags.
- As - Static variable in class chemaxon.core.ChemConst
- ASK - Enum constant in enum class chemaxon.checkers.FixMode
-
on problem requests user interaction
- asProperties(String) - Method in class chemaxon.marvin.common.UserSettings
- asSet() - Method in enum class chemaxon.calculator.CalculatorTag
-
Returns a cached set that contains this element only.
- asymmetricAtomCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates the number of atoms having four different ligands.
- asymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Stereochemistry.asymmetricAtomCount()
- asymmetricAtoms() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Retrieves the indexes of atom having four different ligands.
- asymmetricAtoms() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Stereochemistry.asymmetricAtoms()
- asymmetricEuclidean(float[], float[], double) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric Euclidean distance.
- asymmetricEuclidean(int[], int[], double) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric Euclidean distance.
- asymmetricNormalizedEuclidean(float[], float[], double) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric normalized Euclidean distance.
- asymmetricNormalizedEuclidean(int[], int[], double) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric normalized Euclidean distance.
- asymmetricTanimoto(float[], float[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric Tanimoto dissimilarity for floating point values.
- asymmetricTanimoto(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric Tanimoto dissimilarity for floating point values.
- asymmetricXYZSum - Variable in class chemaxon.descriptors.PFParameters
-
Stores last calculatred asymmetric Tanimoto sum.
- asymmetryFactors - Variable in class chemaxon.descriptors.MDParameters
-
asymmetry ratio of parametrized asymmetric metrics
- AsyncCallback<T> - Interface in chemaxon.marvin.services
-
Callback interface for asynchronous service calls
- At - Static variable in class chemaxon.core.ChemConst
- atom - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
The atom whose the neighbours are processed.
- ATOM - Static variable in class chemaxon.jep.context.AtomContext
- ATOM - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Calculation domain type: calculation refers to atoms.
- ATOM_ATOM_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
-
This
String
represents the key of cloned atom, original atom map - ATOM_COUNT - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
-
Result type with the string id "atomcount".
- ATOM_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomFont"
. - ATOM_FONT_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomFontSize"
. - ATOM_MAP - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that atom maps had found in the molecule
- ATOM_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomMappingVisible"
. - ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomNumberingType"
. - ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Deprecated.in 6.2.0 use atomNumberingType parameter instead.
- ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomPropertiesVisible"
. - ATOM_QUERY_PROPERTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type representing that an atom has a query property set.
- ATOM_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"atomSet"
. - ATOM_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomSetColor"
. - ATOM_SIZE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomsize"
. - ATOM_STRINGS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"atomStrings"
. - ATOM_SYMBOL_VISIBLE_3D - Static variable in class chemaxon.marvin.common.ParameterConstants
- ATOM_SYMBOLS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomSymbolsVisible"
. - ATOM_TYPE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that atom with the specified symbol had found in the molecule
- ATOM_TYPE_COUNT - Static variable in class chemaxon.struc.MolAtom
-
Number of atom types in the elements array
- ATOM_TYPE_MAX - Static variable in class chemaxon.struc.MolAtom
-
Maximum atom number.
- ATOM_TYPES - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColoringScheme
- ATOM_VALUE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that atom values had found in the molecule
- atomChanged(MolAtom) - Method in interface chemaxon.calculations.clean.AtomChangeEventListener
- AtomChangeEventListener - Interface in chemaxon.calculations.clean
- AtomChecker - Class in chemaxon.checkers
-
Descendants of the abstract AtomChecker class check every atom for a specific error or property.
- AtomChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomChecker
-
Constructor to create a Structure checker instance with the given errorType.
- AtomContext - Class in chemaxon.jep.context
-
Expression evaluation context containing an input molecule and an input atom.
- AtomContext() - Constructor for class chemaxon.jep.context.AtomContext
-
Constructor.
- atomCount - Variable in class chemaxon.struc.MoleculeGraph
-
The number of atoms.
- atomCount() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the number of atoms in the molecule.
- atomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the number of atoms in the molecule including implicit hydrogens.
- atomCount() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
-
Calculates the number of atoms in the molecule.
- atomCount(int) - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the number of atoms of a given element in the molecule (including its isotopes).
- atomCount(int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
-
Calculates the number of atoms of a given element in the molecule (including its isotopes).
- atomCount(int, int) - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the number of atoms of a given element in the molecule.
- atomCount(int, int) - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
-
Calculates the number of atoms of a given element in the molecule.
- ATOMCOUNT - Enum constant in enum class chemaxon.standardizer.actions.RemoveFragmentAction.Measurement
-
Atom count of the molecule
- AtomIndexMapper - Interface in com.chemaxon.search.transformation
-
Atom index mapper.
- AtomIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomIterator
-
Constructs an atom iterator for the specified molecule of the factory according to the atom related behavior set in the factory.
- AtomLabels - Class in chemaxon.checkers.util
-
The atom labels storage class.
- AtomLabels() - Constructor for class chemaxon.checkers.util.AtomLabels
-
Initializes the atom labels
- ATOMLIST - Static variable in class chemaxon.sss.search.MarkushFeature
-
Deprecated.Expansion type: atom list.
- AtomMapChecker - Class in chemaxon.checkers
-
A descendant of
AtomChecker
detecting atom maps. - AtomMapChecker() - Constructor for class chemaxon.checkers.AtomMapChecker
-
Default constructor
- atomMapMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets whether atom map numbers should be considered in search.
- atomMapping() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
-
Array of atom - atom mapping.
- AtomNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.AtomNeighbourIterator
-
Constructs an iterator to process the atoms connecting to the specified atom according to the atom and bond related behavior of this factory.
- AtomProperty - Class in chemaxon.struc
-
Class for storing atom property enumerations.
- AtomProperty() - Constructor for class chemaxon.struc.AtomProperty
- AtomProperty.Radical - Enum Class in chemaxon.struc
-
Enumeration of the supported radicals.
- AtomQueryPropertyChecker - Class in chemaxon.checkers
-
A descendant of
AtomChecker
detecting atoms having an query property set. - AtomQueryPropertyChecker() - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
-
Creates a new AtomQueryPropertyChecker instance, it detects all query properties by default.
- AtomQueryPropertyChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomQueryPropertyChecker
-
Creates a new AtomQueryPropertyChecker instance to detect the given query properties.
- AtomQueryPropertyCheckerResult - Class in chemaxon.checkers.result
-
A descendant of
DefaultStructureCheckerResult
for identifying atom query properties, thus errorType property isStructureCheckerErrorType.ATOM_QUERY_PROPERTY
by default. - AtomQueryPropertyCheckerResult(StructureChecker, List<MolAtom>, Molecule, String, List<String>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
-
Constructor which initialize all the properties.
- atoms() - Method in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence
-
Returns list for the atom references in the molecule.
- atoms() - Method in class chemaxon.struc.MoleculeGraph
-
Provides an unmodifiable list view of the atoms in the molecule.
- AtomSelection - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Selection which contains atom indexes.
- AtomSelection(List<Integer>, List<Integer>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
-
Constructs an AtomSelection from lists.
- atomSet - Variable in class chemaxon.struc.Sgroup
-
Set for storing the atoms of the s-group's graph.
- ATOMSTEREO_EITHER - Static variable in interface chemaxon.struc.StereoConstants
-
Either stereo atom type.
- ATOMSTEREO_MASK - Static variable in interface chemaxon.struc.StereoConstants
-
Stereo atom type mask.
- ATOMSTEREO_NONE - Static variable in interface chemaxon.struc.StereoConstants
-
No stereo atom type specified.
- ATOMSTEREO_SPECIFIC - Static variable in interface chemaxon.struc.StereoConstants
-
Specific stereo atom type.
- AtomTypeChecker - Class in chemaxon.checkers
-
A descendant of
AtomChecker
checking different atom types (represented by atom's symbol) in the molecule. - AtomTypeChecker() - Constructor for class chemaxon.checkers.AtomTypeChecker
-
Default constructor.
- AtomTypeChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.AtomTypeChecker
-
Parameterized constructor providing the possibility for descendants to initialize with their own error type.
- AtomTypeChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AtomTypeChecker
-
Parameterized constructor.
- atomTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets whether atom types should be considered in search.
- AtomValueChecker - Class in chemaxon.checkers
-
A descendant of
AtomChecker
detecting atoms with atom value. - AtomValueChecker() - Constructor for class chemaxon.checkers.AtomValueChecker
-
Default constructor.
- ATROP - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
- ATROP - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
-
Atrop stereo center.
- AtropFilter - Class in com.chemaxon.calculations.stereoanal.filters.atrop
-
Filter for atrop stereo centers.
- AtropFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
- ATROPISOMER - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that atropisomers are found in the molecule
- AtropisomerChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting atropisomers in the molecule. - AtropisomerChecker() - Constructor for class chemaxon.checkers.AtropisomerChecker
-
Initializes the atropisomer structure checker
- AtropIsomerDetector - Class in chemaxon.marvin.alignment
-
Molecular mechanics based atropisomer detection.
- AtropIsomerDetector() - Constructor for class chemaxon.marvin.alignment.AtropIsomerDetector
- AtropIsomerDetector.Accuracy - Enum Class in chemaxon.marvin.alignment
- AtropStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Atrop stereo center implementation.
- AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
Constructs a new instance of axial stereo center.
- AtropStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
Constructs a new instance of axial stereo center with attached data.
- AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
Deprecated, for removal: This API element is subject to removal in a future version.
- AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
Deprecated, for removal: This API element is subject to removal in a future version.
- atropStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the atrop stereocenters.
- atropStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the atrop stereocenters with attached data.
- AtropStereoDescriptor - Class in chemaxon.struc
-
Descriptor representing atrop stereo information, the rotation of two aromatic rings connected by a single bond (axis), and at least 3 of the ligands in the ring connected to the axis has a non-ring ligand.
CIPStereoDescriptorIface.CIPValue.AtropStereoValue.ODD
means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is clockwise.CIPStereoDescriptorIface.CIPValue.AtropStereoValue.EVEN
means that if we watch the molecule in the direction of the axis, and the ligand with the maximum index from the ligand connected to the axis is in the back, then from the higher indexed of the two ligands in the front the higher indexed in the back is counter-clockwise.CIPStereoDescriptorIface.CIPValue.AtropStereoValue.UNKNOWN
means that it can not be decided if it is clockwise or counter-clockwise, but there is no wiggly bond - like a 2D structure without wedge information..CIPStereoDescriptorIface.CIPValue.AtropStereoValue.WIGGLY
means that there is a wiggly bond on either ligand in the ring connected to the axis, or the axis is wiggly. - AtropStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AtropStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AtropStereoDescriptor
- ATTACH_BOTH - Static variable in class chemaxon.struc.MolAtom
-
S-group attachment point on first and second site.
- ATTACH_NONE - Static variable in class chemaxon.struc.MolAtom
-
There is no S-group attachment point setting on this atom.
- ATTACH_UNKNOWN - Static variable in class chemaxon.struc.MolAtom
-
S-group attachment point information
- ATTACH1 - Static variable in class chemaxon.struc.MolAtom
-
S-group attachment point on first site.
- ATTACH2 - Static variable in class chemaxon.struc.MolAtom
-
S-group attachment point on second site.
- ATTACHED_DATA - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that attached data had found in the molecule
- ATTACHED_DATA_MATCH_EXACT - Static variable in interface chemaxon.sss.SearchConstants
-
Option value constant for exact match of attached data.
- ATTACHED_DATA_MATCH_GENERAL - Static variable in interface chemaxon.sss.SearchConstants
-
Option value constant for general match of attached data.
- ATTACHED_DATA_MATCH_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
-
Option value constant for ignoring attached data.
- AttachedData - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Data object which contains a name and a data (String).
- AttachedData(String, String) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AttachedData
-
Creates an AttachedData class.
- AttachedDataChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting attached data in the molecule. - AttachedDataChecker() - Constructor for class chemaxon.checkers.AttachedDataChecker
-
Default constructor.
- AttachedDataChecker(Map<String, String>) - Constructor for class chemaxon.checkers.AttachedDataChecker
-
Parameterized constructor.
- ATTACHMENT_ATOM - Static variable in interface chemaxon.sss.SearchConstants
-
Constant for attachment point representation in ligands: sets attachment points by attaching an any-atom.
- ATTACHMENT_LABEL - Static variable in interface chemaxon.sss.SearchConstants
-
Constant for attachment point representation in ligands: sets attachment points by
MolAtom.setExtraLabel(java.lang.String)
Labels with R-group ID: "1" forR1
, "2" forR2
, ... - ATTACHMENT_MAP - Static variable in interface chemaxon.sss.SearchConstants
-
Constant for attachment point representation in ligands: sets attachment points by
MolAtom.setAtomMap(int)
. - ATTACHMENT_NONE - Static variable in interface chemaxon.sss.SearchConstants
-
Constant for attachment point representation in ligands: none (no attachment point data).
- ATTACHMENT_POINT - Static variable in interface chemaxon.sss.SearchConstants
-
Constant for attachment point representation in ligands: R-group attachment.
- ATTACHMENT_RLABEL - Static variable in interface chemaxon.sss.SearchConstants
-
Constant for attachment point representation in ligands: sets attachment points by
MolAtom.setExtraLabel(java.lang.String)
. - AttachmentPoint - Class in chemaxon.struc.sgroup
-
Attachment Point class for the Superatom S-group.
- AttachmentPoint(MolAtom, int, MolBond) - Constructor for class chemaxon.struc.sgroup.AttachmentPoint
-
Constructs an AttachmentPoint object
- Au - Static variable in class chemaxon.core.ChemConst
- AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Automatic check for structures.
- AUTO_SCALE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"autoscale"
. - AUTO_TAB_SCALE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"autoTabScale"
. - AUTO_UNGROUP - Static variable in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.
- AutoMapper - Class in com.chemaxon.mapper
-
AutoMapper
is a tool that performs automated chemical reaction mapping. - AutoMapper() - Constructor for class com.chemaxon.mapper.AutoMapper
-
Initializes an
AutoMapper
object - AutoMapper.Options - Class in com.chemaxon.mapper
-
Option object for set common options when mapping called by static way.
- AUTOMATIC_FOG_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"automaticFogEnabled"
. - AUTOMATIC_REACTION_ENABLED - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"automaticReactionEnabled"
. - AUTORM - Static variable in class chemaxon.marvin.swing.MAction
-
Remove menu items automatically when the menu becomes invisible.
- AWT_IMAGE - Static variable in class chemaxon.formats.MFileFormat
-
Image object (java.awt.Image).
- AXIAL - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
- AXIAL - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
-
Axial stereo center (eg.
- AxialFilter - Class in com.chemaxon.calculations.stereoanal.filters.axial
-
Filter for axial stereo centers.
- AxialFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
- AxialStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Axial stereo center implementation.
- AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
Constructs a new instance of axial stereo center.
- AxialStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
Constructs a new instance of axial stereo center with attached data.
- AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
Deprecated, for removal: This API element is subject to removal in a future version.
- AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
Deprecated, for removal: This API element is subject to removal in a future version.
- axialStereoCenters() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the axial stereocenters.
- axialStereoCentersWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the axial stereocenters with attached data.
- AxialStereoDescriptor - Class in chemaxon.struc
- AxialStereoDescriptor(CIPStereoDescriptorIface.CIPValue.AxialStereoValue, int, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.AxialStereoDescriptor
B
- B - Static variable in class chemaxon.core.ChemConst
- Ba - Static variable in class chemaxon.core.ChemConst
- BACKGROUND - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"background"
. - BACKGROUNDLOAD_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"bgloadEnabled"
. - BACKGROUNDLOAD_PRIORITY - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"bgload"
. - backgroundThread - Variable in class chemaxon.standardizer.runner.BasicStandardizerRunner
- balabanIndex() - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the Balaban distance connectivity of the molecule, which is the average distance sum connectivity.
- BALL_RADIUS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"ballRadius"
. - BASE64 - Static variable in class chemaxon.formats.MFileFormat
-
BASE64 encoded file.
- BASIC - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type
-
Basic aromatization
- BASIC - Enum constant in enum class com.chemaxon.search.AromatizationMethod
-
Basic aromatization.
- BASIC - Enum constant in enum class com.chemaxon.search.transformation.transformers.Aromatizer
- BASIC - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
Constant denoting basic pKa.
- BasicStandardizerRunner - Class in chemaxon.standardizer.runner
-
This is the default implementation of
StandardizerActionRunner
interface. - BasicStandardizerRunner(StandardizerConfigurationReader) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner
-
Initialize a
BasicStandardizerRunner
instance with theStandardizerConfiguration
read from the provided configuration reader. - BasicStandardizerRunner(StandardizerConfiguration) - Constructor for class chemaxon.standardizer.runner.BasicStandardizerRunner
-
Initialize a
BasicStandardizerRunner
instance with specifiedStandardizerConfiguration
. - BBB - Class in chemaxon.calculations.bbb
-
BBB score calculator.
- BBB.Property - Class in chemaxon.calculations.bbb
-
Simple DTO that contains the predicted value, its BBB score and the BBB score multiplied with the corresponding BBB multiplier.
- BBBFunction - Enum Class in chemaxon.calculations.bbb
-
Base phys-chem property calculators and its score functions for BBB score calculation.
- BCUT - Class in chemaxon.descriptors
-
Implements BCUT descriptors.
- BCUT() - Constructor for class chemaxon.descriptors.BCUT
-
Creates a new, empty BCUT descriptor.
- BCUT(BCUT) - Constructor for class chemaxon.descriptors.BCUT
-
Copy constructor.
- BCUT(BCUTParameters) - Constructor for class chemaxon.descriptors.BCUT
-
Creates a new instance according to the parameters.
- BCUT(String) - Constructor for class chemaxon.descriptors.BCUT
-
Creates a new instance according to the parameters.
- BCUTGenerator - Class in chemaxon.descriptors
-
Descriptor generator class for the
BCUT
descriptor. - BCUTGenerator() - Constructor for class chemaxon.descriptors.BCUTGenerator
-
Creates and initializes a
BCUT
descriptor generator object. - BCUTParameters - Class in chemaxon.descriptors
-
Manages parameters for the
BCUT
descriptor class. - BCUTParameters() - Constructor for class chemaxon.descriptors.BCUTParameters
-
Creates an empty object.
- BCUTParameters(File) - Constructor for class chemaxon.descriptors.BCUTParameters
-
Creates a new object based on a given configuration file.
- BCUTParameters(String) - Constructor for class chemaxon.descriptors.BCUTParameters
-
Creates a new object based on a given configuration string.
- Be - Static variable in class chemaxon.core.ChemConst
- beginHourglass() - Method in class chemaxon.marvin.beans.MarvinPane
-
Changes the cursor to hourglass at the beginning of a long operation.
- bemismurcko - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
- bemismurckoloose - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
- Beta - Annotation Interface in com.chemaxon.common.annotations
-
Indicates that a public API entity (public class, method, or field) is subject to incompatible changes, or even removal, in a future release.
- Bh - Static variable in class chemaxon.core.ChemConst
- Bi - Static variable in class chemaxon.core.ChemConst
- BicycloStereoDescriptor - Class in chemaxon.struc
-
This class is the atom index based representation which can be assigned to 'endo', 'exo', 'syn', 'anti' ligands of bicyclo[x.y.z]alkanes in case of 0 dimension molecules.
- BicycloStereoDescriptor(MolAtom, int, MolAtom[], MolAtom[]) - Constructor for class chemaxon.struc.BicycloStereoDescriptor
-
Creates a new stereo descriptor for bicyclo stereo.
- BINARY_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters
-
descriptor type constants
- binaryAsymmetricEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric Euclidean distance of binary descriptors.
- binaryAsymmetricNormalizedEuclidean(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric normalized Euclidean distance of binary descriptors.
- binaryAsymmetricNormalizedEuclidean(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the asymmetric normalized Euclidean distance of binary descriptors.
- binaryAsymmetricTanimoto(int[], int[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates asymmetric Tanimoto dissimilarity for binary descriptors.
- binaryAsymmetricTanimoto(int[], int, int[], int, float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates asymmetricTanimoto dissimilarity for binary descriptors.
- binaryEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the Euclidean distance of two binary descriptors.
- binaryNormalizedEuclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the normalized Euclidean distance of two binary descriptors.
- binaryNormalizedEuclidean(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the normalized Euclidean distance of two binary descriptors.
- binaryTanimoto(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates Tanimoto dissimilarity for binary descriptors.
- binaryTanimoto(int[], int, int[], int) - Static method in class chemaxon.descriptors.Metrics
-
Calculates Tanimoto dissimilarity for binary descriptors.
- binaryTversky(int[], float, int[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates Tversky dissimilarity for binary descriptors.
- binaryWeightedAsymmetricEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the weighted asymmetric Euclidean distance of binary descriptors.
- binaryWeightedAsymmetricNormalizedEuclidean(int[], int[], float[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.
- binaryWeightedAsymmetricNormalizedEuclidean(int[], int, int[], int, float[], float) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the weighted asymmetric normalized Euclidean distance of binary descriptors.
- binaryWeightedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the weighted Euclidean distance of binary descriptors.
- binaryWeightedNormalizedEuclidean(int[], int[], float[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the weighted normalized Euclidean distance of binary descriptors.
- binaryWeightedNormalizedEuclidean(int[], int, int[], int, int[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the weighted normalized Euclidean distance of binary descriptors.
- Bk - Static variable in class chemaxon.core.ChemConst
- BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Constant storing the blue rgb value (the basic pKa result color).
- BOLD - Static variable in class chemaxon.struc.graphics.MFont
-
Bold font style.
- BOLD - Static variable in class chemaxon.struc.MolBond
-
"Bold" attribute of the bond.
- BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"boldBondWidth"
. - BOND_ANGLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that bond angle problem had found in the molecule
- BOND_BOND_MAP - Static variable in class chemaxon.checkers.result.ConvertConstants
-
This
String
represents the key of cloned bond, original bond map - BOND_DRAGGED_ALONG - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"bondDraggedAlong"
. - BOND_HASH_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"bondHashSpacing"
. - BOND_LENGTH - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that bond length problem had found in the molecule
- BOND_LENGTH - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"bondLength"
. - BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"bondLengthVisible"
. - BOND_SET - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"bondSet"
. - BOND_SET_COLOR - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"bondSetColor"
. - BOND_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"bondSpacing"
. - BOND_TOPOLOGY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that molecule contains bond(s) with topology.
- BondAngleChecker - Class in chemaxon.checkers
-
Bond Angle Checker detects wrong bond angles in 2D structures.
- BondAngleChecker() - Constructor for class chemaxon.checkers.BondAngleChecker
-
Default constructor
- BondAngleChecker(double) - Constructor for class chemaxon.checkers.BondAngleChecker
-
Deprecated.Not used.
- BondAngleCheckerResult - Class in chemaxon.checkers.result
-
Bond angle checker result.
- BondAngleCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongAngleBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondAngleCheckerResult
-
Constructor which initialize all the properties.
- BondAngleFixer - Class in chemaxon.fixers
-
Bond Angle Fixer fixes wrong bond angles in 2D structures.
- BondAngleFixer() - Constructor for class chemaxon.fixers.BondAngleFixer
- BondChecker - Class in chemaxon.checkers
-
Descentants of the abstract BondChecker class detect bond related problems.
- BondChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.BondChecker
-
Constructor to create a Structure checker instance with the given errorType.
- bondCount - Variable in class chemaxon.struc.MolAtom
-
Number of bonds.
- bondCount - Variable in class chemaxon.struc.MoleculeGraph
-
The number of bonds.
- bondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the number of bonds in the molecule including bonds of implicit hydrogens.
- BondInfo - Class in chemaxon.marvin.alignment.atrop
-
Encapsulates bond info.
- BondInfo(int, int, int) - Constructor for class chemaxon.marvin.alignment.atrop.BondInfo
-
Construct.
- BondIterator() - Constructor for class chemaxon.util.iterator.IteratorFactory.BondIterator
-
Constructs an iterator to process the bonds of the specified molecule in this factory according to the bond related behavior of this factory.
- bondlength() - Method in class chemaxon.struc.Molecule
-
Calculate the regular bond length for the unified structure.
- bondlength() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the regular bond length.
- BondLengthChecker - Class in chemaxon.checkers
-
Bond Length Checker detects bonds with wrong length in 2D structures.
- BondLengthChecker() - Constructor for class chemaxon.checkers.BondLengthChecker
-
Default constructor
- BondLengthChecker(Map<String, String>) - Constructor for class chemaxon.checkers.BondLengthChecker
-
Deprecated.Checker has no parameters.
- BondLengthCheckerResult - Class in chemaxon.checkers.result
-
Bond angle checker result.
- BondLengthCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, MoleculeCheckerFixer.WrongLengthBonds, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.BondLengthCheckerResult
-
Constructor which initialize all the properties.
- BondLengthFixer - Class in chemaxon.fixers
-
Bond Length Fixer fixes bonds with wrong length in 2D structures.
- BondLengthFixer() - Constructor for class chemaxon.fixers.BondLengthFixer
- BONDLIST - Static variable in class chemaxon.sss.search.MarkushFeature
-
Deprecated.Expansion type: bond list.
- BondNeighbourIterator(MolAtom) - Constructor for class chemaxon.util.iterator.IteratorFactory.BondNeighbourIterator
-
Constructs an iterator to process the bonds connecting to the specified atom.
- bonds() - Method in class chemaxon.struc.MolAtom
-
Provides an unmodifiable list view of the connected bonds of the atom.
- bonds() - Method in class chemaxon.struc.MoleculeGraph
-
Provides an unmodifiable list view of the bonds in the molecule.
- bondSkipped(BondInfo, String) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
-
Called when visited bond is skipped.
- BondTable - Class in chemaxon.core.util
-
Provides easy lookup of bonds between pair of atoms in a molecule graph.
- BondTopologyChecker - Class in chemaxon.checkers
-
Checker detects bonds with reacting center bond marks.
- BondTopologyChecker() - Constructor for class chemaxon.checkers.BondTopologyChecker
-
Default constructor
- bondType(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Determines the type of a bond (aromatic bonds are automatically recognized)
- BondType - Enum Class in chemaxon.struc
-
General chemical bond types.
- bondTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets whether bond types should be considered in search.
- bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom
-
Calculates the average of the bond unit vectors pointing out of this atom.
- BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor
-
Boolean option.
- booleanValue() - Method in class chemaxon.struc.prop.MBooleanProp
-
Gets the boolean value.
- BORDER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"border"
. - BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Deprecated.
- Br - Static variable in class chemaxon.core.ChemConst
- brackets - Variable in class chemaxon.struc.Sgroup
- BRACKETS - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type representing that the molecule contains brackets (S-groups).
- BracketsChecker - Class in chemaxon.checkers
-
Detects brackets (S-groups) in molecules.
- BracketsChecker() - Constructor for class chemaxon.checkers.BracketsChecker
-
Default constructor.
- BRIDGEHEAD_H - Static variable in class chemaxon.struc.MolAtom
-
Hydrogen atom which is connected to a bridgehead atom.
- brightness - Variable in class chemaxon.descriptors.ChemicalFingerprint
-
number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less pausible)
- brightness - Variable in class chemaxon.descriptors.ECFP
-
The number of bits set in the binary vector storage
- brightness - Variable in class chemaxon.descriptors.ReactionFingerprint
-
number of bits set in the fingerprint (sometimes this is called the darkness, but that seems to be less plausible)
- btab - Variable in class chemaxon.struc.MoleculeGraph
-
Bond table.
- bufincRead() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Reads a character and writes into the buffer.
- build() - Method in class chemaxon.calculations.dipole.DipoleCalculator.Builder
- build() - Method in class chemaxon.calculations.nmr.NMRCalculator.Builder
- build() - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
-
Builds a
ValenceCheckOptions
object. - build() - Method in class chemaxon.formats.GeneralExportOptions.Builder
-
Builds an unmodifiable export option.
- build() - Method in class chemaxon.formats.MolConverter.Builder
-
Builds the MolConverter.
- build() - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- build() - Method in class chemaxon.jep.ConstantTableBuilder
-
Creates a new constant table based on this builder.
- build() - Method in class chemaxon.marvin.plugin.gui.ResultView
-
Sets sizes, builds split panes.
- build() - Method in class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
- build() - Method in class chemaxon.standardizer.StandardizerActionFactory.Builder
-
Builds a
StandardizerActionFactory
based on the previously addedInputStream
instances - build() - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
- build() - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Creates a search options object with the settings specified by this builder instance.
- buildButtonBar() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
- buildContentPanel() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
- builder() - Static method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
-
Creates a new builder.
- builder() - Static method in class chemaxon.jep.ConstantTable
-
Creates a new builder for a constant table.
- Builder() - Constructor for class chemaxon.calculations.dipole.DipoleCalculator.Builder
- Builder() - Constructor for class chemaxon.calculations.nmr.NMRCalculator.Builder
- Builder() - Constructor for class chemaxon.core.calculations.valencecheck.ValenceCheckOptions.Builder
- Builder() - Constructor for class chemaxon.formats.GeneralExportOptions.Builder
- Builder() - Constructor for class chemaxon.formats.MolConverter.Builder
-
Constructs an empty Builder object.
- Builder() - Constructor for class chemaxon.marvin.calculations.HlbPlugin.Builder
- Builder() - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
- Builder() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.Builder
- Builder() - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.Builder
- Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Creates a Builder object with the default settings.
- Builder(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Creates a Builder object containing the settings of the given search options object.
- BuildupMcs - Class in com.chemaxon.search.mcs.buildup
-
Implements a heuristic MCS algorithm using the build-up method of Takeshi Kawabata.
- BuildupMcs(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.buildup.BuildupMcs
-
Creates a new
BuildupMcs
object with the given search options. - BUTTON_MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"buttonmenubar"
. - BYTE - Static variable in class chemaxon.naming.document.DocumentToStructure
-
For internal usage only.
C
- C - Static variable in class chemaxon.core.ChemConst
- C_CLOSE_STREAM - Static variable in class chemaxon.formats.MolExporter
-
Close the underlying stream.
- C_FLUSH_STREAM - Static variable in class chemaxon.formats.MolExporter
-
Flush the output stream and force any buffered output bytes to be written out.
- C_SHIFT_PROP_NAME - Static variable in class chemaxon.calculations.nmr.NMRCalculator
-
Name of the 13C chemical shift atom property.
- C13 - Enum constant in enum class chemaxon.calculations.nmr.NMRSpectrum.Nucleus
-
13C NMR
- Ca - Static variable in class chemaxon.core.ChemConst
- CACHE_MOLECULES - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"cacheMols"
. - CACHE_REMOVE_ALL - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for clearing all cached info.
- CACHE_REMOVE_AROMATAMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for remove module used in aromatization.
- CACHE_REMOVE_CACHEMEMORY - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for cacheMemory.
- CACHE_REMOVE_GRINVMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for remove module used in graph invariant calculation.
- CACHE_REMOVE_PARITYMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for remove module used in parity calculation.
- CACHE_REMOVE_SSSRMODULE - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache removal option for remove module used in sssr.
- CACHE_REMOVE_TABS - Static variable in class chemaxon.struc.MoleculeGraph
-
Cache remove option to clear ctab and btab.
- cacheMemory - Variable in class chemaxon.struc.MoleculeGraph
- calcBadness(MoleculeGraph, MoleculeGraph, MolAtom, MolBond[]) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates a "badness" value for the atomic coordinates.
- calcBitCount(int) - Static method in class chemaxon.descriptors.Metrics
-
Counts the number of bits set (1) in the integer parameter.
- calcBitCount(int[]) - Static method in class chemaxon.descriptors.Metrics
-
Counts the number of bits set (1) in a bit vector.
- calcBracketEndPoints(DPoint3[], DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the bracket endpoints from the base line of the bracket.
- calcCenter() - Method in class chemaxon.struc.MDocument
-
Calculates the geometrical center.
- calcCenter() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the geometrical center.
- calcCenter(CTransform3D) - Method in class chemaxon.struc.MDocument
-
Calculates the geometrical center.
- calcCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
-
Calculates the geometrical center.
- calcCenter(DPoint3, CTransform3D) - Method in class chemaxon.struc.MPoint
-
Calculates the geometrical center.
- calcDehydrogenizedGrinv(int[]) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the graph invariants with the assumption that hydrogens are removed.
- calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the division point of a segment with a given ratio.
- calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.CFGenerator
-
Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
- calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.ECFPGenerator
-
Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
- calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.MDGenerator
-
Calculate and store in
freqCount[]
absolute frequency counts per cells. - calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.PFGenerator
-
Calculate and store in
freqCount[]
absolute frequency counts per cells. - calcFreqCount(MolecularDescriptor) - Method in class chemaxon.descriptors.RFGenerator
-
Updates statistics gathered on fingerprints generated and get the number of non-zero cells.
- calcHeight() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the molecule height.
- calcHybridization() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates and sets hybridazation state for each atom.
- calclogD(double) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Returns the logD value at fixed pH.
- calcMaxDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
- calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
Calculates the minimum distance between two atoms in the molecule.
- calcOrderFromLength() - Method in class chemaxon.struc.MolBond
-
Calculate the bond order from the atomic distances.
- calcOrderFromValence() - Method in class chemaxon.struc.MolBond
-
Calculate bond order from the types and charges of the two atoms.
- calcOutRect() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the outer rectangle.
- calcOutRect(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the outer rectangle.
- calcOutRectCenter() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the center of the outer rectangle.
- calcOutRectCenter(DPoint3) - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the center of the outer rectangle.
- CALCRGB_OFF - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Calculator rgb offset.
- calcSimplePolymerBracket(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the points of a simple polymer bracket that belongs to a bond.
- calcStereo2() - Method in class chemaxon.struc.MolBond
-
Computes the stereochemistry of the bond based on the atomic coordinates.
- calcStereo2(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
-
Computes the stereochemistry of the bond based on the atomic coordinates.
- calcStereo2(MolAtom, MolAtom, MolAtom, MolAtom) - Static method in class chemaxon.struc.MolBond
-
Computes the stereochemistry of the atom sequence (scheme a1-a2=a3-a4) based on the atomic coordinates.
- calculate() - Method in class chemaxon.marvin.alignment.MMPAlignment
-
Runs the MCS alignment calculation on the two structures of the constructor.
- calculate(int[]) - Method in class chemaxon.marvin.alignment.MolAligner
-
Calculate best alignment based on the hit map
- calculate(Molecule) - Static method in class chemaxon.calculations.bbb.BBB
-
Calculates the BBB properties and scores of the given Molecule.
- calculate(Molecule) - Method in enum class chemaxon.calculations.bbb.BBBFunction
-
Calculates the BBB property, its score and its multiplied score.
- calculate(Molecule) - Static method in class chemaxon.calculations.cnsmpo.CnsMpo
-
Calculates the CNS MPO properties and scores of the given molecule.
- calculate(Molecule) - Method in enum class chemaxon.calculations.cnsmpo.CnsMpoFunction
-
Calculates the CNS MPO property and its score.
- calculate(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
- calculate(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
-
Calculates NMR spectrum for the given input molecule.
- calculate(Molecule) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Run the atropisomer calculation.
- calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.FastUpperBoundCalculator
- calculate(Molecule, Molecule, McsSearchOptions) - Method in class com.chemaxon.search.mcs.upperbound.StandardUpperBoundCalculator
- calculate(Molecule, Molecule, McsSearchOptions) - Method in interface com.chemaxon.search.mcs.upperbound.UpperBoundCalculator
-
Returns an upper bound for the number of bonds the Maximum Common Substructure of the given molecules may contain.
- calculate(Molecule, ProgressObserver) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Run the atropisomer calculation.
- calculate(Molecule, ProgressObserver, DihedralScanListener) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Run the atropisomer calculation.
- calculateAttachmentPoints() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Calculates the attachment points for the crossing atoms and crossing bonds and sets the calculated values.
- calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
- calculateCIPStereoDescriptors(MoleculeGraph) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
-
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.
- calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
- calculateCIPStereoDescriptors(MoleculeGraph, boolean) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
- calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>) - Static method in class chemaxon.core.calculations.stereo.CIPStereoRecognizer
-
Calculates the Cahn-Ingold-Prelog (CIP) stereo descriptors for a specified molecule.
- calculateCIPStereoDescriptors(MoleculeGraph, EnumSet<CIPStereoDescriptorIface.CIPType>, boolean) - Static method in class chemaxon.calculations.cip.CIPStereoCalculator
-
Calculates the stereo descriptors of the given molecule.
- calculateCoordinates(Molecule, MolBond[], MoleculeGraph, int, boolean, SelectionMolecule, List<Double>) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Calculates the coordinates during expand and contract.
- calculateIntrinsicSolubility(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Calculates intrinsic solubility.
- calculatePhDependentSolubility(Molecule, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Calculates pH-dependent solubility.
- calculatePhDependentSolubility(Molecule, double[]) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Calculates pH-dependent solubilities.
- calculatePhDependentSolubility(Molecule, double, double, double) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
-
Calculates pH-dependent solubilities.
- calculateSimilarityUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
-
Calculates an upper bound on the similarity of the query and target molecules with respect to the specified search options.
- calculateUpperBound() - Method in class com.chemaxon.search.mcs.MaxCommonSubstructure
-
Calculates an upper bound on the number of bonds the maximum common substructure may contain with respect to the specified search options.
- CalculatorError - Interface in chemaxon.calculator
-
An error that might occur when a calculator is initialized.
- CalculatorInputChecker - Interface in chemaxon.calculator
-
Instances of this interface are used by calculators to check if they can process an input molecule.
- CalculatorPlugin - Class in chemaxon.marvin.plugin
-
Common base class for calculator plugins.
- CalculatorPlugin() - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
-
Constructor.
- CalculatorPlugin(Consumer<Molecule>, Consumer<Molecule>) - Constructor for class chemaxon.marvin.plugin.CalculatorPlugin
-
Constructor.
- CalculatorPlugin.HydrogenData - Class in chemaxon.marvin.plugin
- CalculatorPluginCachedResults - Class in com.chemaxon.calculations.cli
-
Provides plugin cached results.
- CalculatorPluginCachedResults(String, String, Molecule[], Molecule, String, String, Throwable, boolean) - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginCachedResults
-
Constructor.
- CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.gui
-
Common base class for calculator plugin displays.
- CalculatorPluginDisplay() - Constructor for class com.chemaxon.calculations.gui.CalculatorPluginDisplay
- CalculatorPluginOutput<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.cli
-
Class providing plugin output in table form.
- CalculatorPluginOutput() - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput
-
Default constructor.
- CalculatorPluginOutput(CalculatorPlugin) - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput
-
Constructor that sets plugin.
- CalculatorPluginService<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin
-
Base class for types that implement a functionality related to a specific
CalculatorPlugin
. - CalculatorPluginService() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginService
- CalculatorResultAccess - Interface in com.chemaxon.calculations.cli
-
Interface providing plugin result access.
- CalculatorTag - Enum Class in chemaxon.calculator
-
List of optional tags that can be reported by a
TaggedCalculator
. - calcWidth() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the molecule width.
- calcWidth(Graphics2D) - Method in class chemaxon.struc.graphics.MNameTextBox
-
Calculates the width of the string in the name text box.
- call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
Performs the calculation and returns the result returned by
PluginWorkUnit.getResult()
. - call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
-
Performs the calculation and returns the result returned by
ReusablePluginWorkUnit.getResult()
. - callback(String, Object) - Method in interface chemaxon.jep.ChemContext
-
Deprecated, for removal: This API element is subject to removal in a future version.Use
ChemContext.callContextFunction(String, List)
instead. - callback(String, Object) - Method in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.No longer used for accessing the context, will be removed without replacement.
- callContextFunction(String, List<Object>) - Method in interface chemaxon.jep.ChemContext
-
Executes the specified context function with the given parameters.
- callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.AtomContext
-
Executes the specified context function with the given parameters.
- callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.MolContext
-
Executes the specified context function with the given parameters.
- callContextFunction(String, List<Object>) - Method in class chemaxon.jep.context.ReactionContext
-
Executes the specified context function with the given parameters.
- callService(HTTPServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.httpservice.HTTPServiceHandler
- callService(JsonServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.json.JsonServiceHandler
- callService(LocalServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.localservice.LocalServiceHandler
- callService(SoapServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.soap.SoapServiceHandler
- callService(XMLRPCServiceDescriptor, Object...) - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceHandler
- callService(DT, AsyncCallback<T>, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
-
Performs thread-safe asynchronous service call.
- callService(DT, Object...) - Method in class chemaxon.marvin.services.ServiceHandler
-
Performs a service call.
- CAN_BE - Static variable in class chemaxon.formats.recognizer.AbbrevGroupRecognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.
- CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.
- canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.
- canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.
- canBeCT(int, int) - Method in class chemaxon.struc.MoleculeGraph
-
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
- canBeCT(int, int, boolean) - Method in class chemaxon.struc.MoleculeGraph
-
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
- canBeCT(int, int, boolean) - Method in class chemaxon.struc.RgMolecule
-
Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
- canBeCT(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Determines whether the given bond can be a CIS/TRANS or not.
- canBeReactionComponent() - Method in class chemaxon.struc.Molecule
-
Tests whether an object of this class can be a reaction component.
- canBeReactionComponent() - Method in class chemaxon.struc.RgMolecule
-
Tests whether an object of this class can be a reaction component.
- canBeReactionComponent() - Method in class chemaxon.struc.RxnMolecule
-
Tests whether an object of this class can be a reaction component.
- canBeSMARTS(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.
- canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.
- cancel() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Stops the background thread
- cancel() - Method in class chemaxon.marvin.alignment.MMPAlignment
-
Cancel the ongoing calculation
- cancel() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
- cancel() - Method in interface chemaxon.standardizer.runner.StandardizerActionRunner
-
Stops the background thread
- CANCELLED - Enum constant in enum class chemaxon.common.swing.io.output.FileSaveResult
- CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
- canonicalName(String) - Static method in class chemaxon.marvin.io.Encoding
-
Standardize a Java encoding.
- canRepeat() - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- canRepeat() - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
- canRepeat() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns
true
if repeatedly running the same plugin object while getting the results on the GUI is allowed,false
otherwise. - carboaliphaticRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of carboaliphatic rings in the molecule (aliphatic rings containing carbon atoms only).
- carboaliphaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.carboaliphaticRingCount()
- carboaromaticRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of carboaromatic rings in the molecule (aromatic rings containing carbon atoms only).
- carboaromaticRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.carboaromaticRingCount()
- carboRingCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of carbocyclic rings in the molecule (rings containing carbon atoms only).
- carboRingCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.carboRingCount()
- carboRingCount(int) - Method in class chemaxon.calculations.Ring
-
Calculates the number of carbocyclic rings in the molecule (rings containing at least a non-carbon atom).
- carboRingCount(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.carboRingCount(int)
- carboRings() - Method in class chemaxon.calculations.Ring
-
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only).
- carboRings() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.carboRings()
- carboRings(int) - Method in class chemaxon.calculations.Ring
-
Identifies carbocyclic rings in the molecule (rings containing carbon atoms only) having the given number of atoms.
- carboRings(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.carboRings(int)
- caretUpdate(CaretEvent) - Method in class chemaxon.marvin.plugin.gui.ResultView
- CBasic - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType
- CCLENGTH - Static variable in class chemaxon.struc.MolBond
-
Default bond length.
- Cd - Static variable in class chemaxon.core.ChemConst
- CDParameters - Class in chemaxon.descriptors
-
Manages parameters the
CustomDescriptor
class. - CDParameters() - Constructor for class chemaxon.descriptors.CDParameters
-
Creates an empty object.
- CDParameters(int) - Constructor for class chemaxon.descriptors.CDParameters
-
Creates an empty object of the given type.
- CDParameters(File) - Constructor for class chemaxon.descriptors.CDParameters
-
Creates a new descriptor configured from the given file.
- CDParameters(String) - Constructor for class chemaxon.descriptors.CDParameters
-
Creates a new object based on a given configuration string.
- CDX - Static variable in class chemaxon.formats.MFileFormat
-
ChemDraw CDX file.
- CDXML - Static variable in class chemaxon.formats.MFileFormat
-
ChemDraw CDXML file.
- Ce - Static variable in class chemaxon.core.ChemConst
- CELL - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"cell"
. - cellSize - Variable in class chemaxon.descriptors.MDParameters
-
size - number of bits - of one descriptor cell
- CELLSIZE - Static variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
The default viewer cell size.
- cellwiseWeights - Variable in class chemaxon.descriptors.MDParameters
-
is cell weights for parametrized metrics
- centralizeMoleculeDisplay() - Method in class chemaxon.marvin.beans.MSketchPane
-
Puts the molecule into the center of the display.
- Cf - Static variable in class chemaxon.core.ChemConst
- CFGenerator - Class in chemaxon.descriptors
-
The
CFGenerator
class generates topological fingerprints of molecular graphs. - CFGenerator() - Constructor for class chemaxon.descriptors.CFGenerator
-
Creates a new instance of
CFGenerator
which can be used to generate chemical fingerprints for an arbitrary number of molecules. - CFNS - Static variable in class chemaxon.jep.context.AtomContext
-
The context function names.
- CFNS - Static variable in class chemaxon.jep.context.ReactionContext
-
The context function names.
- CFParameters - Class in chemaxon.descriptors
-
Manages fingerprint parameters.
- CFParameters() - Constructor for class chemaxon.descriptors.CFParameters
-
Creates an empty object.
- CFParameters(File) - Constructor for class chemaxon.descriptors.CFParameters
-
Creates a new object based on a given configuration file.
- CFParameters(String) - Constructor for class chemaxon.descriptors.CFParameters
-
Creates a new object based on a given configuration string.
- CHAc - Enum constant in enum class chemaxon.calculations.pka.PKaTrainingResult.PKaType
- chainAtomCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of chain atoms in the molecule excluding hydrogens.
- chainAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.chainAtomCount()
- chainBondCount() - Method in class chemaxon.calculations.Ring
-
Calculates the number of chain bonds in the molecule excluding bonds of hydrogen atoms.
- chainBondCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Ring.chainBondCount()
- chainTransformers(Transformer...) - Static method in class com.chemaxon.search.transformation.TransformerFactory
-
Returns a chain transformer.
- chainTransformers(List<Transformer>) - Static method in class com.chemaxon.search.transformation.TransformerFactory
-
Returns a chain transformer.
- changes - Variable in class chemaxon.standardizer.actions.AbstractSgroupAction
- Changes - Class in chemaxon.standardizer
-
The change set of the standardization procedure.
- Changes(Molecule) - Constructor for class chemaxon.standardizer.Changes
-
Initializes the changes object.
- Changes(Molecule, StandardizerAction) - Constructor for class chemaxon.standardizer.Changes
-
Initializes the changes object.
- Changes(Molecule, Molecule) - Constructor for class chemaxon.standardizer.Changes
-
Initializes the changes object.
- CHANGING - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
-
Only reaction center will be mapped
- CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: key of the molecule property which contains the starting character offset since the beginning of the document, for text formats (html, xml, txt).
- characters(char[], int, int) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter
- charAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets a character of the document.
- CHARGE_MATCHING_DEFAULT - Static variable in interface chemaxon.sss.SearchConstants
-
Option value constant for default charge searching (charged query matches only charged target, noncharged query matches all).
- CHARGE_MATCHING_EXACT - Static variable in interface chemaxon.sss.SearchConstants
-
Option value constant for exact charge searching (charged query matches only charged target, noncharged query only matches noncharged).
- CHARGE_MATCHING_IGNORE - Static variable in interface chemaxon.sss.SearchConstants
-
Option value constant for ignore charge searching (charge information is ignored during searching).
- CHARGE_ON_ATOMS - Static variable in class chemaxon.struc.Sgroup
-
Charge is located on atoms and displayed on atoms.
- CHARGE_ON_GROUP - Static variable in class chemaxon.struc.Sgroup
-
Charge is located on atoms but displayed on the whole group (bracket).
- CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"chargeWithCircle"
. - CHARGED_H - Static variable in class chemaxon.struc.MolAtom
-
Include charged Hydrogen atom(s).
- chargeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets whether formal charges of atoms should be considered in search.
- ChargePlugin - Class in chemaxon.marvin.calculations
-
Plugin class for partial charge calculation.
- ChargePlugin() - Constructor for class chemaxon.marvin.calculations.ChargePlugin
-
Constructor.
- check() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
- check() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Invokes a background thread which will run all checkers on the given molecule
- check(Molecule) - Method in class chemaxon.calculations.dipole.DipoleCalculator
- check(Molecule) - Method in class chemaxon.calculations.nmr.NMRCalculator
- check(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
- check(Molecule) - Method in class chemaxon.checkers.InvalidChecker
- check(Molecule) - Method in interface chemaxon.checkers.StructureChecker
-
Detects a specific error in the molecule.
- check(Molecule) - Method in interface chemaxon.jep.MolCondition
-
Deprecated.Returns
true
if molecule should be processed,false
otherwise. - check(Molecule) - Method in class com.chemaxon.calculations.solubility.SolubilityCalculator
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AliasChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomMapChecker
-
Detects atom of the molecule has atom map.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomTypeChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.AtomValueChecker
-
Detects if the current atom of the molecule has atom value.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.ExplicitLonePairChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.IsotopeChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.MissingAtomMapChecker
-
Check the atom of the molecule with index i has no atom map.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.MultiCenterChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.OverlappingAtomsChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.PseudoAtomChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.QueryAtomChecker
-
Detects atom of the molecule is a query atom.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.RacemateChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.RadicalChecker
-
Detects if the current atom has free electrons.
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.RareElementChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.StarAtomChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.StereoInversionRetentionMarkChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.ThreeDimensionChecker
- check(Molecule, MolAtom) - Method in class chemaxon.checkers.ValencePropertyChecker
- check(Molecule, MolBond) - Method in class chemaxon.checkers.BondTopologyChecker
- check(Molecule, MolBond) - Method in class chemaxon.checkers.CrossedDoubleBondChecker
-
Examines if the bond is a crossed double bond.
- check(Molecule, MolBond) - Method in class chemaxon.checkers.OverlappingBondsChecker
-
Detects bond of the molecule is crossing another bond or closer than the limit distance.
- check(Molecule, MolBond) - Method in class chemaxon.checkers.QueryBondChecker
- check(Molecule, MolBond) - Method in class chemaxon.checkers.ReactingCenterBondMarkChecker
- check(Molecule, MolBond) - Method in class chemaxon.checkers.StraightDoubleBondChecker
- check(Molecule, E) - Method in class chemaxon.checkers.ComponentChecker
-
Checks if the component with index i has problem
- check(Stack<Object>) - Method in interface chemaxon.nfunk.jep.function.PostfixMathCommandI
-
Deprecated.Checks the stack.
- Check - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Mode
-
Indicates, that the structurechecker does not automatically fixes.
- check1(Molecule) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
- check1(Molecule) - Method in class chemaxon.checkers.AbsentChiralFlagChecker
-
Determines if a non chiral molecule contains a chiral flag.
- check1(Molecule) - Method in class chemaxon.checkers.AbsoluteStereoConfigurationChecker
-
Determines if all asymmetric centers have absolute stereo configuration
- check1(Molecule) - Method in class chemaxon.checkers.AbstractStructureChecker
-
This method contains the current checking mechanism.
- check1(Molecule) - Method in class chemaxon.checkers.AromaticityErrorChecker
- check1(Molecule) - Method in class chemaxon.checkers.AtropisomerChecker
- check1(Molecule) - Method in class chemaxon.checkers.AttachedDataChecker
-
Detects attached data in the molecule
- check1(Molecule) - Method in class chemaxon.checkers.BondAngleChecker
- check1(Molecule) - Method in class chemaxon.checkers.BondLengthChecker
- check1(Molecule) - Method in class chemaxon.checkers.BracketsChecker
- check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagChecker
- check1(Molecule) - Method in class chemaxon.checkers.ChiralFlagErrorChecker
-
Determines if a non chiral molecule contains a chiral flag.
- check1(Molecule) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
- check1(Molecule) - Method in class chemaxon.checkers.ComponentChecker
-
Iterates through the components and checks every component.
- check1(Molecule) - Method in class chemaxon.checkers.CoordinationSystemErrorChecker
- check1(Molecule) - Method in class chemaxon.checkers.CovalentCounterionChecker
- check1(Molecule) - Method in class chemaxon.checkers.EmptyStructureChecker
- check1(Molecule) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
-
Detects implicitizable hydrogen atoms.
- check1(Molecule) - Method in class chemaxon.checkers.EZDoubleBondChecker
- check1(Molecule) - Method in class chemaxon.checkers.IncorrectTetrahedralStereoChecker
- check1(Molecule) - Method in class chemaxon.checkers.MetalloceneErrorChecker
- check1(Molecule) - Method in class chemaxon.checkers.MissingRGroupChecker
- check1(Molecule) - Method in class chemaxon.checkers.MoleculeChargeChecker
-
Detects if molecule has charge
- check1(Molecule) - Method in class chemaxon.checkers.MultiComponentChecker
- check1(Molecule) - Method in class chemaxon.checkers.MultipleStereocenterChecker
- check1(Molecule) - Method in class chemaxon.checkers.NonStandardWedgeSchemeChecker
- check1(Molecule) - Method in class chemaxon.checkers.NonStereoWedgeBondChecker
- check1(Molecule) - Method in class chemaxon.checkers.OCRErrorChecker
- check1(Molecule) - Method in class chemaxon.checkers.OverlappingAtomsChecker
- check1(Molecule) - Method in class chemaxon.checkers.OverlappingBondsChecker
- check1(Molecule) - Method in class chemaxon.checkers.RacemateChecker
- check1(Molecule) - Method in class chemaxon.checkers.RatomChecker
- check1(Molecule) - Method in class chemaxon.checkers.ReactionChecker
- check1(Molecule) - Method in class chemaxon.checkers.RelativeStereoChecker
- check1(Molecule) - Method in class chemaxon.checkers.RgroupAttachmentErrorChecker
- check1(Molecule) - Method in class chemaxon.checkers.RgroupBridgeRatomChecker
- check1(Molecule) - Method in class chemaxon.checkers.RingStrainErrorChecker
- check1(Molecule) - Method in class chemaxon.checkers.SolventChecker
- check1(Molecule) - Method in class chemaxon.checkers.StereoCareBoxChecker
- check1(Molecule) - Method in class chemaxon.checkers.SubstructureChecker
- check1(Molecule) - Method in class chemaxon.checkers.UnbalancedReactionChecker
- check1(Molecule) - Method in class chemaxon.checkers.UnusedRGroupChecker
- check1(Molecule) - Method in class chemaxon.checkers.ValenceErrorChecker
- check1(Molecule) - Method in class chemaxon.checkers.WedgeErrorChecker
-
Deprecated.In version 15.8.3 the checker logic was replaced with the logic implemented in
Molecule
'sstereoClean()
method. - check1(Molecule) - Method in class chemaxon.checkers.WigglyBondChecker
- check1(Molecule) - Method in class chemaxon.checkers.WigglyDoubleBondChecker
- checkAndWait() - Method in class chemaxon.checkers.runner.AdvancedCheckerRunner
- checkAndWait() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Executes all the checker instances on the given molecule and returns a
List
ofStructureCheckerResult
containing all the identified problems - checkAtno(int) - Static method in class chemaxon.struc.MolAtom
-
Check if the given atomic number is positive and less then atomic type maximum value.
- checkBondConsistency() - Method in class chemaxon.struc.MoleculeGraph
- checkBondConsistency() - Method in class chemaxon.struc.SelectionMolecule
-
Empty implementation, bond consistency is not checked in case of selections.
- checkBondConsistency() - Method in class chemaxon.struc.Sgroup
- checkBonds(MolAtom) - Method in class chemaxon.struc.Sgroup
-
Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.
- checkBonds(MolAtom) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Add the bonds of the given atom to the sgroup if the given atom and the other atom of the selected bond is in the sgroup.
- checkConsistency() - Method in class chemaxon.struc.Molecule
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging. - checkConsistency() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging. - checkConsistency() - Method in class chemaxon.struc.RgMolecule
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging. - checkConsistencyInEmbeddings() - Method in class chemaxon.struc.Sgroup
-
Checks if the sgroup contains all of the child sgroup's atoms and checks consistency between atom and bond references.
- checkDocumentVersion(String, String) - Method in class chemaxon.descriptors.MDParameters
-
Checks if the document is the right version
- CheckerClassDescriptor() - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.CheckerClassDescriptor
-
Initializes an empty checker class descriptor
- CheckerClassDescriptor(String, String, String, String) - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.CheckerClassDescriptor
-
Initializes a checker class descriptor
- CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.Chemaxon's default checker configuration file name
- CheckerFixerFactory - Class in chemaxon.structurechecker.factory
-
Factory for structure checkers and structure fixers.
- CheckerFixerFactory.Builder - Class in chemaxon.structurechecker.factory
-
Builder class for
CheckerFixerFactory
. - CheckerFixerFactory.CheckerClassDescriptor - Class in chemaxon.structurechecker.factory
-
Descriptor of a checker class
- CheckerFixerFactory.ClassDescriptor - Class in chemaxon.structurechecker.factory
-
Descriptor of a class
- CheckerFixerFactory.FixerClassDescriptor - Class in chemaxon.structurechecker.factory
-
Descriptor of a fixer class
- CheckerInfo - Annotation Interface in chemaxon.checkers
-
This annotation is responsible for adding GUI based meta data for
StructureChecker
implementations - CheckerMark(MolAtom[], MolBond[], Color) - Constructor for class chemaxon.struc.MDocument.CheckerMark
- CheckerRunner - Interface in chemaxon.checkers.runner
-
The descendant of CheckerRunner interface has to provide the functionality to run
StructureChecker
instances automatically
on the given molecule and fix the problems with the associatedStructureFixer
instances.
Example:
CheckerRunner can be used directly with thecheckAndWait
method. - CheckerSeverity - Enum Class in chemaxon.checkers
-
This enum defines the constants which represent the severity of the
StructureChecker
implementations - checkFilter(String) - Static method in class chemaxon.sss.search.MolSearch
-
Checks the syntax of the filtering expression.
- checkFilter(String, File) - Static method in class chemaxon.sss.search.MolSearch
-
Checks the syntax of the filtering expression.
- checkLicense() - Method in class chemaxon.marvin.plugin.CalculatorPlugin
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ConformerPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ElementalAnalyserPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.GeometryPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.HBDAPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IonChargePlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IsoelectricPointPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.IUPACNamingPlugin
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logDPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.logPPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MajorMicrospeciesPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MolecularDynamicsPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.MSAPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.pKaPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.PolarizabilityPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.RefractivityPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Deprecated.Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.StructuralFrameworksPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TopologyAnalyserPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.calculations.TPSAPlugin
-
Checks the input molecule.
- checkMolecule(Molecule) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Checks the input molecule.
- checkRlogicRange(int, String) - Method in class chemaxon.struc.RgMolecule
-
Checks an R-logic occurrence range string for syntax errors and returns a "normalized" string.
- checkSgroupConsistency() - Method in class chemaxon.struc.Molecule
-
Checks the internal consisitency of S-groups.
- checkSgroupConsistency() - Method in class chemaxon.struc.RgMolecule
-
Checks the consistency of S-groups.
- checkSgroupConsistency() - Method in class chemaxon.struc.RxnMolecule
-
Checks the consistency of S-groups.
- checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.Sgroup
-
Checks whether the parameter s-group contains the atoms of this s-group.
- checkSgroupGraphConsistency(Sgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Checks whether the parameter s-group contain the proper atoms of this
SuperatomSgroup
. - checkType(String, String[]) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Checks result types.
- checkValence(MolAtom) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
-
Deprecated.
- checkValence(MoleculeGraph) - Method in enum class chemaxon.struc.MoleculeGraph.ValenceCheckState
-
Deprecated.
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MElectronContainer
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.graphics.MPolyline
-
Is it a valid object in the document?
- checkValidity(MDocument, Collection<MolAtom>) - Method in class chemaxon.struc.MObject
-
Is it a valid object in the document?
- CHEMAXON - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod
-
Chemaxon logP calculation method.
- chemaxon.calculations - package chemaxon.calculations
-
Contains chemical computation modules.
- chemaxon.calculations.bbb - package chemaxon.calculations.bbb
-
BBB score calculator.
- chemaxon.calculations.cip - package chemaxon.calculations.cip
- chemaxon.calculations.clean - package chemaxon.calculations.clean
- chemaxon.calculations.cnsmpo - package chemaxon.calculations.cnsmpo
-
CNS MPO score calculator.
- chemaxon.calculations.dipole - package chemaxon.calculations.dipole
- chemaxon.calculations.hydrogenize - package chemaxon.calculations.hydrogenize
- chemaxon.calculations.nmr - package chemaxon.calculations.nmr
- chemaxon.calculations.nmr.io - package chemaxon.calculations.nmr.io
- chemaxon.calculations.pka - package chemaxon.calculations.pka
- chemaxon.calculations.stereo - package chemaxon.calculations.stereo
- chemaxon.calculator - package chemaxon.calculator
- chemaxon.checkers - package chemaxon.checkers
-
Structure checkers can be used to filter drawing mistakes or special structural elements.
- chemaxon.checkers.result - package chemaxon.checkers.result
-
This package is used to identify problems found in molecules.
- chemaxon.checkers.runner - package chemaxon.checkers.runner
-
This package supports the automatic running of structure checkers.
- chemaxon.checkers.runner.configuration.reader - package chemaxon.checkers.runner.configuration.reader
-
Extension package of the automatic runner functionality.
- chemaxon.checkers.util - package chemaxon.checkers.util
- chemaxon.common.swing.io.output - package chemaxon.common.swing.io.output
- chemaxon.common.util - package chemaxon.common.util
-
Provides general utility classes.
- chemaxon.core - package chemaxon.core
- chemaxon.core.calculations.stereo - package chemaxon.core.calculations.stereo
- chemaxon.core.calculations.valencecheck - package chemaxon.core.calculations.valencecheck
- chemaxon.core.util - package chemaxon.core.util
- chemaxon.descriptors - package chemaxon.descriptors
- chemaxon.descriptors.scalars - package chemaxon.descriptors.scalars
- chemaxon.fixers - package chemaxon.fixers
-
Structure fixers can be used to fix problems identified by structure checker instances.
- chemaxon.formats - package chemaxon.formats
-
Provides miscellaneous utility classes for converting between various molecule file formats, importing structures, and compressing Molfiles.
- chemaxon.formats.factory - package chemaxon.formats.factory
- chemaxon.formats.recognizer - package chemaxon.formats.recognizer
-
Provides classes to recognize files of various file formats.
- chemaxon.jep - package chemaxon.jep
-
Chemical Terms Evaluator classes.
- chemaxon.jep.context - package chemaxon.jep.context
-
Specific chemical terms evaluation contexts.
- chemaxon.license - package chemaxon.license
-
Classes related licenses, license handling, validating, GUI and documentation.
- chemaxon.marvin - package chemaxon.marvin
-
Contains utility classes for rendering molecules.
- chemaxon.marvin.alignment - package chemaxon.marvin.alignment
-
The 3D molecular alignment package that can be used to align two or more 3D molecules onto each other.
- chemaxon.marvin.alignment.atrop - package chemaxon.marvin.alignment.atrop
-
Utilities for
AtropIsomerDetector
. - chemaxon.marvin.beans - package chemaxon.marvin.beans
-
Provides bean classes for creating Marvin based user interface.
- chemaxon.marvin.calculations - package chemaxon.marvin.calculations
-
Provides specific plugin, plugin loader and table form output implementations.
- chemaxon.marvin.collecting - package chemaxon.marvin.collecting
- chemaxon.marvin.common - package chemaxon.marvin.common
-
Contains a class for handling user settings.
- chemaxon.marvin.io - package chemaxon.marvin.io
-
Provides classes for molecule import and export through data streams.
- chemaxon.marvin.io.fieldaccess - package chemaxon.marvin.io.fieldaccess
- chemaxon.marvin.io.formats - package chemaxon.marvin.io.formats
-
Core package of any import/export module.
- chemaxon.marvin.io.formats.mdl - package chemaxon.marvin.io.formats.mdl
-
Import and export modules for MDL Molfile, SDfile, RDfile, Rxnfile and (Chemaxon) compressed molfile.
- chemaxon.marvin.io.formats.smiles - package chemaxon.marvin.io.formats.smiles
- chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer
-
Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.
- chemaxon.marvin.plugin - package chemaxon.marvin.plugin
-
Contains the classes responsible for calculator plugin loading, parameter setting, running and displaying mechanism.
- chemaxon.marvin.plugin.concurrent - package chemaxon.marvin.plugin.concurrent
-
Classes to achieve concurrent processing of calculator plugins.
- chemaxon.marvin.plugin.gui - package chemaxon.marvin.plugin.gui
-
Calculator plugin common GUI classes.
- chemaxon.marvin.services - package chemaxon.marvin.services
-
Marvin Services provides API and support for accessing remote services from Marvin Sketch and other tools.
- chemaxon.marvin.services.httpservice - package chemaxon.marvin.services.httpservice
- chemaxon.marvin.services.json - package chemaxon.marvin.services.json
- chemaxon.marvin.services.localservice - package chemaxon.marvin.services.localservice
- chemaxon.marvin.services.soap - package chemaxon.marvin.services.soap
- chemaxon.marvin.services.xmlrpcservice - package chemaxon.marvin.services.xmlrpcservice
- chemaxon.marvin.sketch - package chemaxon.marvin.sketch
-
Contains the sketcher's core classes and various sketching modes.
- chemaxon.marvin.sketch.swing.modules.documentstyle - package chemaxon.marvin.sketch.swing.modules.documentstyle
- chemaxon.marvin.swing - package chemaxon.marvin.swing
- chemaxon.marvin.uif.dialog - package chemaxon.marvin.uif.dialog
- chemaxon.marvin.util - package chemaxon.marvin.util
-
Contains some utilities for example for molecule cleaning and Swing.
- chemaxon.marvin.view - package chemaxon.marvin.view
-
Control records in MarvinView.
- chemaxon.marvin.view.swing - package chemaxon.marvin.view.swing
-
Swing support for MarvinView tables.
- chemaxon.naming - package chemaxon.naming
-
Name to Structure conversion.
- chemaxon.naming.document - package chemaxon.naming.document
-
Document to Structure (D2S) conversion.
- chemaxon.naming.document.annotate - package chemaxon.naming.document.annotate
- chemaxon.nfunk.jep.function - package chemaxon.nfunk.jep.function
- chemaxon.sss - package chemaxon.sss
- chemaxon.sss.formula - package chemaxon.sss.formula
- chemaxon.sss.screen - package chemaxon.sss.screen
-
Classes for screeening.
- chemaxon.sss.search - package chemaxon.sss.search
- chemaxon.sss.search.options - package chemaxon.sss.search.options
- chemaxon.standardizer - package chemaxon.standardizer
-
Contains packages for structure standardization.
- chemaxon.standardizer.actions - package chemaxon.standardizer.actions
-
Contains basic standardizer actions.
- chemaxon.standardizer.advancedactions - package chemaxon.standardizer.advancedactions
-
Contains advanced standardizer actions.
- chemaxon.standardizer.concurrent - package chemaxon.standardizer.concurrent
-
Contains classes for concurrent execution of standardization.
- chemaxon.standardizer.configuration - package chemaxon.standardizer.configuration
-
Contains classes for handling configurations of standardizer.
- chemaxon.standardizer.configuration.reader - package chemaxon.standardizer.configuration.reader
-
Contains classes for handling configuration deserialization.
- chemaxon.standardizer.runner - package chemaxon.standardizer.runner
-
Contains classes for executing standardization based on a configuration.
- chemaxon.struc - package chemaxon.struc
-
Provides classes for implementing and manipulating chemical structures.
Serialization of these classes is `standardized' in Marvin 5.3. - chemaxon.struc.graphics - package chemaxon.struc.graphics
-
Contains graphics MDocument elements.
- chemaxon.struc.prop - package chemaxon.struc.prop
-
Utility classes that represent molecular properties and convert molecular property Strings to values and vice versa.
- chemaxon.struc.sgroup - package chemaxon.struc.sgroup
-
S-group related classes and interfaces.
Serialization of the classes is `standardized' in Marvin 3.1.4. - chemaxon.struc.stereo - package chemaxon.struc.stereo
- chemaxon.structurechecker.factory - package chemaxon.structurechecker.factory
- chemaxon.util - package chemaxon.util
- chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
- chemaxon.util.iterator - package chemaxon.util.iterator
-
Provides iterator classes for molecules and their components.
- chemaxon.util.progress - package chemaxon.util.progress
-
Common components of Calculator APIs.
- ChemConst - Class in chemaxon.core
- ChemConst() - Constructor for class chemaxon.core.ChemConst
- ChemContext - Interface in chemaxon.jep
-
Interface of expression evaluation contexts.
- ChemContext.ProvidesFunction - Annotation Interface in chemaxon.jep
-
Repeatable annotation used on
ChemContext
implementations to declare the context functions supported by theChemContext.callContextFunction(String, List)
method. - ChemContext.ProvidesFunctionContainer - Annotation Interface in chemaxon.jep
-
Container for the repeatable
ChemContext.ProvidesFunction
annotation. - ChemicalFingerprint - Class in chemaxon.descriptors
-
The
ChemicalFingerprint
class implements topological fingerprints as a type ofMolecularDescriptor
s. - ChemicalFingerprint() - Constructor for class chemaxon.descriptors.ChemicalFingerprint
-
Creates a new, empty instance of ChemicalFingerprint without allocating internal storage.
- ChemicalFingerprint(CFParameters) - Constructor for class chemaxon.descriptors.ChemicalFingerprint
-
Creates a new instance of ChemicalFingerprint according to the parameters given.
- ChemicalFingerprint(ChemicalFingerprint) - Constructor for class chemaxon.descriptors.ChemicalFingerprint
-
Copy constructor.
- ChemicalFingerprint(String) - Constructor for class chemaxon.descriptors.ChemicalFingerprint
-
Creates a new instance of ChemicalFingerprint according to the parameters given.
- ChemJEP<C extends ChemContext> - Class in chemaxon.jep
-
Expression parser and evaluator for chemical expressions.
- ChemJEP() - Constructor for class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.Direct creation of a
ChemJEP
object will no longer be supported, use theEvaluator.compile(java.lang.String)
methods instead. - ChemJEP(Class<? extends C>) - Constructor for class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.Direct creation of a
ChemJEP
object will no longer be supported, use theEvaluator.compile(java.lang.String)
methods instead. - CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents molecules marked with "absolute stereo" flag.
- chiralCenterCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates the number of chiral centers.
- chiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Stereochemistry.chiralCenterCount()
- chiralCenters() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Determines the chiral center atoms.
- chiralCenters() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated, for removal: This API element is subject to removal in a future version.as of release 5.5, replaced by
Stereochemistry.chiralCenters()
- ChiralFlagChecker - Class in chemaxon.checkers
-
Implementation of
AbstractStructureChecker
detecting "absolute stereo flag" on molecule. - ChiralFlagChecker() - Constructor for class chemaxon.checkers.ChiralFlagChecker
-
Constructs ChiralFlagChecker instance
- ChiralFlagErrorChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting achiral molecules having a chiral flag set (absolute stereo flag). - ChiralFlagErrorChecker() - Constructor for class chemaxon.checkers.ChiralFlagErrorChecker
-
Default constructor
- CHIRALITY_M - Static variable in interface chemaxon.struc.StereoConstants
-
Axially chiral atom with M configuration.
- CHIRALITY_MASK - Static variable in interface chemaxon.struc.StereoConstants
-
Chirality mask in flags.
- CHIRALITY_P - Static variable in interface chemaxon.struc.StereoConstants
-
Axially chiral atom with P configuration.
- CHIRALITY_r - Static variable in interface chemaxon.struc.StereoConstants
-
Pseudo-asymmetric chiral atom of r configuration.
- CHIRALITY_R - Static variable in interface chemaxon.struc.StereoConstants
-
Chiral atom of R configuration.
- CHIRALITY_s - Static variable in interface chemaxon.struc.StereoConstants
-
Pseudo-asymmetric chiral atom of s configuration.
- CHIRALITY_S - Static variable in interface chemaxon.struc.StereoConstants
-
Chiral atom of S configuration.
- CHIRALITY_SUPPORT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"chiralitySupport"
. - CHIRALITYSUPPORT_ALL - Static variable in interface chemaxon.struc.StereoConstants
-
R/S shown always.
- CHIRALITYSUPPORT_ALL_POSSIBLE - Static variable in interface chemaxon.struc.StereoConstants
-
R/S shown always and highlight possible chiral centers as well.
- CHIRALITYSUPPORT_NONE - Static variable in interface chemaxon.struc.StereoConstants
-
R/S not shown for any molecule.
- CHIRALITYSUPPORT_SELECTED - Static variable in interface chemaxon.struc.StereoConstants
-
R/S shown only if chiral flag is set in molecule or the atom's enhanced stereo type is absolute.
- CIPStereoCalculator - Class in chemaxon.calculations.cip
-
Stereo calculator with the Cahn, Ingold, Prelog priority rules.
- CIPStereoDescriptorIface - Interface in chemaxon.struc
-
Cahn-Ingold-Prelog (CIP) stereodescriptor interface.
- CIPStereoDescriptorIface.CIPType - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue - Interface in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.AtropStereoIUPACValue - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.AtropStereoValue - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.AxialStereoIUPACValue - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.AxialStereoValue - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.CisTransStereoValue - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.TetrahedralStereoIUPACValue - Enum Class in chemaxon.struc
- CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue - Enum Class in chemaxon.struc
- CIPStereoRecognizer - Class in chemaxon.core.calculations.stereo
-
Detection of Cahn-Ingold-Prelog (CIP) stereo descriptors: tetrahedral, axial, cis/trans and atrop stereo features.
- CIPStereoRecognizer() - Constructor for class chemaxon.core.calculations.stereo.CIPStereoRecognizer
- CIRCULAR_RGROUP_REFERENCE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that molecule with circular R-group definition found
- CircularRGroupReferenceChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting circular R-group references. - CircularRGroupReferenceChecker() - Constructor for class chemaxon.checkers.CircularRGroupReferenceChecker
-
Initializes the checker
- CIS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoValue
-
2 dimension: The rigid part's maximal indexed ligands placed in the same half-plane according to the rigid part.
0 dimension: CIS stereo value was set on the double bond for it's maximal indexed ligands. - CIS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.CisTransStereo
-
Deprecated, for removal: This API element is subject to removal in a future version.
- CIS - Static variable in interface chemaxon.struc.StereoConstants
-
Cis double bond.
- CIS_TRANS - Static variable in interface chemaxon.struc.StereoConstants
-
Cis and trans double bond mask.
- CisDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
-
Filter for CIS double bonds.
- CisDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
- cisDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the CIS double bonds.
- CISTRANS - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPType
- CISTRANS - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.Type
-
Cis-trans stereo center.
- CISTRANS - Enum constant in enum class com.chemaxon.calculations.stereoisomers.StereoisomerSettings.StereoisomerType
-
Double bond stereoisomers.
- CisTransDoubleBondFilter - Class in com.chemaxon.calculations.stereoanal.filters.cistrans
-
Filter for cis-trans stereo centers.
- CisTransDoubleBondFilter() - Constructor for class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
- cisTransDoubleBonds() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the CIS-TRANS double bonds.
- cisTransDoubleBondsWithAttachedData() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Calculates the CIS-TRANS double bonds with attached data.
- CisTransStereoCenter - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Cis-trans stereo center implementation.
- CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Constructs a new instance of cis-trans stereo center.
- CisTransStereoCenter(AtomSelection, CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Constructs a new instance of cis-trans stereo center with attached data.
- CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Deprecated, for removal: This API element is subject to removal in a future version.
- CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Deprecated, for removal: This API element is subject to removal in a future version.
- CisTransStereoDescriptor - Class in chemaxon.struc
- CisTransStereoDescriptor(CIPStereoDescriptorIface.CIPValue.CisTransStereoValue, StereoActivePart, StereoActivePart) - Constructor for class chemaxon.struc.CisTransStereoDescriptor
- Cl - Static variable in class chemaxon.core.ChemConst
- CLASS - Static variable in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
-
Property key for Service class name as
String
- ClassDescriptor(String, String, String) - Constructor for class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor
- className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
- className - Variable in class chemaxon.structurechecker.factory.CheckerFixerFactory.ClassDescriptor
- clean(int) - Method in class chemaxon.formats.MolConverter.Builder
-
Enables cleaning.
- clean(int) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- clean(int, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Enables cleaning.
- clean(int, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- clean(int, String) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
Cleaner.clean(MoleculeGraph, int, String)
. - clean(int, String, int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Clean the specified cell.
- clean(int, String, MProgressMonitor) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor)
. - clean(MoleculeGraph, int) - Static method in class chemaxon.calculations.clean.Cleaner
-
Calculates atom coordinates.
- clean(MoleculeGraph, int, String) - Static method in class chemaxon.calculations.clean.Cleaner
-
Calculates atom coordinates.
- clean(MoleculeGraph, int, String, MProgressMonitor) - Static method in class chemaxon.calculations.clean.Cleaner
-
Calculates atom coordinates.
- Clean2DAction - Class in chemaxon.standardizer.advancedactions
-
Clean molecule graph in 2D standardizer action
- Clean2DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.Clean2DAction
-
Initializes the action with parameters
- Clean2DAction.Type - Enum Class in chemaxon.standardizer.advancedactions
-
Type of clean action (partial, full, template based or convert 3D to 2D)
- clean3d(Molecule) - Static method in class chemaxon.marvin.alignment.MMPAlignment
-
Utility for preprocessing structure for alignment.
- clean3d(Molecule, int) - Static method in class chemaxon.marvin.alignment.MMPAlignment
-
Utility for preprocessing structure for alignment.
- Clean3DAction - Class in chemaxon.standardizer.advancedactions
-
Clean molecule graph in 3D standardizer action
- Clean3DAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.Clean3DAction
-
Initializes the action with parameters
- cleanAll(int, String, MProgressMonitor, String[]) - Method in class chemaxon.marvin.view.MDocStorage
-
Clean all cells.
- Cleaner - Class in chemaxon.calculations.clean
-
Class to clean MoleculeGraphs, Molecules, SelectionMolecules and Sgroups.
- Cleaner() - Constructor for class chemaxon.calculations.clean.Cleaner
- CleanFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which cleans the molecule in 2d - CleanFixer() - Constructor for class chemaxon.fixers.CleanFixer
- CLEANING_2D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"clean2dOpts"
. - CLEANING_3D_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"clean3dOpts"
. - CLEANING_DIMENSION - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"cleanDim"
. - CLEANING_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"cleanOpts"
. - cleanupRemovedRgroupMember(MoleculeGraph, int) - Method in class chemaxon.struc.RgMolecule
-
Clean-up after R-group removal.
- CleanUtil - Class in chemaxon.marvin.util
-
Utility methods for cleaning.
- CleanUtil() - Constructor for class chemaxon.marvin.util.CleanUtil
- clear() - Method in class chemaxon.descriptors.BCUT
-
Clears the descriptor, all values are set to zero.
- clear() - Method in class chemaxon.descriptors.ChemicalFingerprint
-
Clears the fingerprint: sets all bins to store zero value.
- clear() - Method in class chemaxon.descriptors.CustomDescriptor
-
Clears the descriptor: sets all cells to store zero value.
- clear() - Method in class chemaxon.descriptors.ECFP
-
Clears the fingerprint, all values are set to zero.
- clear() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
Clears the fingerprint: sets all bins to store zero value.
- clear() - Method in class chemaxon.descriptors.ReactionFingerprint
-
Clears the fingerprint: sets all bins to store zero value.
- clear() - Method in class chemaxon.descriptors.ScalarDescriptor
-
Clears the descritor: sets its value to zero value.
- clear() - Method in class chemaxon.descriptors.ShapeDescriptor
-
Clears the fingerprint, all values are set to zero.
- clear() - Method in class chemaxon.formats.MolConverter.Builder
-
Clears all settings.
- clear() - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- clear() - Method in interface chemaxon.jep.ChemContext
-
Clears the context.
- clear() - Method in class chemaxon.jep.context.AtomContext
-
Clears the context.
- clear() - Method in class chemaxon.jep.context.MolContext
-
Clears the context.
- clear() - Method in class chemaxon.jep.context.ReactionContext
-
Clears the context.
- clear() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
-
Clears the configuration of action
- clear() - Method in class chemaxon.struc.MDocument
-
Clears the document.
- clear() - Method in class chemaxon.struc.MolAtom
-
Clear query properties, charge, and hcount.
- clear() - Method in class chemaxon.struc.Molecule
-
Clears the molecule.
- clear() - Method in class chemaxon.struc.MoleculeGraph
-
Clears the molecule.
- clear() - Method in class chemaxon.struc.MPropertyContainer
-
Clears properties.
- clear() - Method in class chemaxon.struc.MSelectionDocument
-
Clears the document.
- clear() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Clears the display.
- CLEAR - Enum constant in enum class chemaxon.standardizer.actions.AbsoluteStereoAction.Type
-
Deprecated.Remove absolute stereo
- clearAssigned() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
- clearCachedInfo(int) - Method in class chemaxon.struc.MoleculeGraph
-
Deletes the cached information depending on the given options.
- clearChangesInUserComparators() - Method in class chemaxon.sss.search.SearchOptions
-
Used in initializing searches.
- clearCheckerMarks() - Method in class chemaxon.struc.MDocument
-
Clears the checker marks
- clearComparators() - Method in class chemaxon.sss.search.MolSearch
-
Delete all comparator from the search object.
- clearExtraLabel() - Method in class chemaxon.struc.MolAtom
-
Clears the extra label.
- clearExtraLabels() - Method in class chemaxon.struc.Molecule
-
Clears extra atom labels.
- clearForImport(String) - Method in class chemaxon.struc.Molecule
-
Initializes molecule for import.
- clearForImport(String) - Method in class chemaxon.struc.MoleculeGraph
-
Clears the bonds vector, the properties, the flags, and sets the origin coordinates to 0.
- clearForImport(String) - Method in class chemaxon.struc.RgMolecule
-
Clear the edges vector and the properties.
- clearForImport(String) - Method in class chemaxon.struc.RxnMolecule
-
Clear the edges vector and the properties.
- clearHistory() - Method in class chemaxon.marvin.beans.MSketchPane
-
Reset undo queue.
- clearInactiveTasks(Standardizer) - Static method in class chemaxon.standardizer.StandardizerUtil
-
Clears the inactive tasks list.
- ClearIsotopesAction - Class in chemaxon.standardizer.actions
-
Clear isotopes standardizer action
- ClearIsotopesAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearIsotopesAction
-
Initializes the action
- clearLines() - Method in class chemaxon.struc.graphics.MTextBox
-
Clears all lines.
- clearMark() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Disables the mark (if any) on this stream.
- clearMatch() - Method in class chemaxon.sss.search.MolSearch
- clearMatch() - Method in class chemaxon.sss.search.Search
-
Clears the extra prerequisites of the structure search specified using addMatch calls.
- clearObjects() - Method in class chemaxon.struc.Molecule
- clearObjects() - Method in class chemaxon.struc.RgMolecule
- clearObjects() - Method in class chemaxon.struc.RxnMolecule
-
Deletes the graphical objects from this.
- clearObjects() - Method in class chemaxon.struc.Sgroup
-
Clears all MObject-s that belong to this S-groups.
- clearProperties() - Method in class chemaxon.struc.MolAtom
-
Removes all properties from this atom.
- clearProperties() - Method in class chemaxon.struc.MolBond
-
Removes all properties from this bond.
- clearProperties() - Method in class chemaxon.struc.Molecule
-
Clears RDfile/SDfile properties.
- clearQProps() - Method in class chemaxon.struc.MolAtom
-
Clears query props.
- clearSavedAtomIndices() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
- clearSets() - Method in class chemaxon.struc.MDocument
-
Clears the atomSets and the bondSets.
- ClearStereoAction - Class in chemaxon.standardizer.actions
-
Clear stereo standardizer action
- ClearStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ClearStereoAction
-
Initializes the action with parameters
- ClearWedgeFixer - Class in chemaxon.fixers
-
Clears wedges.
- ClearWedgeFixer() - Constructor for class chemaxon.fixers.ClearWedgeFixer
- CLIPBOARD_OPERATION_GET - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Flag that indicates an import operation
- CLIPBOARD_OPERATION_PUT - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Flag that indicates an export operation
- CLIPBOARD_OPERATION_UNDEFINED - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Undefined clipboard operation state identifier
- CLIPBOARD_ORIGIN_IS_FILE - Static variable in interface chemaxon.marvin.modules.datatransfer.MTransferable
-
Temporary property name to mark the molecule if it comes from a file via the clipboard
- clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Clipboard operation type.
- clone() - Method in class chemaxon.checkers.AbstractStructureChecker
- clone() - Method in class chemaxon.checkers.StructureCheckerDescriptor
- clone() - Method in class chemaxon.checkers.SubstructureChecker
- clone() - Method in class chemaxon.core.util.BondTable
- clone() - Method in class chemaxon.descriptors.BCUT
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.ChemicalFingerprint
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.CustomDescriptor
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.ECFP
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.MolecularDescriptor
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.ReactionFingerprint
-
Creates a copy with identical internal state.
- clone() - Method in class chemaxon.descriptors.ScalarDescriptor
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.scalars.HAcc
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.scalars.HDon
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.scalars.Heavy
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.scalars.LogD
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.scalars.LogP
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.scalars.Mass
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.scalars.TPSA
-
Creates a new instance with identical internal state.
- clone() - Method in class chemaxon.descriptors.ShapeDescriptor
- clone() - Method in class chemaxon.fixers.StructureFixerDescriptor
- clone() - Method in class chemaxon.formats.MolConverter.Builder
-
Clones the object.
- clone() - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated, for removal: This API element is subject to removal in a future version.
- clone() - Method in class chemaxon.sss.search.MolSearchOptions
- clone() - Method in class chemaxon.sss.search.SearchOptions
-
Makes an identical copy of this SearchObject.
- clone() - Method in class chemaxon.standardizer.AbstractStandardizerAction
- clone() - Method in class chemaxon.standardizer.actions.AbsoluteStereoAction
-
Deprecated.
- clone() - Method in class chemaxon.standardizer.actions.AbstractSgroupAction
- clone() - Method in class chemaxon.standardizer.actions.AliasToGroupAction
- clone() - Method in class chemaxon.standardizer.actions.AromatizeAction
- clone() - Method in class chemaxon.standardizer.actions.ClearStereoAction
- clone() - Method in class chemaxon.standardizer.actions.ConvertDoubleBondsAction
- clone() - Method in class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
- clone() - Method in class chemaxon.standardizer.actions.ExpandAction
- clone() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
- clone() - Method in class chemaxon.standardizer.actions.RemoveExplicitHydrogensAction
- clone() - Method in class chemaxon.standardizer.actions.RemoveFragmentAction
- clone() - Method in class chemaxon.standardizer.actions.ReplaceAtomsAction
- clone() - Method in class chemaxon.standardizer.actions.SetHydrogenIsotopeSymbolAction
- clone() - Method in class chemaxon.standardizer.actions.TautomerizeAction
- clone() - Method in class chemaxon.standardizer.advancedactions.Clean2DAction
- clone() - Method in class chemaxon.standardizer.advancedactions.CreateGroupAction
- clone() - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
- clone() - Method in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
- clone() - Method in class chemaxon.standardizer.advancedactions.StripSaltsAction
- clone() - Method in class chemaxon.standardizer.advancedactions.TransformAction
- clone() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
- clone() - Method in class chemaxon.standardizer.runner.BasicStandardizerRunner
- clone() - Method in class chemaxon.standardizer.StandardizerActionDescriptor
- clone() - Method in class chemaxon.struc.CTransform3D
- clone() - Method in class chemaxon.struc.DPoint3
-
Make an identical copy.
- clone() - Method in class chemaxon.struc.graphics.MAnalysisBox
- clone() - Method in class chemaxon.struc.graphics.MAssigner
- clone() - Method in class chemaxon.struc.graphics.MAtomSetPoint
- clone() - Method in class chemaxon.struc.graphics.MBracket
- clone() - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Creates a clone.
- clone() - Method in class chemaxon.struc.graphics.MEFlow
- clone() - Method in class chemaxon.struc.graphics.MEFlowBasePoint
- clone() - Method in class chemaxon.struc.graphics.MElectron
- clone() - Method in class chemaxon.struc.graphics.MElectronContainer
- clone() - Method in class chemaxon.struc.graphics.MEllipse
- clone() - Method in class chemaxon.struc.graphics.MFont
-
Creates a clone.
- clone() - Method in class chemaxon.struc.graphics.MMidPoint
- clone() - Method in class chemaxon.struc.graphics.MMidPoint.Sticky
- clone() - Method in class chemaxon.struc.graphics.MMoleculeMovie
-
Creates a clone.
- clone() - Method in class chemaxon.struc.graphics.MNameTextBox
- clone() - Method in class chemaxon.struc.graphics.MPolyline
- clone() - Method in class chemaxon.struc.graphics.MRArrow
- clone() - Method in class chemaxon.struc.graphics.MRectangle
- clone() - Method in class chemaxon.struc.graphics.MRectanglePoint
- clone() - Method in class chemaxon.struc.graphics.MRectanglePoint.Sticky
- clone() - Method in class chemaxon.struc.graphics.MRoundedRectangle
- clone() - Method in class chemaxon.struc.graphics.MTextBox
- clone() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- clone() - Method in class chemaxon.struc.MObject
-
Creates a clone.
- clone() - Method in class chemaxon.struc.MolAtom
-
Clones the atom.
- clone() - Method in class chemaxon.struc.MolBond
-
Make a copy of this object.
- clone() - Method in class chemaxon.struc.Molecule
-
Makes an identical copy of the molecule.
- clone() - Method in class chemaxon.struc.MoleculeGraph
-
Make an identical copy of the molecule.
- clone() - Method in class chemaxon.struc.MPoint
- clone() - Method in class chemaxon.struc.MPropertyContainer
-
Clones this object.
- clone() - Method in class chemaxon.struc.PageSettings
-
Clones this object.
- clone() - Method in class chemaxon.struc.prop.MBooleanProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MCollectionProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MDoubleProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MIntegerProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MObjectProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.prop.MStringProp
-
Clones the object.
- clone() - Method in class chemaxon.struc.QueryBond
-
Make a copy of this object.
- clone() - Method in class chemaxon.struc.RgMolecule
-
Clone the markush structure.
- clone() - Method in class chemaxon.struc.RxnMolecule
-
Make an identical copy of the reaction structure.
- clone() - Method in class chemaxon.struc.SelectionMolecule
-
Create a clone of this SelectionMolecule.
- clone() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Clones the S-group superatom and it's
SuperatomSgroup
as well. - clone() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Clones the SuperatomSgroup (and not the Molecule).
- cloneAsMTextBox() - Method in class chemaxon.struc.graphics.MAnalysisBox
- cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Copies the specified atoms.
- cloneAtoms(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Copies the specified atoms.
- cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.MolBond
-
Clones this bond.
- cloneBond(MolAtom, MolAtom) - Method in class chemaxon.struc.QueryBond
-
Clones this bond.
- cloneBondTable(BondTable) - Static method in class chemaxon.core.util.BondTable
-
Clones the bond table.
- cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MCollectionProp
-
Clones the object.
- cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MHashProp
-
Clones the object.
- cloneCollectionProp(Set) - Method in class chemaxon.struc.prop.MListProp
-
Clones the object.
- cloneConfiguration() - Method in class chemaxon.standardizer.configuration.StandardizerConfiguration
-
Clones the configuration
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Copies the specified atoms and bonds of this molecule to another one.
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Copies the specified atoms of this molecule graph to another one.
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
-
Copies the specified atoms of this graph to another one.
- clonecopy(int[], MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Copies the specified nodes and edges of this graph to another one.
- clonecopy(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions
-
Copies parameters to
other
. - clonecopy(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions
-
Copies all search options to other.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Makes another molecule identical to this one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Make another molecule identical to this one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
-
Make another molecule identical to this one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Make another molecule identical to this one.
- clonecopy(MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
-
Copies the clones of atoms and bonds of this graph to another one.
- clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Copies the specified atoms and bonds of this molecule graph to another one.
- clonecopyMoleculeGraphWithoutSgroups(int[], MolBond[], int, MoleculeGraph) - Method in class chemaxon.struc.SelectionMolecule
-
Copies the specified atoms and bonds of this graph to another one.
- clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.MolSearchOptions
- clonecopyOptions(SearchOptions) - Method in class chemaxon.sss.search.SearchOptions
-
Copies all search options except search type to other.
- clonecopyWithoutSgroups(Molecule) - Method in class chemaxon.struc.Molecule
-
Copies the all the contents except the S-groups into another molecule object.
- cloneDocument() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- cloneDocument() - Method in class chemaxon.struc.MSelectionDocument
-
Creates a clone.
- cloneFromSgroupCopy() - Method in class chemaxon.struc.sgroup.SgroupAtom
-
Clones the S-group superatom partially.
- cloneItem() - Method in class chemaxon.checkers.AbstractStructureChecker
- cloneItem() - Method in class chemaxon.checkers.InvalidChecker
- cloneItem() - Method in interface chemaxon.checkers.StructureChecker
-
Returns a clone of this StructureChecker instance
- cloneItem() - Method in class chemaxon.standardizer.AbstractStandardizerAction
- cloneItem() - Method in class chemaxon.standardizer.actions.InvalidStandardizerAction
- cloneItem() - Method in interface chemaxon.standardizer.StandardizerAction
-
Returns a clone of this
StandardizerAction
instance - clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.Molecule
-
Deprecated.as of Marvin 6.3.
Not supported feature. - clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.as of Marvin 6.3.
Not supported feature. - clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RgMolecule
-
Deprecated.as of Marvin 6.3.
Not supported feature. - clonelesscopy(MoleculeGraph) - Method in class chemaxon.struc.RxnMolecule
-
Deprecated.as of Marvin 6.3.
Not supported feature. - cloneMainMolecule() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- cloneMainMoleculeGraph() - Method in class chemaxon.struc.MDocument
-
Creates a clone.
- cloneMFont() - Method in class chemaxon.struc.graphics.MFont
-
Creates a clone.
- cloneMolecule() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
- cloneMolecule() - Method in class chemaxon.struc.Molecule
-
Deprecated, for removal: This API element is subject to removal in a future version.as of Marvin 2014.09.01.0 use
Molecule.clone()
instead - cloneMoleculeWithDocument() - Method in class chemaxon.struc.Molecule
-
Makes an identical copy of the molecule and its document.
- cloneMoleculeWithDocument() - Method in class chemaxon.struc.RgMolecule
- cloneMoleculeWithDocument() - Method in class chemaxon.struc.RxnMolecule
- cloneProp() - Method in class chemaxon.struc.MDocument.Prop
-
Creates a clone.
- cloneProp() - Method in class chemaxon.struc.MProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MBooleanProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MCollectionProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MDoubleProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MFontProp
- cloneProp() - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MIntegerProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MMoleculeProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MMoleculeStringProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MObjectProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MStringProp
-
Clones the object.
- cloneSets(MDocument) - Method in class chemaxon.struc.MDocument
-
Clones the atom/bond sets from doc.
- cloneSgroup(Molecule, Sgroup) - Method in class chemaxon.struc.Sgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.Sgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.DataSgroup
-
Gets a new DataSgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MulticenterSgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Gets a new Sgroup instance.
- cloneSgroup(Molecule, Sgroup, int[]) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Gets a new Sgroup instance.
- cloneStructure() - Method in class chemaxon.struc.Sgroup
-
Gets the clone of the structure stored.
- cloneTemporraryObjects(MDocument) - Method in class chemaxon.struc.MDocument
- close() - Method in class chemaxon.formats.MolConverter
-
Closes the exporter and the output stream.
- close() - Method in class chemaxon.formats.MolExporter
-
Closes the
MolExportModule
and the underlying stream. - close() - Method in class chemaxon.formats.MolImporter
-
Close the underlying input stream.
- close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Interrupts parsing.
- close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
- close() - Method in interface chemaxon.marvin.io.formats.MoleculeImporterIface
-
Close the underlying input stream.
- close() - Method in class chemaxon.marvin.io.MDocSource
-
Closes the underlying input stream(s).
- close() - Method in class chemaxon.marvin.io.MolExportModule
-
Close the stream.
- close() - Method in class chemaxon.marvin.io.MRecordImporter
-
Closes the input stream.
- close() - Method in interface chemaxon.marvin.io.MRecordReader
-
Closes the input stream.
- close() - Method in class chemaxon.naming.document.annotate.DocumentAnnotator
- close() - Method in class chemaxon.util.concurrent.marvin.MolInputProducer
-
Closes the importers.
- close() - Method in interface chemaxon.util.progress.ProgressObserver
-
Notifies that the represented task has completed (either successfully or because of a failure), and no further work will be done.
- close() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
-
Closes the output.
- close() - Method in interface com.chemaxon.util.concurrent.CloseableIterator
- close(int) - Method in class chemaxon.formats.MolConverter
-
Closes the exporter.
- close(int) - Method in class chemaxon.formats.MolExporter
-
Closes the
MolExportModule
and, optionally, the underlying stream. - close(int) - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
-
Closes the output.
- closeableIterator(Iterator<Molecule>) - Static method in class com.chemaxon.mapper.AutoMapper
-
Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator.
NOTE: the returned iterator provides the same molecule instances with maps added - closeableIterator(Iterator<Molecule>, StandardizerConfiguration, int, StandardizerRunner.ErrorHandlingPolicy, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
-
Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.
- closeableIterator(Iterator<Molecule>, AutoMapper.Options) - Static method in class com.chemaxon.mapper.AutoMapper
-
Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator using the specified number of threads for mapping.
NOTE: the returned iterator provides the same molecule instances with maps added - closeableIterator(Iterator<Molecule>, Mapper<RxnMolecule>...) - Static method in class com.chemaxon.mapper.AutoMapper
-
Returns an auto-closeable iterator that will return the mapped molecules from the specified iterator using the specified mappers for mapping.
- CloseableIterator<T> - Interface in com.chemaxon.util.concurrent
-
An auto-closeable wrapper for the
Iterator
class, so you should use this class with try-with-resources statements! - closeableResultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
-
Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.
- closeableResultIterator(Iterator<Molecule>, StandardizerConfiguration, int, String, boolean) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
-
Returns an auto-closeable iterator that will wrap the specified iterator and standardizes all molecules.
- CLOSED_FLAG - Static variable in class chemaxon.struc.graphics.MPolyline
-
Closed flag.
- closeSketcher(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Closes the sketcher window that belongs the the specified cell.
- closeWindow(int) - Method in class chemaxon.marvin.beans.MViewPane
-
Closes the detached viewer window of the specified cell.
- closeWindows() - Method in class chemaxon.marvin.beans.MarvinPane
-
Closes all windows opened by this MarvinPane.
- Cm - Static variable in class chemaxon.core.ChemConst
- CML - Static variable in class chemaxon.formats.MFileFormat
-
Chemical Markup Language.
- Cn - Static variable in class chemaxon.core.ChemConst
- CnsMpo - Class in chemaxon.calculations.cnsmpo
-
CNS MPO score calculator.
- CnsMpo.Property - Class in chemaxon.calculations.cnsmpo
-
Simple DTO that contains the predicted value and its CNS MPO score.
- CnsMpoFunction - Enum Class in chemaxon.calculations.cnsmpo
-
Base phys-chem property calculators and its score functions for CNS MPO calculation.
- Co - Static variable in class chemaxon.core.ChemConst
- codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
Add mass number information to the given code.
- COL_MOLECULE - Static variable in class chemaxon.sss.search.RGroupDecomposition
-
Constant for adding query-target column to ligand table.
- COL_SCAFFOLD - Static variable in class chemaxon.sss.search.RGroupDecomposition
-
Constant for adding scaffold column to ligand table.
- colDec - Variable in class chemaxon.descriptors.PFParameters
-
atom set colors
- collectLonePairContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
- collectLonePairsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
- collectMElectronContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
-
Collects all MElectronContainers of an atom, if the atom is part of a Molecule, which has an MDocument.
- collectMElectronsOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectron
-
Deprecated, for removal: This API element is subject to removal in a future version.
- collectRadicalContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
- collectRadicalsLikeContainersOfAtom(MolAtom) - Static method in class chemaxon.struc.graphics.MElectronContainer
- color() - Method in class chemaxon.sss.search.Decomposition
-
Colors ligands, scaffold, query and target by setting color data in atoms by calling
MolAtom.setSetSeq(int)
. - color(Molecule) - Static method in class chemaxon.sss.search.Decomposition
-
Colors a molecule by setting color data in atoms by calling
MolAtom.setSetSeq(int)
. - color(Molecule, String) - Static method in class chemaxon.sss.search.Decomposition
-
Colors a molecule by setting color data in the specified molecule property (SDF tag).
- color(String) - Method in class chemaxon.sss.search.Decomposition
-
Colors ligands, scaffold, query and target by setting color data in the specified molecule property (SDF tag).
- COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"colorScheme"
. - ColorGenerator - Class in chemaxon.marvin.util
-
A final class which provides a static access to a color distant color creator class.
- ColorGenerator() - Constructor for class chemaxon.marvin.util.ColorGenerator
- COLORING_ALL - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for setting all coloring options, currently scaffold and R-groups.
- COLORING_NONE - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for no hit coloring.
- COLORING_RGROUPS - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for R-group coloring.
- COLORING_SCAFFOLD - Static variable in class chemaxon.marvin.calculations.MarkushEnumerationPlugin
-
Constant for scaffold coloring.
- COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"cols"
. - com.chemaxon.calculations.admet - package com.chemaxon.calculations.admet
- com.chemaxon.calculations.cli - package com.chemaxon.calculations.cli
- com.chemaxon.calculations.elemanal - package com.chemaxon.calculations.elemanal
-
API of the elemental analysis functionality.
- com.chemaxon.calculations.elemanal.factory - package com.chemaxon.calculations.elemanal.factory
- com.chemaxon.calculations.gui - package com.chemaxon.calculations.gui
- com.chemaxon.calculations.solubility - package com.chemaxon.calculations.solubility
- com.chemaxon.calculations.stereoanal - package com.chemaxon.calculations.stereoanal
-
API of the Stereo Analysis Plugin.
- com.chemaxon.calculations.stereoanal.filters - package com.chemaxon.calculations.stereoanal.filters
-
Core filter classes.
- com.chemaxon.calculations.stereoanal.filters.atrop - package com.chemaxon.calculations.stereoanal.filters.atrop
-
Atrop stereo filter implementations.
- com.chemaxon.calculations.stereoanal.filters.axial - package com.chemaxon.calculations.stereoanal.filters.axial
-
Axial stereo filter implementations.
- com.chemaxon.calculations.stereoanal.filters.cistrans - package com.chemaxon.calculations.stereoanal.filters.cistrans
-
Cis-trans stereo filter implementations.
- com.chemaxon.calculations.stereoanal.filters.tetrahedral - package com.chemaxon.calculations.stereoanal.filters.tetrahedral
-
Tetrahedral stereo filter implementations.
- com.chemaxon.calculations.stereoanal.stereocenters - package com.chemaxon.calculations.stereoanal.stereocenters
-
Stereocenter implementations of Stereo Analysis API.
- com.chemaxon.calculations.stereoisomers - package com.chemaxon.calculations.stereoisomers
- com.chemaxon.common.annotations - package com.chemaxon.common.annotations
-
Provides annotations for Chemaxon classes.
- com.chemaxon.mapper - package com.chemaxon.mapper
- com.chemaxon.search - package com.chemaxon.search
-
Tools for chemical search.
- com.chemaxon.search.mcs - package com.chemaxon.search.mcs
-
Contains classes for finding the maximum common substructure (MCS) of molecular structures.
- com.chemaxon.search.mcs.buildup - package com.chemaxon.search.mcs.buildup
-
Contains MCS algorithm implementation based on the "build up" method.
- com.chemaxon.search.mcs.maxclique - package com.chemaxon.search.mcs.maxclique
-
Contains MCS algorithm implementation based on the "maximum clique" method.
- com.chemaxon.search.mcs.upperbound - package com.chemaxon.search.mcs.upperbound
-
Contains classes for calculating upper bound estimations for maximum common substructure (MCS) search.
- com.chemaxon.search.transformation - package com.chemaxon.search.transformation
- com.chemaxon.search.transformation.transformers - package com.chemaxon.search.transformation.transformers
- com.chemaxon.search.transformation.util - package com.chemaxon.search.transformation.util
- com.chemaxon.util.concurrent - package com.chemaxon.util.concurrent
-
This package contains an
Iterator
wrapper that can be used to perform calculations simultaneously on multiple elements provided by the wrapped iterator, and returns the calculation results while preserving the original order of elements. - com.chemaxon.version - package com.chemaxon.version
- combine(Collection<? extends CalculatorInputChecker>) - Static method in interface chemaxon.calculator.CalculatorInputChecker
-
Combines the given checkers into a single one that reports all errors reported by the given checkers.
- compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator
- compareAtoms(int, int) - Method in class chemaxon.sss.search.MolComparator
-
Compares atoms of indices a1 and a2.
- compareBonds(int, int) - Method in class chemaxon.sss.search.MolComparator
-
Compares bonds of indices b1 and b2.
- compareHit(int[], int) - Method in class chemaxon.sss.search.MolComparator
-
Checks a partial hit during the search algorithm.
- compareTo(TransferableDescriptor) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
-
Comparison method which uses the priority field for ordering.
- compareTo(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
- compareTo(BicycloStereoDescriptor) - Method in class chemaxon.struc.BicycloStereoDescriptor
-
Compares two bicyclostereo descriptors.
- compareTo(RgroupBridgeId) - Method in class chemaxon.struc.RgroupBridgeId
- compareTo(AttachmentPoint) - Method in class chemaxon.struc.sgroup.AttachmentPoint
-
Compares two attachment points by their order.
- compareTo(Object) - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
- compile(String) - Method in class chemaxon.jep.ChemJEP
-
Compiles the expression string to an inner structure.
- compile(String) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP
object. - compile(String, C) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP
object. - compile(String, C, ConstantTable) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP
object. - compile(String, Class<? extends C>) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP
object. - compile(String, Class<? extends C>, ConstantTable) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP
object. - compile(String, Class<? extends C>, SymbolTable) - Method in class chemaxon.jep.Evaluator
-
Deprecated, for removal: This API element is subject to removal in a future version.Use
Evaluator.compile(String, Class, ConstantTable)
instead. - COMPILE_ERROR - Static variable in class chemaxon.jep.ChemJEP
-
The compilation error message.
- COMPLETE - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
-
All atoms will be mapped
- COMPONENT - Enum constant in enum class chemaxon.struc.SgroupType
- ComponentChecker<E> - Class in chemaxon.checkers
-
Descendants of the abstract ComponentChecker class implement detect problems related to disconnected components (fragments).
- ComponentChecker(StructureCheckerErrorType) - Constructor for class chemaxon.checkers.ComponentChecker
-
Constructor to create a Structure checker instance with the given errorType.
- 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.
- componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MViewPane
- componentShown(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Shows windows if the parent frame is hidden.
- composition() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
-
Gets the elemental analysis, the relative percent composition of a pure chemical substance by element (w/w%).
- 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%).
- COMPOSITION - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
-
Result type with the string id "composition".
- COMPRESS - Static variable in class chemaxon.formats.MdlCompressor
-
Compression flag.
- compressedData - Variable in class chemaxon.descriptors.PFParameters
-
Buffer for compressed data, used in
MolecularDescriptor.toData( final int[] )
. - 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
- computeNext() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
- ConcurrentStandardizerProcessor - Class in chemaxon.standardizer
-
Performs standardization of molecules in concurrent mode.
- ConcurrentStandardizerProcessor() - Constructor for class chemaxon.standardizer.ConcurrentStandardizerProcessor
- ConcurrentStandardizerProcessor.MolTransformer - Interface in chemaxon.standardizer
-
Molecule transformer.
- CONFIDENCE - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the confidence that the structure is correct.
- config - Variable in class chemaxon.checkers.StructureCheckOptions
-
The configuration of the structure check.
- CONFIG_DIR - Static variable in class chemaxon.jep.Evaluator
-
Default directory for storing configuration files.
- CONFIG_PATH_KEY - Static variable in class chemaxon.standardizer.AbstractStandardizerAction
-
The key of configuration path parameter of the abstract action.
- configFilePath - Variable in class chemaxon.descriptors.MDParameters
-
location of the configuration file
- ConfigurationReader - Interface in chemaxon.checkers.runner.configuration.reader
-
This interface is provided for classes which can read the configuration of
CheckerRunner
. - ConfigurationUtility - Class in chemaxon.standardizer.configuration
-
Utility to manage standardizer configuration
- ConfigurationUtility() - Constructor for class chemaxon.standardizer.configuration.ConfigurationUtility
- CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"confirmTransfer"
. - CONFORMATION - Enum constant in enum class chemaxon.calculator.CalculatorTag
- CONFORMER_CONFORMERS - Enum constant in enum class chemaxon.calculator.CalculatorTag
- CONFORMER_HASVALIDCONFORMER - Enum constant in enum class chemaxon.calculator.CalculatorTag
- CONFORMER_LECONFORMER - Enum constant in enum class chemaxon.calculator.CalculatorTag
- ConformerPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for conformer calculation.
- ConformerPlugin() - Constructor for class chemaxon.marvin.calculations.ConformerPlugin
- CONJUGATED - Enum constant in enum class chemaxon.struc.BondType
-
Conjugation state of the bond.
- CONJUGATED - Static variable in class chemaxon.struc.MolBond
-
Conjugation state of the bond.
- connectedMode(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets whether the common substructures should be connected or they can consist of multiple fragments.
- connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.Molecule
- connectOriginalBondsToNewAtom(MolAtom, MolAtom, MolBond[]) - Method in class chemaxon.struc.MoleculeGraph
-
Sets the original connections to the new atom.
- connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
- connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
- connectToSgroupOfAtom(SuperatomSgroup, MolAtom) - Method in class chemaxon.struc.MObject
- CONSENSUS - Enum constant in enum class chemaxon.marvin.calculations.LogPMethod
-
Consensus model using Chemaxon and Klopman's models and the PhysProp database.
- Consent - Enum Class in chemaxon.marvin.collecting
- constant - Variable in class chemaxon.marvin.services.ServiceArgument
-
field indicates constant argument
- constants() - Method in class chemaxon.jep.ConstantTable
-
Returns an immutable set containing the names of the constants in this table.
- constantTable() - Method in class chemaxon.jep.ChemJEP
-
Returns the constant table used by this parser.
- constantTable() - Method in class chemaxon.jep.Evaluator
-
Returns the table of predefined constants (molecules, molecule sets and other constants defined in the built-in and the user-defined jep.script).
- ConstantTable - Class in chemaxon.jep
-
Immutable table of constants used in a Chemical Terms evaluator.
- ConstantTableBuilder - Class in chemaxon.jep
-
A builder for a
ConstantTable
. - contains(MElectron) - Method in class chemaxon.struc.graphics.MElectronContainer
- contains(MDocument) - Method in class chemaxon.struc.MDocument
-
Tests whether the document contains all objects of another document.
- contains(MObject) - Method in class chemaxon.struc.MDocument
-
Searches an object in the document.
- contains(MolAtom) - Method in class chemaxon.struc.MolBond
- 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(MolAtom) - Method in class chemaxon.struc.RgMolecule
-
Checks if the root structure or an R-group contains the specified node.
- contains(MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
Checks if a reactant, agent or product structure contains the specified node.
- contains(MolAtom) - Method in class chemaxon.struc.Sgroup
-
Is this atom contained by the s-group?
- contains(MolBond) - Method in class chemaxon.struc.MoleculeGraph
-
Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.
- contains(MolBond) - Method in class chemaxon.struc.RgMolecule
-
Checks if the root structure or an R-group contains the specified edge.
- contains(MolBond) - Method in class chemaxon.struc.RxnMolecule
-
Checks if a reactant, agent or product structure contains the specified edge.
- 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(String) - Method in class chemaxon.checkers.util.AtomLabels
-
Gets whether the atom labels contain the specified atom label
- contains(String) - Method in class chemaxon.checkers.util.DataExclusionList
- 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.MElectronContainer
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MMoleculeMovie
-
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.
- containsConstant(String) - Method in class chemaxon.jep.ConstantTable
-
Returns true if this table contains the given constant.
- 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
-
Deprecated, for removal: This API element is subject to removal in a future version.
- 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.
- CONTEXT - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the context of the structure recognized in the text.
- CONTEXT_INDEX - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: index of the hit inside the context.
- 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.
- contractSgroups(int) - Method in class chemaxon.struc.Molecule
-
Contracts all S-groups.
- ContractSgroupsAction - Class in chemaxon.standardizer.actions
-
Standardizer action contracting s-groups of the target molecule
- ContractSgroupsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ContractSgroupsAction
-
Initializes the action
- convert() - Method in class chemaxon.formats.MdlCompressor
-
Compression/decompression
- convert() - Method in class chemaxon.formats.MolConverter
-
Convert the next molecule.
- convert(byte[], int) - Static method in class chemaxon.formats.MdlCompressor
-
(Un)compress the specified molfile or SDfile.
- convert(byte[], int, int) - Method in class chemaxon.marvin.io.Encoding
-
Converts a byte array to a string.
- convert(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy
- convert(double, double) - Method in class chemaxon.calculations.nmr.Multiplet
-
Multiplies the parameters of this multiplet (unit conversion).
- 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(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
- convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
- convert(Molecule, Map<String, Map<?, ?>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
- convert(Molecule, Map<String, Map<?, ?>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
This method converts the entities contained in this result according to the convertData.
- convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.ModeConverter
- convert(String) - Method in class chemaxon.checkers.StructureCheckOptions.TypeConverter
- convert(String, boolean) - Method in interface chemaxon.naming.NameConverter
-
Convert a name into the corresponding structure.
- convert(String, int) - Static method in class chemaxon.formats.MdlCompressor
-
(Un)compress the specified molfile or SDfile.
- 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
- ConvertConstants - Class in chemaxon.checkers.result
-
This class contains convert relevant constants
- ConvertConstants() - Constructor for class chemaxon.checkers.result.ConvertConstants
- 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.
- ConvertDoubleBondsAction - Class in chemaxon.standardizer.actions
-
Convert double bonds standardizer action
- ConvertDoubleBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertDoubleBondsAction
-
Initializes the action with parameters
- ConvertDoubleBondsAction.Type - Enum Class in chemaxon.standardizer.actions
-
Type of conversion
- convertExplicitHToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts 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
-
Converts 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.
- convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts implicit Hydrogen atoms of the molecule to explicit.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts 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.
- 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.
- ConvertPiMetalBondsAction - Class in chemaxon.standardizer.actions
-
Convert Pi-Metal coordinate bond to coordinate bond action.
- ConvertPiMetalBondsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertPiMetalBondsAction
-
Initializes a convert pi-metal bond action
- 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(StructureCheckerResult) - Method in class chemaxon.checkers.runner.SketchCheckerRunner
-
Deprecated.This method converts the result by changing the atoms and bonds back to the original instead of the cloned ones
- 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.BracketsChecker
-
This implementation does nothing.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.CircularRGroupReferenceChecker
-
This implementation does nothing.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.MissingRGroupChecker
-
This implementation does nothing.
- convertResult(Molecule, Molecule, StructureCheckerResult, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.UnusedRGroupChecker
-
This implementation does nothing.
- 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
- convertToBondType(int) - Static method in enum class chemaxon.struc.BondType
-
Creates BondType from the given number.
- ConvertToCarbonFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which converts pseudo atoms to carbon atoms - ConvertToCarbonFixer() - Constructor for class chemaxon.fixers.ConvertToCarbonFixer
- ConvertToCrossedDoubleBondFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which sets wiggly bond to crossed double bond - ConvertToCrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToCrossedDoubleBondFixer
- ConvertToElementalFormFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which converts the isotopes to non isotope atoms - ConvertToElementalFormFixer() - Constructor for class chemaxon.fixers.ConvertToElementalFormFixer
- ConvertToEnhancedStereoAction - Class in chemaxon.standardizer.actions
-
Convert to enhanced stereo standardizer action
- ConvertToEnhancedStereoAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ConvertToEnhancedStereoAction
-
Initializes the action with parameters
- 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.
- ConvertToIonicFormFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which converts the incorrectly drawn (connected to bond, no charge) covalent counter ion representation into ionic form. - ConvertToIonicFormFixer() - Constructor for class chemaxon.fixers.ConvertToIonicFormFixer
- ConvertToPlainDoubleBondFixer - Class in chemaxon.fixers
-
Converts non-stereo double bonds with invalid stereo mark (crossed, wiggly) to plain double bonds.
- ConvertToPlainDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToPlainDoubleBondFixer
- ConvertToSingleBondFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which converts the bond to single bond. - ConvertToSingleBondFixer() - Constructor for class chemaxon.fixers.ConvertToSingleBondFixer
- 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(MPropertyContainer, String) - Static method in class chemaxon.marvin.io.MPropHandler
-
Converts the value associated with the given key in the given MPropertyContainer to string.
- convertToString(MProp, String) - Static method in class chemaxon.marvin.io.MPropHandler
-
Converts the property to text format.
- convertToString(String) - Method in class chemaxon.struc.MProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop
-
Deprecated, for removal: This API element is subject to removal in a future version.As of release 5.7, replaced by
MolExporter.convertToString(MDocument, String, int)
- convertToString(String, int) - Method in class chemaxon.struc.MProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
. - convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
. - convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MFontProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
. - convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- ConvertToWigglyDoubleBondFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which converts crossed double bond to wiggly - ConvertToWigglyDoubleBondFixer() - Constructor for class chemaxon.fixers.ConvertToWigglyDoubleBondFixer
- convertTransform(CTransform3D, boolean) - Method in class chemaxon.struc.graphics.MRectangle
- COORDDEP - Static variable in class chemaxon.struc.MProp
-
Coordinate dependent property.
- COORDINATE - Enum constant in enum class chemaxon.struc.BondType
-
Coordinate bond.
- COORDINATE - Static variable in class chemaxon.struc.MolBond
-
Coordinate bond flag.
- 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"
. - 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
-
Deprecated, for removal: This API element is subject to removal in a future version.As of Marvin 6.2, no replacement.
Not supported feature. - COPOLYMER - Enum constant in enum class chemaxon.struc.SgroupType
- COPOLYMER_ALT - Enum constant in enum class chemaxon.struc.SgroupType
- COPOLYMER_BLK - Enum constant in enum class chemaxon.struc.SgroupType
- COPOLYMER_RAN - Enum constant in enum class chemaxon.struc.SgroupType
- 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, for removal: This API element is subject to removal in a future version.
- COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated, for removal: This API element is subject to removal in a future version.
- COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated, for removal: This API element is subject to removal in a future version.
- COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated, for removal: This API element is subject to removal in a future version.
- COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Deprecated, for removal: This API element is subject to removal in a future version.since 5.3.3 has no sense
- copyOf(ShapeData) - Static method in class chemaxon.marvin.alignment.ShapeData
- CopyOptConstants - Interface in chemaxon.marvin.util
-
Deprecated, for removal: This API element is subject to removal in a future version.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(MAssigner) - Method in class chemaxon.struc.graphics.MAssigner
-
Copies the assigner properties to another assigner object.
- copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket
-
Copies line properties to another line object.
- copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow
- copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline
-
Copies line properties to another line object.
- copyProperties(MRArrow) - Method in class chemaxon.struc.graphics.MRArrow
-
Copies arrow properties to another arrow 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, for removal: This API element is subject to removal in a future version.
- COVALENT_COUNTER_ION - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that incorrectly drawn covalent counter ion had found in the molecule
- COVALENT_HYDRATION_ERROR_REMARK - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Covalent hydration error remark.
- CovalentCounterionChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting covalently bonded counterions (alkaline alcoholates, carboxylates an thio analogs). - CovalentCounterionChecker() - Constructor for class chemaxon.checkers.CovalentCounterionChecker
-
Default constructor
- covalentRadiusOf(int, int) - Static method in class chemaxon.struc.MolAtom
-
Gets the covalent radius in C-C bond length units.
- Cr - Static variable in class chemaxon.core.ChemConst
- crdMolRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
- crdSafeRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
- create() - Static method in class com.chemaxon.calculations.stereoisomers.StereoisomerSettings
-
Constructs a new
StereoisomerSettings
object with default settings. - create(byte[]) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule
-
Deprecated, for removal: This API element is subject to removal in a future version.
- create(byte[], AlignmentProperties.DegreeOfFreedomType) - Static method in class chemaxon.marvin.alignment.AlignmentMolecule
-
Deserializes an AlignmentMolecule from a byte array.
- create(ShapeData, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
- create(Molecule) - Static method in class chemaxon.marvin.alignment.Pharmacophore3D
- create(Molecule, AlignmentProperties.DegreeOfFreedomType) - Method in class chemaxon.marvin.alignment.AlignmentMoleculeFactory
- create(Molecule, Molecule) - Method in interface com.chemaxon.search.mcs.McsCustomMatcherFactory
-
Creates a custom matcher for atom and bond pairs of the given query and target structures.
- create(String) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
-
Creates a similarity calculator object according to the user defined parameters.
- create(String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Loads a plugin from the classpath based on its fully qualified name.
- create(String, int, int) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
-
Creates a similarity calculator object according to the user defined parameters.
- create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Deprecated, for removal: This API element is subject to removal in a future version.Loading plugins from plugin-specific jars is no longer supported, use
CalculatorPlugin.create(String)
instead. - createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.factory.MolecularFormulas
-
Constructs an elemental analysis from molecular formula.
- createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
-
Deprecated.Constructs an elemental analysis from molecular formula.
- createArgument(String, T) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value
- createArgument(T) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value
- createArgumentAs(String, T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value and type
- createArgumentAs(T, Class<T>) - Static method in class chemaxon.marvin.services.ServiceArgument
-
Returns a service argument based on value and type
- createAromatizedSearcher(AromatizationMethod) - Static method in class com.chemaxon.search.SimpleSearcherFactory
-
Creates a searcher that considers aromatization differences of the input molecule.
- createAromatizedSearcher(AromatizationMethod, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
-
Creates a searcher which considers aromatization according to the specified rules and initializes it with the specified search options.
- 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.
- 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.
- createBondTable(int, int) - Static method in class chemaxon.core.util.BondTable
-
Creates a new bond table for a molecule graph with the specified number of atoms and bonds.
- createBondType(int) - Static method in enum class chemaxon.struc.BondType
-
Deprecated, for removal: This API element is subject to removal in a future version.since 2014.06.04. use
BondType.convertToBondType(int)
instead. - createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil
- createChecker(String, Map<String, String>) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory
-
This method creates a requested (type represented in checkerId) StructureChecker instance with the give parameters
- createCompatible(MTextAttributes, MTextAttributes, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
- createConstantFromString(String, Class<?>) - Static method in class chemaxon.marvin.services.ServiceArgument
- createDefaultParameterPanel(Class, String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory
- createDefaultParameterPanel(String, Component) - Static method in class com.chemaxon.calculations.gui.PluginFactory
-
Creates default parameter panel based on XML config.
- 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.
- createErrorMessage(StandardizerConfiguration) - Static method in class chemaxon.standardizer.configuration.StandardizerConfiguration
-
Creates an error message based on an invalid configuration
- createExportModule() - Method in class chemaxon.formats.MFileFormat
-
Creates the export module.
- createExportModule(String) - Method in interface chemaxon.formats.factory.MolExportModuleFactory
-
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.
- createFixer(String) - Method in class chemaxon.structurechecker.factory.CheckerFixerFactory
-
This method creates a
StructureFixer
instance identified by fixerId parameters - 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
- createGroup() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
- CreateGroupAction - Class in chemaxon.standardizer.advancedactions
-
Create Group standardizer action
- CreateGroupAction(Map<String, String>) - Constructor for class chemaxon.standardizer.advancedactions.CreateGroupAction
-
Initializes a create group standardizes action
- createImporter(InputStream) - Method in interface chemaxon.formats.ImportOptions
-
Creates a
MolImporter
from the given input stream. - 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 interface chemaxon.formats.factory.MolImportModuleFactory
-
Creates the molecule import module.
- createImportModule() - Method in class chemaxon.formats.MFileFormat
-
Creates the molecule import module.
- createInDocumentAt(DPoint3, MDocument) - Static method in class chemaxon.struc.NoStructure
-
Creates a NoStructure at the given location.
- createInDocumentFrom(Molecule, MDocument) - Static method in class chemaxon.struc.NoStructure
-
Creates a NoStructure from the given component.
- createMElectronContainer(DPoint3[], MolAtom, boolean) - Static method in class chemaxon.struc.graphics.MElectronContainer
- createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated, for removal: This API element is subject to removal in a future version.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) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a menu 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, Class<?>, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a menu item 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.IsoelectricPointPlugin
-
Returns the major tautomeric form of the molecule.
- 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.
- createMol() - Method in class chemaxon.formats.MolImporter
-
Deprecated, for removal: This API element is subject to removal in a future version.As of 23.15, no replacement
- 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.
- 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() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Creates a molecule object that contains only one
SuperatomSgroup
identical to this one. - createMolecule(Molecule) - Method in class chemaxon.struc.Sgroup
-
Creates a cloned sgroup instance and a molecule object that contains only this sgroup.
- createMoleculeFromInputStream(InputStream) - Method in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Helper function to get Molecule or MacroMolecule from the given InputStream with MolImporter.
- createMoleculeIterator(Molecule[]) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
-
Creates a
MoleculeIterator
object for iterating through a molecule array (Molecule
[]). - createMoleculeIterator(Collection<Molecule>) - Static method in class chemaxon.util.iterator.MoleculeIteratorFactory
-
Creates a
MoleculeIterator
object for iterating through collection of molecules (Molecule
objects). - createMolIfNeeded() - Method in class chemaxon.marvin.io.MRecordImporter
-
Creates an empty target molecule for import if non-concurrent mode, returns
null
if concurrent mode. - createNew() - Static method in class chemaxon.marvin.calculations.HlbPlugin.Builder
-
Constructs a new HlbPlugin instance.
- createNew(Molecule) - Static method in class chemaxon.marvin.alignment.MCSAlignment.Factory
-
Constructs a new instance of ConformationAlignment class.
- createNext() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Creates identical attributes for the next section.
- createParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Creates the parameter panel.
- createPreConcatenatedAffineTransform(Graphics2D) - Method in class chemaxon.struc.graphics.MTextBoxTransformation
- createReaction(MoleculeGraph, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
-
Creates a reaction.
- createReaction(Molecule, DPoint3[], int) - Static method in class chemaxon.struc.RxnMolecule
-
Creates a reaction.
- createRecognizer() - Method in interface chemaxon.formats.factory.RecognizerFactory
-
Creates a recognizer module.
- createRecognizer() - Method in class chemaxon.formats.MFileFormat
-
Creates a recognizer module.
- createRecognizer(String) - Method in class chemaxon.formats.MFileFormat
-
Deprecated, for removal: This API element is subject to removal in a future version.as of Marvin 2014.07.21.0 use
MFileFormat.createRecognizer()
instead - createRecordReader(MolInputStream, String) - Method in interface chemaxon.formats.factory.MRecordReaderFactory
-
Creates the record reader.
- 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<StructureCheckerResult>) - Method in class chemaxon.checkers.ReactionChecker
-
This method a merged StructureCheckerResult from the
List
ofStructureCheckerResult
which contains the problems of the components in the reaction - 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<MolAtom>) - Method in class chemaxon.checkers.PseudoAtomChecker
- createResult(Molecule, List<MolBond>) - Method in class chemaxon.checkers.BondChecker
- createResult(Molecule, List<E>) - Method in class chemaxon.checkers.ComponentChecker
-
Creates a
StructureCheckerResult
from aList
containing the components. - createResultView(String, MolPanel) - Method in class com.chemaxon.calculations.gui.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.
- createSearcher(Transformer, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
-
Constructs a searcher with the specified parameters.
- createSearcherWithoutAromatization() - Static method in class com.chemaxon.search.SimpleSearcherFactory
-
Creates a searcher that does not handle aromatization.
- createSearcherWithoutAromatization(MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
-
Creates a searcher that doesn't consider aromatization.
- createSearcherWithoutAromatization(SimpleSearcher, MolSearchOptions) - Static method in class com.chemaxon.search.SimpleSearcherFactory
-
Creates a searcher with the specified search options, other parameters (query, target, etc.) are copied from the specified searcher if possible (in case of
BaseMolSearch
). - createServiceHandler() - Method in class chemaxon.marvin.services.httpservice.HTTPServiceDescriptor
- createServiceHandler() - Method in class chemaxon.marvin.services.json.JsonServiceDescriptor
- createServiceHandler() - Method in class chemaxon.marvin.services.localservice.LocalServiceDescriptor
- createServiceHandler() - Method in class chemaxon.marvin.services.ServiceDescriptor
-
Creates a new service handler for this descriptor.
- createServiceHandler() - Method in class chemaxon.marvin.services.soap.SoapServiceDescriptor
- createServiceHandler() - Method in class chemaxon.marvin.services.xmlrpcservice.XMLRPCServiceDescriptor
- createSgroupIterator() - Method in class chemaxon.util.iterator.IteratorFactory
-
Constructs an s-group iterator for the specified molecule of the factory.
- createSmolecule() - Method in class chemaxon.struc.MoleculeGraph
-
Creates a
Smolecule
represenation of this molecule. - createSpacePanel(Molecule[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Creates space panel with given molecules, creates colored surface to each molecule.
- 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) - 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) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Creates standardized molecule, the original input molecule is cloned.
- createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.ResonancePlugin
-
Deprecated, for removal: This API element is subject to removal in a future version.
- createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.calculations.TautomerizationPlugin
-
Deprecated, for removal: This API element is subject to removal in a future version.
- createStandardizedMolecule(Molecule, boolean) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Deprecated, for removal: This API element is subject to removal in a future version.
- createStatistics - Variable in class chemaxon.descriptors.MDGenerator
-
indicates if statistical data has to be gathered during generation
- createSubPanel(String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a sub-panel with a title.
- createTautomerMoleculeBasedOnDecoration(Molecule, boolean) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode
- createTopLeftConstraints() - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates GridBagConstraints for the top left component.
- createUserDefined(String, String, String, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, String, long) - Static method in class chemaxon.formats.MFileFormat
-
Creates a user-defined format descriptor.
- createUserDefined(String, List<String>, List<String>, MRecordReaderFactory, MolImportModuleFactory, MolExportModuleFactory, RecognizerFactory, Map<String, Integer>, long) - Static method in class chemaxon.formats.MFileFormat
-
Creates a user-defined format descriptor.
- createViewPanel(Molecule[]) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Creates view panel with given molecules, places molecule properties in formatted texts.
- createViewPanel(Molecule[], int, int, int, int) - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Creates view panel with given molecules, places molecule properties in formatted texts.
- createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.AtropFilter
- createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.KnownAtropFilter
-
Constructs the specified visitor implementation.
- createVisitor(Consumer<AtropStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.atrop.UnknownAtropFilter
- createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.AxialFilter
- createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.KnownAxialFilter
- createVisitor(Consumer<AxialStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.axial.UnknownAxialFilter
- createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisDoubleBondFilter
- createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.CisTransDoubleBondFilter
- createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.KnownDoubleBondFilter
- createVisitor(Consumer<CisTransStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.cistrans.TransDoubleBondFilter
- createVisitor(Consumer<StereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.HasAttachedDataFilter
- createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.KnownResolvedTetrahedralFilter
- createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.RacemicTetrahedralFilter
- createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.TetrahedralFilter
- createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnknownResolvedTetrahedralFilter
- createVisitor(Consumer<TetrahedralStereoCenter>) - Method in class com.chemaxon.calculations.stereoanal.filters.tetrahedral.UnresolvedTetrahedralFilter
- createVisitor(Consumer<T>) - Method in class com.chemaxon.calculations.stereoanal.filters.AbstractStereoFilter
-
Constructs the specified visitor implementation.
- 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
- CROSSED - Enum constant in enum class chemaxon.standardizer.actions.ConvertDoubleBondsAction.Type
-
Crossed double bond type
- CROSSED_DOUBLE_BOND - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that crossed double bond had found in the molecule
- 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
-
Deprecated, for removal: This API element is subject to removal in a future version.
- CrossedDoubleBondFixer() - Constructor for class chemaxon.fixers.CrossedDoubleBondFixer
-
Deprecated.
- CROSSLINK - Enum constant in enum class chemaxon.struc.SgroupType
- Cs - Static variable in class chemaxon.core.ChemConst
- 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.
- cssr - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
- CSSR - Enum constant in enum class chemaxon.sss.search.options.SetOfSmallestRingsOption
-
Complete set of smallest rings.
- CSV - Static variable in class chemaxon.formats.MFileFormat
- ctab - Variable in class chemaxon.struc.MoleculeGraph
-
Connection table.
- CTransform3D - Class in chemaxon.struc
-
3D transformation matrix.
- CTransform3D() - Constructor for class chemaxon.struc.CTransform3D
-
Constructs an identity transformation.
- CTransform3D(CTransform3D) - Constructor for class chemaxon.struc.CTransform3D
-
Copy constructor.
- CTSPECIFIC_H - Static variable in class chemaxon.struc.MolAtom
-
Deprecated.As of Marvin 5.11
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
-
Deprecated.As of Marvin 6.1,
Usage:In the specified methods the CIS|TRANS or CIS|TRANS|CTUNSPEC values are used instead.
- CTUNSPEC - Static variable in interface chemaxon.struc.StereoConstants
-
Unspecified double bond.
- Cu - Static variable in class chemaxon.core.ChemConst
- CubeRecognizer - Class in chemaxon.formats.recognizer
-
Deprecated, for removal: This API element is subject to removal in a future version.No longer used, will be removed.
- CubeRecognizer() - Constructor for class chemaxon.formats.recognizer.CubeRecognizer
-
Deprecated.
- currentBond - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
Current bond pointer of the iterator.
- currentMetricIndex - Variable in class chemaxon.descriptors.MDParameters
-
index of the parametrized metric currently in use
- cursorDown(boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Move the cursor down.
- cursorLeft(boolean) - Method in class chemaxon.struc.graphics.MTextBox
- cursorRight(boolean) - Method in class chemaxon.struc.graphics.MTextBox
- 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.
- CUSTOM_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
custom name property
- CustomDescriptor - Class in chemaxon.descriptors
-
The
CustomDescriptor
class implements a generic molecular descriptor class which supports third party or use defined descriptors. - CustomDescriptor() - Constructor for class chemaxon.descriptors.CustomDescriptor
-
Creates a new, empty instance of CustomDescriptor without allocating internal storage for its value.
- CustomDescriptor(int, int) - Constructor for class chemaxon.descriptors.CustomDescriptor
-
Creates a new, empty instance of CustomDescriptor and allocates internal storage to store values.
- CustomDescriptor(CDParameters) - Constructor for class chemaxon.descriptors.CustomDescriptor
-
Creates a new instance of CustomDescriptor according to the parameters given.
- CustomDescriptor(CustomDescriptor) - Constructor for class chemaxon.descriptors.CustomDescriptor
-
Copy constructor.
- CustomDescriptor(String) - Constructor for class chemaxon.descriptors.CustomDescriptor
-
Creates a new instance of CustomDescriptor according to the parameters given.
- CustomFunction - Interface in chemaxon.jep
-
Base interface for custom Chemical Terms functions.
- CUSTOMIZATION_ENABLED - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"customizationEnabled"
. - customMatching(McsCustomMatcherFactory) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets the factory to be used to create a custom matcher.
- CXON - Static variable in class chemaxon.formats.MFileFormat
-
Chemaxon Object Notation.
- 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.
D
- D2S - Static variable in class chemaxon.formats.MFileFormat
-
Any document format recognized by Document to Structure (doc, odt, ...).
- data - Variable in class chemaxon.descriptors.MDParameters
-
buffer for external data format generation, used in
MolecularDescriptor.toData()
- DATA - Enum constant in enum class chemaxon.struc.SgroupType
- DATA_COLLECTION_CONSENT - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- DATA_COLLECTION_SERVER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
- DataExclusionList - Class in chemaxon.checkers.util
-
A list of Strings to be excluded by
AttachedDataChecker
. - DataExclusionList(String) - Constructor for class chemaxon.checkers.util.DataExclusionList
- DataSgroup - Class in chemaxon.struc.sgroup
-
Data Sgroup.
- DataSgroup(Molecule) - Constructor for class chemaxon.struc.sgroup.DataSgroup
-
Creates a Data S-group with the specified parent.
- DataSgroup(DataSgroup, Molecule, Sgroup) - Constructor for class chemaxon.struc.sgroup.DataSgroup
-
Copy constructor.
- DataSgroup(DataSgroup, Molecule, Sgroup, int[]) - Constructor for class chemaxon.struc.sgroup.DataSgroup
-
Copy constructor.
- DataSgroupCheckerResult - Class in chemaxon.checkers.result
-
A descendant of
DefaultStructureCheckerResult
for identifyingSgroup
problems. - DataSgroupCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, List<Sgroup>, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DataSgroupCheckerResult
-
Constructor which initialize all the properties.
- date() - Element in annotation interface com.chemaxon.common.annotations.SubjectToRemoval
- Db - Static variable in class chemaxon.core.ChemConst
- DBS_ALL - Static variable in interface chemaxon.struc.StereoConstants
-
Double bond stereo checking for all double bonds.
- DBS_MARKED - Static variable in interface chemaxon.struc.StereoConstants
-
Double bond stereo checking for marked double bonds only.
- DBS_NONE - Static variable in interface chemaxon.struc.StereoConstants
-
No double bond stereo checking.
- DEAROM_GENERAL - Static variable in class chemaxon.struc.MoleculeGraph
-
General dearomatization.
- DEAROM_HUCKELCHECK - Static variable in class chemaxon.struc.MoleculeGraph
-
Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
- DEAROM_HUCKELCHECK_EX - Static variable in class chemaxon.struc.MoleculeGraph
-
Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
- DEAROMATIZATION_GENERAL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
General dearomatization method.
- DEAROMATIZATION_HUCKEL - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
Dearomatization method with Hückel rule checking.
- DEAROMATIZATION_HUCKEL_EX - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
Dearomatization method with Hückel rule checking.
- dearomatize() - Method in class chemaxon.struc.Molecule
-
Dearomatize molecule.
- dearomatize() - Method in class chemaxon.struc.MoleculeGraph
-
Dearomatize molecule.
- dearomatize(int) - Method in class chemaxon.struc.MoleculeGraph
-
Dearomatize molecule.
- DearomatizeAction - Class in chemaxon.standardizer.actions
-
Dearomatization standardizer action
- DearomatizeAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DearomatizeAction
-
Initializes the action
- DearomatizeFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which converts the aromatic rings in the molecule into Kekule representation. - DearomatizeFixer() - Constructor for class chemaxon.fixers.DearomatizeFixer
- DEBUG - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"debug"
. - Debye - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit
-
Debye unit.
- DEBYE_TO_EA - Static variable in class chemaxon.calculations.dipole.DipoleResult
-
Debye to eA conversion upon multiplication.
- decForm - Variable in class chemaxon.descriptors.MDParameters
-
to format floating point output
- DECLINE - Enum constant in enum class chemaxon.marvin.collecting.Consent
- decode(String, MFont, MTextAttributes.MFontCreator) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Reads attributes of the next section from a string.
- decode(String, MFont, MTextAttributes.MFontCreator, double) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Reads attributes of the next section from a string.
- decodeHIsotopeMass(int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
Extract H isotope information from the given Chemaxon compressed mol format code of the atom.
- Decomposition - Class in chemaxon.sss.search
-
Class storing
RGroupDecomposition
results. - Decomposition(Molecule, Molecule, int[][], Molecule[], Molecule) - Constructor for class chemaxon.sss.search.Decomposition
-
Constructor.
- decompress(byte[]) - Method in class chemaxon.descriptors.PharmacophoreFingerprint
-
Uncompresses input byte array and stores the uncompressed array in params.data.
- DECOMPRESS - Static variable in class chemaxon.formats.MdlCompressor
-
Decompression.
- decorateSubPanel(JPanel, String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates border and title for a panel.
- decorateTautomerRegions(Molecule, int, OptionalInt) - Method in enum class chemaxon.sss.search.options.TautomerTransformationMode
- decQProp(String) - Method in class chemaxon.struc.MolAtom
-
Decrements the value of a query property.
- decValenceProp() - Method in class chemaxon.struc.MolAtom
-
Decrements the value of the valence property.
- DEF_IONICSTRENGTH - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
The default ionic strength of the pKa calculation models (small and large).
- DEF_MAXIONS - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
The default value of the number of ionizable atoms to consider.
- DEF_TEMPERATURE - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
The default temperature in Kelvins.
- Default - Enum constant in enum class chemaxon.marvin.io.MolImportModule.PreferredView
- DEFAULT - Enum constant in enum class chemaxon.descriptors.MetricsType
- DEFAULT - Enum constant in enum class chemaxon.formats.GeneralExportOptions.AromatizationMethod
-
No aromatization.
- DEFAULT - Enum constant in enum class chemaxon.formats.GeneralExportOptions.HydrogenizeOption
-
No change in hydrogens.
- DEFAULT - Enum constant in enum class chemaxon.sss.search.options.HaltOnErrorOption
-
Default error handling.
- DEFAULT - Static variable in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.default factory id
- DEFAULT - Static variable in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
-
The default options: both
ValenceCheckOptions.isLocalAromatic()
andValenceCheckOptions.isTraditionalNitrogensAllowed()
return true. - DEFAULT - Static variable in class chemaxon.marvin.io.Encoding
-
The system's default encoding.
- DEFAULT - Static variable in class chemaxon.standardizer.StandardizerActionFactory
-
default factory id
- DEFAULT - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Default attributes object.
- DEFAULT - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory
-
default factory id
- DEFAULT_ARROW_HEAD_LENGTH - Static variable in class chemaxon.struc.graphics.MPolyline
-
Default arrow head length.
- DEFAULT_ARROW_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline
-
Default arrow head width.
- DEFAULT_ASYMMETRY_FACTOR - Static variable in class chemaxon.descriptors.MDParameters
- DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.CFParameters
- DEFAULT_BITS_SET - Static variable in class chemaxon.descriptors.RFParameters
- DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.CFParameters
- DEFAULT_BOND_COUNT - Static variable in class chemaxon.descriptors.RFParameters
- DEFAULT_CACHE_SIZE - Static variable in class com.chemaxon.mapper.AutoMapper
-
default cache size
- DEFAULT_CACHE_SIZE_PROPERTY - Static variable in class com.chemaxon.mapper.AutoMapper
-
cache size property key
- DEFAULT_CHECKERS_CONFIG_PATH - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
-
path to default checker configuration list
- DEFAULT_CONFIG_FILE - Static variable in class com.chemaxon.calculations.gui.PluginFactory
-
The default config file name.
- DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.Chemaxon's default checker configuration path
- DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.standardizer.StandardizerActionFactory
-
Chemaxon's default standardizer action configuration path
- DEFAULT_CONFIGURATION_PATH - Static variable in class chemaxon.structurechecker.factory.CheckerFixerFactory
-
Chemaxon's default checker configuration path
- DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.runner.configuration.reader.XMLBasedConfigurationReader
-
The default location of Chemaxon standard checker runner configuration
- DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.Chemaxon's default checker configuration file schema path
- DEFAULT_CONFIGURATION_SCHEMA - Static variable in class chemaxon.standardizer.StandardizerActionFactory
-
Chemaxon's default standardizer action configuration file schema path
- DEFAULT_DIAMETER - Static variable in class chemaxon.descriptors.ECFPParameters
- DEFAULT_DISSIMILARITY_THRESHOLD - Static variable in interface chemaxon.sss.SearchConstants
-
Default threshold value for similarity search.
- DEFAULT_EQUILIBRIUM_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline
-
Default equilibrium head width.
- DEFAULT_FUZZINESS_FACTOR - Static variable in class chemaxon.descriptors.PFParameters
- DEFAULT_FUZZY_CUTOFF - Static variable in class chemaxon.descriptors.PFParameters
- DEFAULT_FUZZY_LOWER_BOUND - Static variable in class chemaxon.descriptors.PFParameters
- DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.CFParameters
-
default values for parameters
- DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.ECFPParameters
-
default values for parameters
- DEFAULT_LENGTH - Static variable in class chemaxon.descriptors.RFParameters
-
default values for parameters
- DEFAULT_LOWER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters
-
default values for parameters
- DEFAULT_MAX_CONSIDERED_RING_SIZE - Static variable in class com.chemaxon.search.mcs.McsSearchOptions
-
Default value for
McsSearchOptions.Builder.maxConsideredRingSize(int)
. - DEFAULT_MAX_CROSS_SIZE - Static variable in class chemaxon.struc.graphics.MPolyline
-
Default maximum cross size.
- DEFAULT_OPTIONS - Static variable in interface chemaxon.struc.sgroup.Expandable
-
Default expansion/contraction options.
- DEFAULT_OUTPUT_PRECISION - Static variable in class chemaxon.descriptors.MDParameters
- DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.HBParameters
-
default values for parameters
- DEFAULT_PH - Static variable in class chemaxon.descriptors.scalars.LDParameters
- DEFAULT_PRIORITY - Static variable in class chemaxon.fixers.StructureFixerDescriptor
-
the default priority value
- DEFAULT_RANDOM_SEED - Static variable in class com.chemaxon.search.mcs.MaxCommonSubstructure
-
Default random seed.
- DEFAULT_RECURSION_LEVEL - Static variable in class chemaxon.sss.screen.HashCode
- DEFAULT_RESOLUTION - Static variable in class chemaxon.descriptors.PFParameters
-
default values
- DEFAULT_RETROSYNTHETIC_HEAD_WIDTH - Static variable in class chemaxon.struc.graphics.MPolyline
-
Default retrosynthetic head width.
- DEFAULT_RLOGIC_RANGE - Static variable in class chemaxon.struc.RgMolecule
-
Default R-logic range.
- DEFAULT_SALT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction
-
Default salt dictionary file path.
- DEFAULT_SAMPLING_ACCURACY - Static variable in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Default for parameter
AtropIsomerDetector.setSamplingAccuracy(int)
. - DEFAULT_SAVE_FORMAT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"defaultSaveFormat"
. - DEFAULT_SCALE_FACTOR - Static variable in class chemaxon.descriptors.MDParameters
-
constants, default parameter values
- DEFAULT_SEARCHTYPE - Static variable in interface chemaxon.sss.SearchConstants
-
Default search type equals SUBSTRUCTURE.
- DEFAULT_SOLVENT_DICTIONARY_PATH - Static variable in class chemaxon.standardizer.advancedactions.RemoveSolventsAction
-
Default solvent dictionary file path.
- DEFAULT_STANDARDIZERS_CONFIG_PATH - Static variable in interface chemaxon.standardizer.configuration.reader.StandardizerConfigurationReader
-
path to default standardizer action configuration list
- DEFAULT_STEP_SIZE - Static variable in class chemaxon.descriptors.scalars.LDParameters
- DEFAULT_SUPERSCRIPT_DELTAY - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Default value of the y shift attribute in superscripts
- DEFAULT_SUPERSCRIPT_SCALE - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Default value of the font scale attribute in superscripts
- DEFAULT_SUPERSCRIPT_SUBLEVEL - Static variable in class chemaxon.struc.graphics.MTextAttributes
-
Default value of the superscript level attribute in superscripts
- DEFAULT_TAG_NAME - Static variable in class chemaxon.jep.Evaluator
-
Default SDFile tag to store the evaluation result.
- DEFAULT_THICKNESS - Static variable in class chemaxon.struc.graphics.MPolyline
-
Default line thickness.
- DEFAULT_TIMEOUT_LIMIT - Static variable in class chemaxon.sss.search.SearchOptions
- DEFAULT_TOOL - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"defaultTool"
. - DEFAULT_UNGROUP - Static variable in class chemaxon.struc.Molecule
-
Do not ungroup and do not expand S-group's children.
- DEFAULT_UPPER_BOUND - Static variable in class chemaxon.descriptors.scalars.LDParameters
- DEFAULT_USER_CHECKER_FILENAME - Static variable in interface chemaxon.checkers.runner.configuration.reader.ConfigurationReader
-
Default user defined checker file name for fallback.
- DEFAULT_VALUE - Static variable in class chemaxon.core.util.BondTable
-
The default (null) value in the matrix.
- DEFAULT_WEIGHT - Static variable in class chemaxon.descriptors.MDParameters
- DEFAULT_XML_CONFIG - Static variable in class chemaxon.descriptors.PFParameters
- defaultCategories() - Static method in class com.chemaxon.calculations.solubility.SolubilityCategories
-
Creates default categories.
- DefaultExternalStructureCheckerResult - Class in chemaxon.checkers.result
-
This descendant of
DefaultStructureCheckerResult
also implements theExternalStructureCheckerResult
interface thus providing a default implementation base class for external structure checkers' results. - DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
-
Constructor which initialize all the properties.
- DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
- DefaultExternalStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule, String, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
-
Constructor which initialize all the properties.
- DefaultPluginWorkUnit - Class in chemaxon.marvin.plugin.concurrent
-
Work unit performing plugin calculation and returning the cached results.
- DefaultPluginWorkUnit(CalculatorPluginOutput<?>, boolean) - Constructor for class chemaxon.marvin.plugin.concurrent.DefaultPluginWorkUnit
-
Constructor.
- DefaultSolubilityCategory - Enum Class in com.chemaxon.calculations.solubility
-
Default solubility categories.
- DefaultStructureCheckerResult - Class in chemaxon.checkers.result
-
This class is the default implementation of
StructureCheckerResult
- DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
- DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, StructureCheckerErrorType, Molecule, String, String, String, String, Icon, int) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
-
Constructor which initialize all the properties.
- DefaultStructureCheckerResult(StructureChecker, List<MolAtom>, List<MolBond>, Molecule) - Constructor for class chemaxon.checkers.result.DefaultStructureCheckerResult
-
Constructor which initialize all the properties.
- defaultWeight - Variable in class chemaxon.descriptors.MDParameters
-
value for all missing weight parameters
- dehydrogenize(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Deprecated, for removal: This API element is subject to removal in a future version.
Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)
with parameterMolAtom.ALL_H
does the same. - deleteAllUserComparators() - Method in class chemaxon.sss.search.SearchOptions
-
Deletes all comparator added by the user.
- deleteChar() - Method in class chemaxon.struc.graphics.MTextBox
-
Removes the character under the cursor.
- deleteCharBackward() - Method in class chemaxon.struc.graphics.MTextBox
-
Removes the character before the cursor (backspace).
- deleteUserComparator(MolComparator) - Method in class chemaxon.sss.search.SearchOptions
-
Deletes a given user defined comparator if found.
- density - Variable in class chemaxon.descriptors.MDGenerator
- DENY_IF_NOT_SPECIFIED - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
- description() - Element in annotation interface chemaxon.checkers.CheckerInfo
-
Returns the description of the checker
- description() - Element in annotation interface chemaxon.fixers.FixerInfo
-
Returns the description of the fixer.
- description() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
-
Returns the description of the action
- description() - Method in enum class com.chemaxon.calculations.solubility.DefaultSolubilityCategory
- description() - Method in class com.chemaxon.calculations.solubility.SolubilityCategories.UndefinedSolubilityCategory
- description() - Method in interface com.chemaxon.calculations.solubility.SolubilityCategory
-
Description.
- DESCRIPTION - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
description of checker
- DESCRIPTION - Static variable in class chemaxon.fixers.StructureFixerDescriptor
-
description of fixer
- DESCRIPTION - Static variable in class chemaxon.marvin.services.ServiceDescriptor
-
Property key for Service description as
String
- DESCRIPTION - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
-
description of action
- DESCRIPTOR_URI - Static variable in class chemaxon.marvin.services.json.JsonServiceDescriptor
-
Property key for Service descriptor as
String
- DescriptorGenerator - Class in chemaxon.descriptors
-
Simple class for generating molecular descriptors (fingerprints).
- DescriptorGenerator(String) - Constructor for class chemaxon.descriptors.DescriptorGenerator
-
Creates a new instance using the given descriptor type with its default configuration parameters.
- DescriptorGenerator(String, String) - Constructor for class chemaxon.descriptors.DescriptorGenerator
-
Creates a new instance using the given descriptor type with the given XML configuration.
- descrType - Variable in class chemaxon.descriptors.CDParameters
-
descriptor type
- descrValue - Variable in class chemaxon.descriptors.ScalarDescriptor
-
descriptor value
- desiredLength(int, int, int, int) - Static method in class chemaxon.struc.MolBond
-
Desired length of a bond between two atoms in Angstroms.
- destroySketcher() - Method in class chemaxon.marvin.beans.MViewPane
-
Closes all detached sketcher windows.
- DETACH - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"detach"
. - DETACHABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"detachable"
. - detectRecordPositions(IntVector) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Deprecated.
- detectRecordPositions(IntVector) - Method in interface chemaxon.marvin.io.MRecordReader
-
Deprecated.
- determinant() - Method in class chemaxon.struc.CTransform3D
-
Computes the determinant of the matrix.
- determinant2D() - Method in class chemaxon.struc.CTransform3D
-
Computes the determinant of the 2D matrix.
- determineArrowDistance(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
-
Project the point (x,y,z) to the line of the reaction arrow 'ar'.
- determinePosition(DPoint3, boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Deprecated, for removal: This API element is subject to removal in a future version.use
MTextBox.determinePosition(Graphics, DPoint3, boolean)
in case you have a special graphics context to be used for font calculations. - determinePosition(Graphics, DPoint3, boolean) - Method in class chemaxon.struc.graphics.MTextBox
-
Determines the character index based on the passed view coordinate.
- determineType(double, double, double) - Method in class chemaxon.struc.RxnMolecule
-
Determines whether a point should be in a reactant, in a product or in an agent.
- determineType(double, double, double, DPoint3[]) - Static method in class chemaxon.struc.RxnMolecule
-
Determines whether a point should be in a reactant, in a product or in an agent.
- DICE - Enum constant in enum class chemaxon.descriptors.MetricsType
- DihedralRotator - Class in chemaxon.marvin.alignment
-
Rotates a dihedral in a 3D molecule
- DihedralRotator(Molecule) - Constructor for class chemaxon.marvin.alignment.DihedralRotator
-
creates a rotator object
- DihedralScanListener - Interface in chemaxon.marvin.alignment.atrop
-
Callback to track dihedral scan steps.
- DihedralScanResult - Class in chemaxon.marvin.alignment.atrop
-
Results of a dihedral scan.
- DihedralScanResult(BondInfo) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanResult
-
Construct for a dihedral.
- dihedralScanStep(BondInfo, DihedralScanStep, Molecule, Molecule) - Method in interface chemaxon.marvin.alignment.atrop.DihedralScanListener
-
Called when a dihedral scan step is performed.
- DihedralScanStep - Class in chemaxon.marvin.alignment.atrop
-
One step in a dihedral scan.
- DihedralScanStep(double, double) - Constructor for class chemaxon.marvin.alignment.atrop.DihedralScanStep
-
Construct.
- DIM_MASK - Static variable in class chemaxon.struc.MoleculeGraph
-
Dimension bits in flags.
- DIPOLE - Enum constant in enum class chemaxon.calculator.CalculatorTag
- DipoleCalculator - Class in chemaxon.calculations.dipole
-
Calculates the components of the dipole vector.
- DipoleCalculator.Builder - Class in chemaxon.calculations.dipole
-
Builder class for dipole moment calculation.
- DipoleResult - Class in chemaxon.calculations.dipole
-
Dipole moment calculation result.
- DipoleResult(double, double, double, DipoleResult.Unit, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult
-
Constructor.
- DipoleResult(double, double, double, Molecule) - Constructor for class chemaxon.calculations.dipole.DipoleResult
-
Constructor.
- DipoleResult.Unit - Enum Class in chemaxon.calculations.dipole
-
Dipole moment units.
- dirty - Variable in class chemaxon.sss.search.SearchOptions
-
This flag is set to true whenever any of the options change.
- DISABLE_ACCELERATOR - Static variable in class chemaxon.marvin.swing.MAction
-
Disables the keyboard shortcut while still displaying its name in the menu.
- DISABLE_SPECIAL_NODES - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"disableSpecialNodes"
. - disableNewEmfGenerator() - Static method in class chemaxon.util.ImageExportUtil
-
Disables the new .NET based EMF generator.
- Discarded - Enum constant in enum class chemaxon.checkers.StructureCheckOptions.Type
-
Indicates, that the structure checker puts invalid structures to the discarded file.
- discardedPath - Variable in class chemaxon.checkers.StructureCheckOptions
-
The path of the invalid/unfixable output structures
- DisconnectMetalAtomsAction - Class in chemaxon.standardizer.actions
-
Disconnect metal atoms standardizer action
- DisconnectMetalAtomsAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.DisconnectMetalAtomsAction
-
Initializes the disconnect metal atoms action
- DISPLAY_QUALITY - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Deprecated, for removal: This API element is subject to removal in a future version.Deprecated since Marvin 6.4. No settings is used intead of this, only High Quality exists from now on.
- displayInMarvinSpace - Variable in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Display in MarvinSpace is enabled or not.
- DISSIMILARITY_PROPERTY_NAME - Static variable in interface chemaxon.sss.SearchConstants
-
Name of the mrv/sdf property which stores the dissimilarity values.
- distance(DPoint3) - Method in class chemaxon.struc.DPoint3
-
Calculates the distance between two points.
- distance2D(DPoint3) - Method in class chemaxon.struc.DPoint3
-
Calculates the distance between two points in the XY plane.
- DistanceBasedMetalloceneFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which converts incorrectly drawn metallocenes into multicenter based coordinate bond representation. - DistanceBasedMetalloceneFixer() - Constructor for class chemaxon.fixers.DistanceBasedMetalloceneFixer
- distanceCount(int, int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Counts the given value in a row of the distance matrix.
- distanceDegree(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the distance degree of an atom, which is the sum of the corresponding row values in the distance matrix.
- distanceFrom(double, double) - Method in class chemaxon.struc.MObject
-
Gets the 2D distance from the specified point.
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Gets the 2D distance from the specified point.
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MEFlow
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MElectronContainer
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MMoleculeMovie
-
Gets the 2D distance from the specified point.
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MPolyline
-
Gets the 2D distance from the specified point.
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.graphics.MRectangle
-
Gets the 2D distance from the specified point.
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MObject
-
Gets the 2D distance from the specified point.
- distanceFrom(double, double, CTransform3D) - Method in class chemaxon.struc.MPoint
-
Gets the 2D distance from the specified point.
- distanceFrom(MoleculeGraph, double, double, CTransform3D) - Static method in class chemaxon.struc.graphics.MChemicalStruct
-
Gets the 2D distance from the specified point.
- DIVALENT - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
-
Divalent radical center.
- DIVALENT_SINGLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
-
Divalent radical center with singlet electronic configuration.
- DIVALENT_TRIPLET - Enum constant in enum class chemaxon.struc.AtomProperty.Radical
-
Divalent radical center with triplet electronic configuration.
- DNA - Static variable in class chemaxon.formats.MFileFormat
-
DNA sequence.
- DO_NOT_FIX - Enum constant in enum class chemaxon.checkers.FixMode
-
on problem do nothing
- doAction(ActionEvent) - Method in class chemaxon.marvin.swing.MAction
-
Performs a custom action.
- DOC_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: name of the principal author(s) of a document.
- DOC_CREATION_DATE - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the date on which the document was created.
- DOC_LAST_AUTHOR - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: name of the last (most recent) author of a document.
- DOC_PATENT_ASSIGNEES - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the assignees of the patent, separated by newline characters.
- DOC_PATENT_ID - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the patent identifier.
- DOC_PATENT_INVENTORS - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the inventors of the patent, separated by newline characters.
- DOC_PATENT_IPC - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the IPC classification(s) for the patent, separated by newline characters.
- DOC_PATENT_IPCR - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the IPCR classification(s) for the patent, separated by newline characters.
- DOC_TITLE - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the title of the document.
- docProduced(MDocStorage, MDocument, int) - Method in interface chemaxon.marvin.view.MDocStorage.Listener
-
Document retrieved from source.
- document - Variable in class chemaxon.descriptors.MDParameters
-
contains the XML document
- DOCUMENT - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: the file name of the source document.
- DocumentAnnotator - Class in chemaxon.naming.document.annotate
-
Generate a chemically annotated HTML view of a document.
- DocumentAnnotator(File) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
-
Constructs a DocumentAnnotator to annotate the given document file.
- DocumentAnnotator(InputStream) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
-
Constructs a DocumentAnnotator to annotate the given document.
- DocumentAnnotator(InputStream, DocumentAnnotator.DocumentType) - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotator
-
Constructs a DocumentAnnotator to annotate the given document.
- DocumentAnnotator.DocumentType - Enum Class in chemaxon.naming.document.annotate
-
Document type enum for
DocumentAnnotator
. - DocumentAnnotator.Listener - Interface in chemaxon.naming.document.annotate
-
The interface for a
DocumentAnnotator
progress event listener. - DocumentAnnotator.ProgressInfo - Class in chemaxon.naming.document.annotate
-
Represents the state of progress during a document annotation process.
- DocumentAnnotatorOptions - Class in chemaxon.naming.document.annotate
-
Represents various options regarding how a document should be annotated, both in terms of input and output.
- DocumentAnnotatorOptions.Builder - Class in chemaxon.naming.document.annotate
-
A builder for
DocumentAnnotatorOptions
, allowing for options to be built using a fluent interface. - DocumentAnnotatorOptions.ImageFormat - Enum Class in chemaxon.naming.document.annotate
-
A list of supported image formats for popups in the annotated document.
- DocumentStyleAPI - Class in chemaxon.marvin.sketch.swing.modules.documentstyle
-
API for DocumentStyle management.
- DocumentStyleAPI() - Constructor for class chemaxon.marvin.sketch.swing.modules.documentstyle.DocumentStyleAPI
- DocumentToStructure - Class in chemaxon.naming.document
-
A convenience class for dealing with String-based documents, such as TXT, HTML, or XML files.
- DocumentToStructure() - Constructor for class chemaxon.naming.document.DocumentToStructure
- done() - Method in interface chemaxon.util.progress.ProgressObserver
-
Deprecated, for removal: This API element is subject to removal in a future version.Implement
ProgressObserver.close()
instead, and create instances of this interface in a try-with-resources block. - DONOR_SIGN - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
-
Donor sign displayed in GUI.
- DONR - Static variable in class chemaxon.marvin.alignment.Pharmacophore3D
- DONT_REMOVE_LAST_COMPONENT_KEY - Static variable in class chemaxon.standardizer.advancedactions.StripSaltsAction
-
Property key for "Don't Remove Last Component" option
- DOODLE - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that molecule with serious scanning or drawing issue had found
- doPaste() - Method in class chemaxon.marvin.beans.MarvinPane
-
Invokes Paste actions.
- doPaste() - Method in class chemaxon.marvin.beans.MSketchPane
-
Invokes Paste action.
- doPaste() - Method in class chemaxon.marvin.beans.MViewPane
-
Invokes Paste action.
- doSetSetSeqs(Molecule[], int, String) - Method in class chemaxon.marvin.view.MDocStorage
- DOT_DISCONNECTED_FRAGMENTS - Enum constant in enum class com.chemaxon.calculations.elemanal.FormulaGenerationRule
-
Dot-disconnected molecular formula of a multifragment molecule.
For example:C7H5O2.Na
for sodium benzoate. - DOTDISCONNECTED_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
-
Result type with the string id "dotdisconnectedformalchargeformula".
- DOTDISCONNECTED_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
-
Result type with the string id "dotdisconnectedformula".
- DOTDISCONNECTED_ISOTOPE_FORMAL_CHARGE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
-
Result type with the string id "dotdisconnectedisotopeformalchargeformula".
- DOTDISCONNECTED_ISOTOPE_FORMULA - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
-
Result type with the string id "dotdisconnectedisotopeformula".
- dotDisconnectedFormula() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the dot-disconnected molecular formula of a multifragment molecule.
- dotDisconnectedIsotopeFormula() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the dot-disconnected isotope formula of a multifragment molecule.
- dotDisconnectedIsotopeFormula(boolean) - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the dot-disconnected isotope formula of a multifragment molecule.
- DOUBLE - Enum constant in enum class chemaxon.struc.BondType
-
Double bond type.
- DOUBLE - Static variable in class chemaxon.struc.MolBond
-
Double bond type.
- DOUBLE_BOND - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Deprecated.
- DOUBLE_BOND_STEREO - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that molecule contains either double bonds which are not valid
- DOUBLE_OR_AROMATIC - Enum constant in enum class chemaxon.struc.BondType
-
Double or aromatic query bond type.
- DOUBLE_OR_AROMATIC - Static variable in class chemaxon.struc.MolBond
-
Double or aromatic query bond type.
- doubleStringWidth(String, MFont, FontMetrics, Graphics) - Method in class chemaxon.struc.graphics.MTextDocument.Section
-
Gets the width of a string as a floating point number.
- doubleValue() - Method in class chemaxon.struc.prop.MDoubleProp
-
Gets the double floating point value.
- DOWN - Static variable in class chemaxon.struc.MolBond
-
Single bond down flag.
- DOWN_WEDGE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"downWedge"
. - DPoint3 - Class in chemaxon.struc
-
Point in three dimensional space.
- DPoint3() - Constructor for class chemaxon.struc.DPoint3
-
Construct a zero point.
- DPoint3(double, double, double) - Constructor for class chemaxon.struc.DPoint3
-
Construct a point from the specified coordinates.
- DPoint3(DPoint3) - Constructor for class chemaxon.struc.DPoint3
-
Copy constructor.
- DRAGGABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"draggable"
. - dropBinaryVector() - Method in class chemaxon.descriptors.ECFP
-
Drops the binary vector storage.
- Ds - Static variable in class chemaxon.core.ChemConst
- DT_FORMATTED - Static variable in class chemaxon.struc.sgroup.DataSgroup
-
Field type: formatted.
- DT_NUMERIC - Static variable in class chemaxon.struc.sgroup.DataSgroup
-
Field type: numeric.
- DT_TEXT - Static variable in class chemaxon.struc.sgroup.DataSgroup
-
Field type: text.
- DT_UNSPEC - Static variable in class chemaxon.struc.sgroup.DataSgroup
-
Field type: unspecified.
- DT_URL - Static variable in class chemaxon.struc.sgroup.DataSgroup
-
Field type: url.
- DUPLICATE - Static variable in interface chemaxon.sss.SearchConstants
-
Duplicate search (formerly called perfect).
- Dy - Static variable in class chemaxon.core.ChemConst
- DynamicArgument<CT,
RT> - Class in chemaxon.marvin.services -
ServiceArgument
s implementing this interface should support automatic evaluation of arguments before service call based on context.
NOTE: subclasses MUST HAVE default constructor to use from Marvin Sketch - DynamicArgument() - Constructor for class chemaxon.marvin.services.DynamicArgument
- DynamicArgument(String) - Constructor for class chemaxon.marvin.services.DynamicArgument
- DYNAMICpKaPREFIX - Static variable in class chemaxon.marvin.calculations.pKaPlugin
-
pKa's prefix (acidic/basic) does depend on the submitted micro state
E
- E - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.CisTransStereoIUPACValue
- E - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration
- E_OR_UNSPEC - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration
- E_OR_Z - Enum constant in enum class chemaxon.struc.stereo.EZConfiguration
- E_SINK - Static variable in class chemaxon.struc.graphics.MEFlow
-
Electron sink.
- E_SOURCE - Static variable in class chemaxon.struc.graphics.MEFlow
-
Electron source.
- eA - Enum constant in enum class chemaxon.calculations.dipole.DipoleResult.Unit
-
Atomic charge unit * Angstrom.
- eccentricity(int) - Method in class chemaxon.calculations.TopologyAnalyser
-
Calculates the eccentricity of an atom, which is the greatest value in the corresponding row of the distance matrix.
- ECFP - Class in chemaxon.descriptors
-
The
ECFP
class implements Extended-Connectivity Fingerprints (ECFPs) as a type ofMolecularDescriptor
s. - ECFP() - Constructor for class chemaxon.descriptors.ECFP
-
Creates a new, empty instance of ECFP without allocating internal storage.
- ECFP(ECFP) - Constructor for class chemaxon.descriptors.ECFP
-
Copy constructor.
- ECFP(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFP
-
Creates a new instance of ECFP according to the parameters given.
- ECFP(String) - Constructor for class chemaxon.descriptors.ECFP
-
Creates a new instance of ECFP according to the parameters given.
- ECFPFeature - Class in chemaxon.descriptors
-
Class for representing the substructural features of ECFP fingerprints.
- ECFPFeatureLookup - Class in chemaxon.descriptors
-
Class for retrieving the substructural features of ECFP fingerprints.
- ECFPFeatureLookup() - Constructor for class chemaxon.descriptors.ECFPFeatureLookup
-
Creates a new
ECFPFeatureLookup
instance with the default ECFP configuration parameters. - ECFPFeatureLookup(ECFPParameters) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup
-
Creates a new
ECFPFeatureLookup
instance with the given ECFP configuration parameters. - ECFPFeatureLookup(String) - Constructor for class chemaxon.descriptors.ECFPFeatureLookup
-
Creates a new
ECFPFeatureLookup
instance with the given ECFP configuration parameters. - ECFPGenerator - Class in chemaxon.descriptors
-
The
ECFPGenerator
class generates ECFP fingerprints of molecular graphs. - ECFPGenerator() - Constructor for class chemaxon.descriptors.ECFPGenerator
-
Creates a new instance of
ECFPGenerator
, which can be used to generate ECFP fingerprints for an arbitrary number of molecules. - ECFPParameters - Class in chemaxon.descriptors
-
Manages ECFP fingerprint parameters.
- ECFPParameters() - Constructor for class chemaxon.descriptors.ECFPParameters
-
Creates an empty object.
- ECFPParameters(File) - Constructor for class chemaxon.descriptors.ECFPParameters
-
Creates a new object based on a given configuration file.
- ECFPParameters(String) - Constructor for class chemaxon.descriptors.ECFPParameters
-
Creates a new object based on a given configuration string.
- EDITABLE - Static variable in class chemaxon.marvin.beans.MViewPane
-
Editing mode identifier meaning the structures can be edited with the Edit > Structure menu or double click and launches MarvinView in a new window.
- EDITABLE - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"editable"
. - EDITOR_CLASS_NAME - Static variable in class chemaxon.checkers.StructureCheckerDescriptor
-
editor class name property of checker
- EDITOR_CLASS_NAME - Static variable in class chemaxon.standardizer.StandardizerActionDescriptor
-
editor class name property of standardizer action
- editorClassName() - Element in annotation interface chemaxon.checkers.CheckerInfo
-
Returns the name of the checker's editor
- editorClassName() - Element in annotation interface chemaxon.standardizer.StandardizerActionInfo
-
Returns the editor class name of the action
- electronegOf(int) - Static method in class chemaxon.struc.MolAtom
-
Gets 10 times the electronegativity value for the specified element.
- electronRadious - Static variable in class chemaxon.struc.graphics.MEFlowBasePoint
- ELEMENT_COUNT - Static variable in class chemaxon.core.ChemConst
-
Number of elements in the periodic system
- ELEMENT_COUNT - Static variable in class chemaxon.struc.MolAtom
-
Number of elements in the periodic system
- ElementalAnalyser - Class in chemaxon.calculations
-
Calculates molecular formula, mass, MS mass and composition.
- ElementalAnalyser() - Constructor for class chemaxon.calculations.ElementalAnalyser
- ElementalAnalyserPlugin - Class in chemaxon.marvin.calculations
-
Calculates molecular formula, mass, MS mass and composition.
- ElementalAnalyserPlugin() - Constructor for class chemaxon.marvin.calculations.ElementalAnalyserPlugin
- ElementalAnalyserPlugin.ResultType - Enum Class in chemaxon.marvin.calculations
-
Represents the different result types of the elemental analyser plugin.
- ElementalAnalysis - Interface in com.chemaxon.calculations.elemanal
-
Calculates molecular formula, mass, MS mass and composition.
- ELEMENTS - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"elements"
. - EMF - Static variable in class chemaxon.formats.MFileFormat
-
Windows Enhanced Metafiles.
- EMPTY - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents that molecule structure was empty
- EMPTY - Static variable in class chemaxon.jep.ConstantTable
-
An empty constant table.
- EMPTY - Static variable in class chemaxon.struc.MolAtom
-
Empty atom type.
- EMPTY_MOLECULE - Enum constant in enum class chemaxon.standardizer.concurrent.StandardizerRunner.ErrorHandlingPolicy
-
In case of standardization error an empty molecule is provided on the output
- EmptyStructureChecker - Class in chemaxon.checkers
-
A descendant of
AbstractStructureChecker
detecting structures having no atoms. - EmptyStructureChecker() - Constructor for class chemaxon.checkers.EmptyStructureChecker
-
Default constructore
- ENABLED_2D_VIEWER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"2dviewerEnabled"
. - ENABLED_3D_VIEWER - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"3dviewerEnabled"
. - enableDefaultHeavyAtomLimits() - Static method in interface chemaxon.calculator.TaggedCalculator
-
Sets the global input checker to one that uses the default heavy atom limits.
- enclosesPoint(double, double) - Method in class chemaxon.struc.graphics.MBracket
-
Checks if a specified point is enclosed by this bracket.
- encode(MFont, MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Returns the string representation of the attributes.
- encoding - Variable in class chemaxon.marvin.io.PositionedInputStream
-
The encoding.
- Encoding - Class in chemaxon.marvin.io
-
File encoding information.
- Encoding(String, int, ByteOrder) - Constructor for class chemaxon.marvin.io.Encoding
-
Creates an Encoding for the specified name, word length and byte order.
- END_CHARACTER - Static variable in class chemaxon.naming.document.DocumentToStructure
-
Molecule property key on results: key of the molecule property which contains the ending character offset since the beginning of the document, for text formats (html, xml, txt).
- endElement(String, String, String) - Method in class chemaxon.naming.document.annotate.XmlToHtmlConverter
- endGrabLines() - Method in class chemaxon.marvin.io.PositionedInputStream
-
Deprecated, for removal: This API element is subject to removal in a future version.
- endHourglass() - Method in class chemaxon.marvin.beans.MarvinPane
-
Changes the hourglass cursor back to normal at the end of a long operation.
- ENDO - Static variable in interface chemaxon.struc.StereoConstants
-
Non-CIP stereodescriptor, endo (relative configuration).
- endRecord(boolean) - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
It must be called at the end of record.
- endReuse(int) - Method in class chemaxon.struc.Molecule
-
End reusing atoms.
- endReuse(int) - Method in class chemaxon.struc.RgMolecule
-
End reusing atoms.
- endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument
-
Tests whether the document ends with the specified character.
- endsWith(char) - Method in class chemaxon.struc.graphics.MTextDocument.Portion
-
Tests whether this text portion ends with the specified character.
- EnhancedStereo - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Please note that this class is marked with @Beta annotation, so it can be subject of incompatible changes or removal in later releases.
- EnhancedStereo(StereoConstants.EnhancedStereoType) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
-
Creates enhanced stereo representation.
- EnhancedStereo(StereoConstants.EnhancedStereoType, int) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereo
-
Creates enhanced stereo representation.
- EnhancedStereoGroup - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Enhanced stereo descriptor class.
- EnhancedStereoGroup(EnhancedStereo, List<TetrahedralStereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.EnhancedStereoGroup
-
Creates enhanced stereo group.
- enqueueUpdate() - Method in class chemaxon.marvin.view.swing.TableSupport
-
Enqueues an update task.
- ensureValidity() - Method in class chemaxon.struc.graphics.MElectronContainer
- ENTRY_SEPARATOR - Static variable in class chemaxon.standardizer.configuration.reader.StandardizerActionStringReader
-
Configuration entry separator token of the action string
- EPS - Static variable in class chemaxon.formats.MFileFormat
-
Encapsulated PostScript vector image format.
- EPSILON - Static variable in class chemaxon.marvin.calculations.HBDAPlugin
- EPSILON - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
The microspecies is ignored if its distribution is less than EPSILON for all pH values.
- equals(Encoding) - Method in class chemaxon.marvin.io.Encoding
-
Tests whether two encodings are equal.
- equals(CTransform3D, double) - Method in class chemaxon.struc.CTransform3D
- equals(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Tests whether two attributes objects equal or not.
- equals(Object) - Method in class chemaxon.calculations.pka.PKaTrainingResult
- equals(Object) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
- equals(Object) - Method in class chemaxon.checkers.AbstractStructureChecker
- equals(Object) - Method in class chemaxon.checkers.AromaticityErrorChecker
- equals(Object) - Method in class chemaxon.checkers.AtomQueryPropertyChecker
- equals(Object) - Method in class chemaxon.checkers.AttachedDataChecker
- equals(Object) - Method in class chemaxon.checkers.ExplicitHydrogenChecker
- equals(Object) - Method in class chemaxon.checkers.result.AromaticityCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.AtomQueryPropertyCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.BondAngleCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.BondLengthCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.DefaultExternalStructureCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.ExplicitHydrogenResult
- equals(Object) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.ReactionCheckerResult
-
Deprecated.
- equals(Object) - Method in class chemaxon.checkers.result.RgroupCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.SgroupCheckerResult
- equals(Object) - Method in class chemaxon.checkers.result.SubstructureCheckerResult
- equals(Object) - Method in class chemaxon.checkers.StructureCheckerDescriptor
- equals(Object) - Method in class chemaxon.checkers.util.AtomLabels
- equals(Object) - Method in class chemaxon.checkers.util.DataExclusionList
- equals(Object) - Method in class chemaxon.checkers.ValencePropertyChecker
- equals(Object) - Method in class chemaxon.core.calculations.valencecheck.ValenceCheckOptions
- equals(Object) - Method in class chemaxon.fixers.StructureFixerDescriptor
- equals(Object) - Method in class chemaxon.marvin.io.Encoding
-
Tests whether two encodings are equal.
- equals(Object) - Method in class chemaxon.marvin.modules.datatransfer.TransferableDescriptor
- equals(Object) - Method in class chemaxon.sss.search.Decomposition
-
Returns
true
if this decomposition is equivalent to the specified decomposition. - equals(Object) - Method in class chemaxon.sss.search.MarkushFeature
-
Deprecated.
- equals(Object) - Method in class chemaxon.sss.search.SearchHit
- equals(Object) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
- equals(Object) - Method in class chemaxon.standardizer.StandardizerActionDescriptor
- equals(Object) - Method in class chemaxon.struc.AtropStereoDescriptor
- equals(Object) - Method in class chemaxon.struc.AxialStereoDescriptor
- equals(Object) - Method in class chemaxon.struc.CisTransStereoDescriptor
- equals(Object) - Method in class chemaxon.struc.CTransform3D
- equals(Object) - Method in class chemaxon.struc.DPoint3
-
Two points equal if their coordinates equal.
- equals(Object) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Two points equal if their atoms equal.
- equals(Object) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Two points equal if their atoms equal.
- equals(Object) - Method in class chemaxon.struc.graphics.MElectron
- equals(Object) - Method in class chemaxon.struc.graphics.MElectronContainer
- equals(Object) - Method in class chemaxon.struc.graphics.MFont
-
Tests whether two font objects equal.
- equals(Object) - Method in class chemaxon.struc.graphics.MMidPoint
-
Two midpoints equal if their parent lines are the same and the polyline point indices also equal.
- equals(Object) - Method in class chemaxon.struc.graphics.MRectanglePoint
-
Two rectangle points equal if their parent rectangles are the same and they are on the same corner or edge.
- equals(Object) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Tests whether two attributes objects equal or not.
- equals(Object) - Method in class chemaxon.struc.MPoint
-
Two points equal if their location equals.
- equals(Object) - Method in class chemaxon.struc.prop.MBooleanProp
- equals(Object) - Method in class chemaxon.struc.prop.MCollectionProp
- equals(Object) - Method in class chemaxon.struc.prop.MDoubleArrayProp
- equals(Object) - Method in class chemaxon.struc.prop.MDoubleProp
- equals(Object) - Method in class chemaxon.struc.prop.MFontProp
- equals(Object) - Method in class chemaxon.struc.prop.MHashProp
- equals(Object) - Method in class chemaxon.struc.prop.MHCoords3DProp
- equals(Object) - Method in class chemaxon.struc.prop.MIntegerArrayProp
- equals(Object) - Method in class chemaxon.struc.prop.MIntegerProp
- equals(Object) - Method in class chemaxon.struc.prop.MListProp
- equals(Object) - Method in class chemaxon.struc.prop.MMoleculeProp
- equals(Object) - Method in class chemaxon.struc.prop.MMoleculeStringProp
- equals(Object) - Method in class chemaxon.struc.prop.MObjectProp
- equals(Object) - Method in class chemaxon.struc.prop.MStringProp
- equals(Object) - Method in class chemaxon.struc.RgroupBridgeId
- equals(Object) - Method in class chemaxon.struc.StereoActivePart
- equals(Object) - Method in class chemaxon.struc.TetrahedralStereoDescriptor
- equalsHead(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Decides whether the head bonds equal the given bonds.
- equalsNext(MTextAttributes) - Method in class chemaxon.struc.graphics.MTextAttributes
-
Tests whether the attributes of two neighboring sections equal or not.
- equalsTail(MolBond[]) - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Decides whether the tail bonds equal the given bonds.
- equalsTo(Object, int[]) - Method in class chemaxon.struc.AtropStereoDescriptor
- equalsTo(Object, int[]) - Method in class chemaxon.struc.AxialStereoDescriptor
- equalsTo(Object, int[]) - Method in interface chemaxon.struc.CIPStereoDescriptorIface
- equalsTo(Object, int[]) - Method in class chemaxon.struc.CisTransStereoDescriptor
- equalsTo(Object, int[]) - Method in class chemaxon.struc.StereoActivePart
- equalsTo(Object, int[]) - Method in class chemaxon.struc.TetrahedralStereoDescriptor
- EQUILIBRIUM - Static variable in class chemaxon.struc.RxnMolecule
-
Resonance arrow, the same as the two-headed double reaction arrow.
- Er - Static variable in class chemaxon.core.ChemConst
- ERROR - Enum constant in enum class chemaxon.checkers.CheckerSeverity
-
This severity level should used for
StructureChecker
implementations which search for serious problems in aMolecule
- errorList - Variable in class chemaxon.jep.ChemJEP
-
Deprecated, for removal: This API element is subject to removal in a future version.This class no longer collects exceptions but throws them when they are encountered. The list this method uses is filled but otherwise ignored.
- ErrorProcessor - Interface in chemaxon.util
-
Error processing interface.
- ErrorReport - Class in com.chemaxon.calculations.stereoanal
-
Error reporting class.
- ErrorReport(AtomSelection, String) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport
-
Constructs new error report.
- ErrorReport(AtomSelection, String, Optional<? extends StereoCenter>) - Constructor for class com.chemaxon.calculations.stereoanal.ErrorReport
-
Constructs new error report.
- errors() - Method in class com.chemaxon.calculations.stereoanal.StereoAnalysis
-
Error reports.
- errorType - Variable in class chemaxon.checkers.AbstractStructureChecker
-
The error type of the current checker.
- Es - Static variable in class chemaxon.core.ChemConst
- ESCAPE_CHAR - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"escapeChar"
. - estimateNumRecords() - Method in class chemaxon.formats.MolImporter
-
Estimates the total number of records.
- estimateNumRecords() - Method in class chemaxon.marvin.io.ArrayMDocSource
-
Estimates the total number of records.
- estimateNumRecords() - Method in class chemaxon.marvin.io.MDocSource
-
Estimates the total number of records.
- estimateNumRecords() - Method in class chemaxon.marvin.plugin.PluginMDocSource
-
Estimates the total number of records.
- estimateProgress() - Method in interface chemaxon.util.iterator.MoleculeIterator
-
Estimates the iteration progress.
- Eu - Static variable in class chemaxon.core.ChemConst
- euclidean(float[], float[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the Euclidean distance.
- euclidean(int[], int[]) - Static method in class chemaxon.descriptors.Metrics
-
Calculates the Euclidean distance.
- EUCLIDEAN - Enum constant in enum class chemaxon.descriptors.MetricsType
- evaluate(C) - Method in class chemaxon.jep.ChemJEP
-
Evaluates the expression.
- evaluate(StandardizerRunner.ErrorHandlingPolicy, StandardizerResult) - Static method in class chemaxon.standardizer.concurrent.StandardizerRunner
- evaluate(CT) - Method in class chemaxon.marvin.services.DynamicArgument
-
Evaluates the dynamic argument based on context
- evaluate(Map<String, String>, List<Object>, ChemContext) - Method in interface chemaxon.jep.CustomFunction
-
Evaluates this function.
- evaluate_boolean(C) - Method in class chemaxon.jep.ChemJEP
-
Evaluates the expression and converts the result
boolean
. - evaluate_booleans(C) - Method in class chemaxon.jep.ChemJEP
-
Evaluates the expression and converts the result to
boolean[]
. - evaluate_double(C) - Method in class chemaxon.jep.ChemJEP
-
Evaluates the expression and converts the result to
double
. - evaluate_doubles(C) - Method in class chemaxon.jep.ChemJEP
-
Evaluates the expression and converts the result to
double[]
. - EVALUATION_ERROR - Static variable in class chemaxon.jep.ChemJEP
-
The evaluation error message.
- Evaluator - Class in chemaxon.jep
-
Evaluates Chemical Terms expressions.
- Evaluator() - Constructor for class chemaxon.jep.Evaluator
-
Default constructor.
- Evaluator(Standardizer) - Constructor for class chemaxon.jep.Evaluator
-
Constructor for internal use only.
- Evaluator(File) - Constructor for class chemaxon.jep.Evaluator
-
Constructor.
- Evaluator(File, Standardizer) - Constructor for class chemaxon.jep.Evaluator
-
Constructor for internal use only.
- Evaluator(File, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator
-
Deprecated, for removal: This API element is subject to removal in a future version.
- Evaluator(String) - Constructor for class chemaxon.jep.Evaluator
-
Constructor.
- Evaluator(String, Standardizer) - Constructor for class chemaxon.jep.Evaluator
-
Constructor for internal use only.
- Evaluator(String, Standardizer, MolImporter, String) - Constructor for class chemaxon.jep.Evaluator
-
Deprecated, for removal: This API element is subject to removal in a future version.
- EVALUATOR_DEFAULTS_FILE - Static variable in class chemaxon.jep.Evaluator
-
Default Function/Plugin settings filename.
- EVALUATOR_NAMED_MOLS_FILE - Static variable in class chemaxon.jep.Evaluator
-
Deprecated, for removal: This API element is subject to removal in a future version.No longer used, will be removed.
- EVALUATOR_SCRIPT_FILE - Static variable in class chemaxon.jep.Evaluator
-
Initial script filename.
- EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AtropStereoValue
- EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.AxialStereoValue
- EVEN - Enum constant in enum class chemaxon.struc.CIPStereoDescriptorIface.CIPValue.TetrahedralStereoValue
- EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AtropStereo
-
Deprecated, for removal: This API element is subject to removal in a future version.
- EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.AxialStereo
-
Deprecated, for removal: This API element is subject to removal in a future version.
- EVEN - Enum constant in enum class com.chemaxon.calculations.stereoanal.StereoConstants.StereoValue.TetrahedralStereo
-
Deprecated, for removal: This API element is subject to removal in a future version.
- EVEN - Static variable in class chemaxon.calculations.stereo.Stereochemistry
- EVERY_WEIGHT_IS_ONE - Enum constant in enum class chemaxon.marvin.alignment.AlignmentProperties.ColorNotSpecifiedCase
- EXACT - Static variable in class chemaxon.sss.formula.FormulaSearch
-
Constant value specifying the exact search type.
- EXACT_KEY - Static variable in class chemaxon.standardizer.advancedactions.TransformAction
-
Key of exact for parsing and property change
- EXACT_MASS - Enum constant in enum class chemaxon.marvin.calculations.ElementalAnalyserPlugin.ResultType
-
Result type with the string id "exactmass".
- EXACT_SUBFORMULA - Static variable in class chemaxon.sss.formula.FormulaSearch
-
Constant value specifying the exact sub formula search type.
- exactMass() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the weight of the molecular ion measured in Mass Spectrometry using the mass of the most frequent natural isotope of the atoms.
- exactMass() - Method in interface com.chemaxon.calculations.elemanal.ElementalAnalysis
-
Calculates the weight of the MS molecule ion using the mass of the most frequent natural isotope for element atoms.
- exactMassPrecision() - Method in class chemaxon.calculations.ElementalAnalyser
-
Calculates the precision of the monoisitopic weight (number of significant decimal digits).
- exactQueryAtomMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets whether generic query atoms should be matched only to atoms of exactly the same type.
- exactQueryBondMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Sets whether generic query bonds should be matched only to bonds of exactly the same type.
- EXCLUDE_KEY - Static variable in class chemaxon.standardizer.actions.AbstractSgroupAction
-
Key of exclude for parsing and property change
- EXCLUDE_XX - Enum constant in enum class chemaxon.sss.search.options.TargetHomologyMatchingMode
- excludeString - Variable in class chemaxon.standardizer.actions.ContractSgroupsAction
- excludeString - Variable in class chemaxon.standardizer.actions.ExpandSgroupsAction
- excludeString - Variable in class chemaxon.standardizer.actions.UngroupSgroupsAction
- exit() - Method in class chemaxon.marvin.beans.MarvinPane
-
Closes all windows opened by this MarvinPane and saves user initialization file.
- EXO - Static variable in interface chemaxon.struc.StereoConstants
-
Non-CIP stereodescriptor, exo (relative configuration).
- expand(int) - Method in class chemaxon.struc.Sgroup
-
Sets the state to
Sgroup.XSTATE_X
orSgroup.XSTATE_XC
. - expand(int) - Method in interface chemaxon.struc.sgroup.Expandable
-
Expands the S-group.
- expand(int) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Expands this S-group unless it has expandable child s-group because in that case our calculations' behaviour can not be predicted.
- expand(int) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Expands this S-group.
- Expandable - Interface in chemaxon.struc.sgroup
-
Expandable interface for S-groups.
- ExpandAction - Class in chemaxon.standardizer.actions
-
Expand stoichiometry standardizer action
- ExpandAction(Map<String, String>) - Constructor for class chemaxon.standardizer.actions.ExpandAction
-
Initializes the action with parameters
- ExpandGroupFixer - Class in chemaxon.fixers
-
A descendant of
AbstractStructureFixer
which expands all abbreviated groups in the molecule - ExpandGroupFixer() - Constructor for class chemaxon.fixers.ExpandGroupFixer
- expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbbreviatedGroupChecker
-
This implementation does nothing.
- expandMolecule(Molecule, Map<MolAtom, MolAtom>, Map<MolBond, MolBond>) - Method in class chemaxon.checkers.AbstractStructureC