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.as of Marvin 2014.07.21.0 intended for internal use only
- 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_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Absolute stereoconfiguration label visibility flag.
- ABS_STEREO_ALWAYS_ON - Static variable in interface chemaxon.sss.SearchConstants
-
Option for absolute stereo matching.
- ABS_STEREO_CHIRAL_FLAG - Static variable in interface chemaxon.sss.SearchConstants
-
Option for absolute stereo matching.
- ABS_STEREO_TABLE_OPTION - Static variable in interface chemaxon.sss.SearchConstants
-
Option for absolute stereo matching.
- 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.
- AbsentChiralFlagFixer() - Constructor for class chemaxon.fixers.AbsentChiralFlagFixer
-
Deprecated.
- ABSOLUTE_LABEL_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Show absolute stereo label.
- 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.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.
- 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
- AbstractShapeComparator<T extends ShapeDescriptor> - Class in com.chemaxon.descriptors.alignment
- AbstractShapeComparator(DescriptorGenerator<T>) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeComparator
- AbstractShapeGenerator<D extends ShapeDescriptor,
P extends AbstractShapeGeneratorParameter> - Class in com.chemaxon.descriptors.alignment - AbstractShapeGenerator(P) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGenerator
- AbstractShapeGeneratorParameter - Class in com.chemaxon.descriptors.alignment
-
Helper class without the requested getDescriptorGenerator method.
- AbstractShapeGeneratorParameter(AtomTyping) - Constructor for class com.chemaxon.descriptors.alignment.AbstractShapeGeneratorParameter
- 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 class chemaxon.marvin.util.MolFragLoader.RgroupAttachmentCountFilter
-
Accepts molecule if the number of R-group attachments in the molecule is exactly the attachment count specified in the constructor of this filter.
- 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(T) - Method in interface com.chemaxon.calculations.io.Sink
-
Deprecated.
- 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.
- ACCEPTOR_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
- ACCESS - Static variable in class chemaxon.jchem.db.DatabaseConstants
- ACCESS_DRIVER - Static variable in class chemaxon.jchem.db.DatabaseConstants
-
JDBC driver for MS Access database
- ACCESS_TYPE_NAME - Static variable in class chemaxon.jchem.db.DatabaseConstants
- ACCESS_URL_EXAMPLE - Static variable in class chemaxon.jchem.db.DatabaseConstants
-
JDBC URL example for Access database
- ACCESS_URL_TEMPLATE - Static variable in class chemaxon.jchem.db.DatabaseConstants
-
JDBC URL template for Access database
- 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.
- 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
- activateContainerCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
-
The containing cell of the GraphicComponent will be the active cell of the scene.
- active - Variable in class chemaxon.marvin.space.GraphicComponent
-
Is this component selected or not.
- adaptiveSPHEX(int, int, DissimilarityInput, ProgressObserver) - Static method in class com.chemaxon.clustering.sphex.SphereExclusion
-
Sphere exclusion clustering with sphere radius inference.
- add(MDSet) - Method in interface chemaxon.descriptors.MDHypothesisGenerator
-
Adds a MDSet component to be considered in the hypothesis.
- 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
-
Adds a bond to the 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(InputStream) - 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.standardizer.StandardizerActionFactory.Builder
-
Adds an input stream containing standardizer 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 - 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
- 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.
- addAtom(int) - Method in interface chemaxon.struc.WSmolecule
-
Adds an atom.
- 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.
- addAtom(Smolecule, int) - Method in interface chemaxon.struc.WSmolecule
-
Adds an atom from another Smolecule.
- 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
-
Adds an atom to a fragment.
- addAtomToFragment(MolAtom) - Method in class chemaxon.struc.RxnMolecule
-
Adds an atom to a fragment.
- 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.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.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.
- addBond(int, int, int) - Method in interface chemaxon.struc.WSmolecule
-
Adds a bond.
- 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.
- addCanvas(Container) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace viewer to the container.
- 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.
- addChildCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
-
Add a cluster to another cluster as a child cluster.
- 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.
- addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
-
Adds a new component to this cell.
- addComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
-
Adds a component to the active or to the first cell.
- addComponent(GraphicComponent, int) - Method in class chemaxon.marvin.space.GraphicScene
-
Adds a component to the cell having the given index.
- addComponent(Molecule, int) - Method in class chemaxon.struc.RxnMolecule
-
Adds a reactant, product or agent.
- addComponent(Molecule, int, boolean) - Method in class chemaxon.struc.RxnMolecule
-
Adds a reactant, product or agent.
- addComponentToEmptyCell(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
-
Adds a component to an empty cell.
- 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.
- addCoordinateSystem(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Adds a dummy graphic component that represents the coordinate system.
- 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.
- addDataPoint(double, double) - Method in class com.chemaxon.clustering.util.Util.StringScatterPlot
-
Add new point to put.
- addDescriptor(MolecularDescriptor) - Method in class chemaxon.descriptors.MDSet
-
Appends the next component to the
MDSet
object. - addDihedralStep(DihedralScanStep) - Method in class chemaxon.marvin.alignment.atrop.DihedralScanResult
-
Add a new step.
- addDrawProperties(Properties) - Method in class chemaxon.marvin.space.GraphicComponent
-
Forces the component to set all drawing property stored in drawProperties, and leaves the old settings which are not overidden.
- addExplicitHydrogens(int) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.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.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.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
-
Adds a new function to the parser.
- 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.since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph) instead
- addHAtoms(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.since Marvin 5.11 use convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) instead
- addHAtoms(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.since Marvin 5.11 use 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.
- addHydrogens() - Method in class chemaxon.util.MolHandler
-
Adds explicit H atoms instead of the current implicit ones.
- addHydrogensToAromaticHeteroAtoms() - Method in class chemaxon.util.MolHandler
-
Adds the implicit Hydrogen atoms to heteroatoms in aromatic rings.
- 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.
- 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.
- 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.
- addInputChecker(CalculatorInputChecker) - Method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Adds the specified input checker to this plugin.
- additionalInformation - Variable in class chemaxon.jchem.db.Updater.UpdateInfo
-
Additional information for the entities in same order, if needed.
- 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.
- addListToDelete(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Adds a gl list id to the deletion list
- addLogger(ProgressWriter.Logger) - Method in class chemaxon.jchem.file.ProgressWriter
-
Adds a
ProgressWriter.Logger
to retrieve suppressed (error) messages. - addLonePairs(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Deprecated.since Marvin 5.11 use convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) isntead
- 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.
- addMDConfig(String, String, File) - Method in class chemaxon.descriptors.GenerateMD
-
Adds a new parameter configuration to the descriptor.
- addMDConfig(String, String, String) - Method in class chemaxon.descriptors.GenerateMD
-
Adds a new parameter configuration to the descriptor.
- addMenuBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace menubar to the container.
- addMenuBarChangeListener(MenuBarChangeListener) - Method in class chemaxon.marvin.beans.MarvinPane
-
Adds a menubar change listener.
- addMessage(int, String, Throwable) - Method in interface chemaxon.jchem.file.ProgressWriter.Logger
- 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) - Method in class chemaxon.clustering.libmcs.LibraryMcs
-
Adds a new molecule to the set of structures to be clustered.
- addMolecule(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds a
Molecule
object to the actual cell of the viewer. - addMolecule(Molecule) - Method in class com.chemaxon.clustering.common.MolInputBuilder
-
Add a new structure.
- addMolecule(Molecule, boolean, boolean) - Method in class chemaxon.marvin.alignment.Alignment
-
Add molecule to align
- addMolecule(String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Reads the molecule file, and adds molecule component(s) to the actual cell of the viewer.
- addMolecules(Collection<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
-
Add multiple structures.
- addMolecules(Iterator<? extends Molecule>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
-
Add multiple structures.
- addMolecules(Iterator<? extends Molecule>, StandardizerWrapper) - Method in class com.chemaxon.clustering.common.MolInputBuilder
-
Add multiple structures with preprocessing.
- addMoleculeTo(Molecule, int) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Makes the given cell to be the active cell, and adds the molecule to it.
- addMoleculeToEmptyCell(Molecule) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the molecule to the next empty cell, or creates a new empty cell if all existing cell contains at least 1 component.
- addMoleculeToEmptyCell(String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Reads the molecule, and adds molecule(s) to the next empty cell of the viewer, creating new cell if necessary.
- addMoleculeWithoutChange(Molecule, boolean) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds a
Molecule
object to the actual cell of the viewer and resets the view only if required. - addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
-
Allocate a new cluster.
- addNewCluster() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
-
Allocate a new cluster.
- 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.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. - addPDB(String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Loads a pdb file from the RCSB Protein Data Bank (http://www.rcsb.org/)
- addPopupMenu() - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace popup menu to the JPanel.
- addProperty(String, String) - Method in class chemaxon.jchem.db.DatabaseProperties
-
Inserts the property with the specified key and value into the
JChemProperties
table. - 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.
- addPropertyColumnName(String, String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Sets the displayed name in the header column of the given property
- addQueries(MDReader) - Method in class chemaxon.descriptors.MDSimilarity
-
Adds new query molecules as their set of descriptors from a chemical descriptor reader.
- addQueries(MDSet[]) - Method in class chemaxon.descriptors.MDSimilarity
-
Adds new query molecules as their set of descriptors from an array.
- addQuery(MDSet) - Method in class chemaxon.descriptors.MDSimilarity
-
Adds a new query molecule as its set of descriptors.
- addRepeatingUnitAtom(MolAtom) - Method in class chemaxon.struc.sgroup.MultipleSgroup
-
Adds an atom to the list of paradigmatic repeating unit atoms.
- addResultWriter(MDSimilarityResultWriter) - Method in class chemaxon.descriptors.MDSimilarity
-
Adds a
MDSimilarityResultWriter
object. - 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
- addSelectionPanel(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace selection panel to the container.
- addSelectionPanelAndProgressBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace selection panel to the container.
- 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
- 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.
- addStructure(byte[], String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(byte[], String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(byte[], String, Map<String, String>) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(byte[], String, Map<String, String>, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(IMoleculeData) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
-
Adds the molecule and its properties into the predefined template.
- addStructure(IMoleculeData) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Adds the molecule structure to the end of the document without it's properties
- addStructure(IMoleculeData, ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Adds the molecule structure to the the document with the given settings without properties
- addStructure(IMoleculeData, ITemplateWriterOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
-
Adds the molecule and its properties into the predefined template.
- addStructure(Molecule, String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(Molecule, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(String, int, int, byte[]) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, byte[], String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, byte[], String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, byte[], String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, Molecule, String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, Molecule, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, String, String) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, int, int, String, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.JChemExcelAPI
-
Adds a structure to the cell in the given column/row on the sheet with the given name.
- addStructure(String, String, String) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(String, String, String, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(String, String, String, Map<String, String>) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructure(String, String, String, Map<String, String>, String, boolean) - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
A single structure can be added to the worksheet, in the current row
- addStructureAndProperties(IMoleculeData, ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Adds the molecule structure and all corresponding properties to the document with the give settings
- addStructures(IMoleculeData[]) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
-
Adds the array of molecule structures and their corresponding properties to the predefined template.
- addStructures(IMoleculeData[]) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Adds the array of molecule structures and their corresponding properties to the end of the document.
- addStructures(IMoleculeData[], ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Adds the array of molecule structures and their corresponding properties to the location given in the settings.
- addStructures(IMoleculeData[], ISettings, int) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Adds the array of molecule structures and their corresponding properties to the document with the give settings
- addStructures(IMoleculeData[], ITemplateWriterOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
-
Adds the array of molecule structures and their corresponding properties to the predefined template.
- addStructuresToCluster(Collection<Integer>, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
-
Add multiple structures to a cluster.
- addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
-
Set a structure to be a part of a cluster as a leaf.
- addStructureToCluster(int, int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
-
Add a structure to a cluster as an immediate leaf.
- addTable(ITableModel) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Adds the table custom table to the and of the Document
- addThreadLocal(NameConverter, int) - Static method in class chemaxon.naming.NameConverters
-
Add a thread-local name to structure converter.
- addTimestamp(String, Connection) - Method in class chemaxon.jchem.db.CacheRegistrationUtil
- addToolBar(RootPaneContainer) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Adds the basic MarvinSpace toolbar to the container.
- addToolsMenu(Container) - Method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.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
- addTransferable(TransferableDescriptor) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Add a
TransferableDescriptor
to theMTransferable
Registry. - addTransferable(String, String, Integer, Integer, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Deprecated.
- addTransferable(String, String, Integer, Integer, boolean, boolean, boolean) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Add a
TransferableDescriptor
to the registry, and constructing it by the given parameters. - 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.
- adjustMultiChiralFlag() - Method in class chemaxon.struc.MoleculeGraph
-
Checks whether the molecule has multiple chiral centres
- 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. - AdvancedCheckerRunner(ConfigurationReader, CheckerFixerFactory) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
-
Constructs
CheckerRunner
with more advanced fixing capabilities. - AdvancedCheckerRunner(List<StructureChecker>) - Constructor for class chemaxon.checkers.runner.AdvancedCheckerRunner
-
Constructs
CheckerRunner
with more advanced fixing capabilities. - 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_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
-
Execute 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, int[]) - Method in class chemaxon.util.MolHandler
-
Alignes (rotates) a specified molecule realtive to the contained molecule according to the specified atom pairs.
- 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
- ALIGNMENT - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Alignment
- ALIGNMENT_OFF - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
The structure is displayed with the original coordinates.
- ALIGNMENT_PARTIAL_CLEAN - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
The substructure part of the target will get the exact coordinates of the query, and new coordinates will be generated for the remainder of the structure.
- ALIGNMENT_ROTATE - Static variable in class chemaxon.util.HitColoringAndAlignmentOptions
-
The structure is rotated according to the substructure.
- AlignmentAccuracyMode - Enum Class in chemaxon.marvin.alignment
-
Settings for the representation of a molecular shape.
- 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.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.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.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.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.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.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
- ambient - Static variable in class chemaxon.marvin.space.monitor.Control
- 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(StandardizerWrapper) - Method in interface com.chemaxon.overlap.io.StandardizerWrapper
-
Create a new wrapper representing an additional step.
- 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.
- AngleMonitor - Class in chemaxon.marvin.space.monitor
-
Monitor for measuring angle between 3 components, the first 2 determines a line, the second 2 another.
- AngleMonitor() - Constructor for class chemaxon.marvin.space.monitor.AngleMonitor
-
Creates a new instance of AngleMonitor
- 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"
. - ANIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
- ANTI - Static variable in interface chemaxon.struc.StereoConstants
-
Non-CIP stereodescriptor, anti (relative configuration).
- 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
- anybond_auto - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues
- ANYBOND_AUTO - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - ANYBOND_AUTO_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - anybond_dashed - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues
- ANYBOND_DASHED - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - ANYBOND_DASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - ANYBOND_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - ANYBOND_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - anybond_solid - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.anyBondValues
- ANYBOND_SOLID - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - ANYBOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - ANYBOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.Use
AnyBondStyle
instead. - anyBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the drawing style for ANY bonds.
- AnyBondStyle - Enum Class in chemaxon.marvin.paint.constants
-
Holds the values for the possible rendering styles for Any bonds.
- 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
- anyCancelled(CancelObserver...) - Static method in class com.chemaxon.calculations.common.ProgressObservers
-
Returns a cancel observer which cancels when any of the specified observer is cancelled.
- 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.
- APPEND_TO_RESULT_TABLE - Static variable in class chemaxon.jchem.db.JChemSearch
-
Constant for the generation of result tables.
- 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.
- appendLongAsBinaryString(StringBuilder, long) - Method in enum class com.chemaxon.descriptors.common.BinaryVectors.Endianness
-
Convert 64 bit long to binary string.
- appendMEnd(Molecule) - 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(Molecule) - Method in interface chemaxon.calculator.CalculatorInputChecker
-
Checks the given molecule and returns the found errors, or an empty list of the molecule is valid.
- apply(BinaryVectorMetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.BinaryVectorMetricFactory.ToLinenote
- apply(MetricFactory<C>) - Method in class com.chemaxon.descriptors.metrics.MetricFactory.ToLinenote
- APPLY_DEPTH_CUE - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.As of Marvin 5.4.1, replaced by
DispOptConsts.AUTOMATIC_FOG
- 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.
- areArrowsAndLikelyTheSame(MPolyline, MPolyline) - Static method in class chemaxon.marvin.modules.reaction.ReactionEditUtils
-
Compares type and checks perfect equality of location.
- 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?
- areRGroupsHidden() - Method in class chemaxon.marvin.io.image.ImageExporter
- 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 - 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
- AROMATIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
- 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.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.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.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.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.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.as of release 5.5, replaced by
Ring.aromaticRings(int)
- 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() - Method in class chemaxon.util.MolHandler
-
Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds.
- 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) - Method in class chemaxon.util.MolHandler
-
Converts the bonds in an aromatic system entered using single and double bonds to aromatic bonds.
- 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.
- aromatizeBasic() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
-
Wrap basic aromatization.
- aromatizeGeneral() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
-
Wrap general aromatization.
- aromatizeLoose() - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
-
Wrap loose aromatization.
- Aromatizer - Enum Class in com.chemaxon.search.transformation.transformers
-
Aromatizer transformer.
- arrangeComponents() - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.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.
- arrangeCrossingBonds(MolBond, Molecule, boolean) - Static method in class chemaxon.marvin.util.MoleculeUtil
-
Deprecated.as of Marvin 5.11.1 use
MoleculeGraph.setBond(int, MolBond)
- 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.
- arrangeRgroupMembers(RgMolecule) - Method in class chemaxon.marvin.util.MolFragLoader
-
Arranges R-group definition member coordinates.
- 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 - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.LineType
- ARROW - Enum constant in enum class chemaxon.marvin.paint.constants.CoordinateBondStyle
-
Arrow is used when rendering Coordinate bonds.
- 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
- Assign(ICellFormat) - Method in interface chemaxon.formats.documents.jchemoffice.ICellFormat
-
Assign an existing cell format to the cell
- Assign(IMoleculeData) - Method in interface chemaxon.formats.documents.jchemoffice.ICellData
-
Assigns the structure to the cell and sets the molecule data and format
- Assign(String) - Method in interface chemaxon.formats.documents.jchemoffice.ICellData
-
Assigns the string content and string format to the cell
- associate(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicComponent
-
The given component will depend on this component.
- associatedComponents - Variable in class chemaxon.marvin.space.GraphicComponent
-
Strores components that depend on this component.
- asymmetricAtomCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates the number of atoms having four different ligands.
- asymmetricAtomCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated.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.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
- ATMAP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Show atom mapping flag.
- ATNUM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Show atom numbers flag.
- atom - Variable in class chemaxon.util.iterator.IteratorFactory.NeighbourIterator
-
The atom whose the neighbours are processed.
- 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_COUNT_UPPER_BOUND - Static variable in class chemaxon.clustering.libmcs.LibraryMcs
-
structures above this size are not searched for pair-wise mcs as it would take to long to calculate the MCS
- ATOM_FONT - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomFont"
. - ATOM_FONT - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Sets the atom font.
- 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_MAPPING_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Displays atom mapping.
- ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomNumberingType"
. - ATOM_NUMBERING_TYPE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Atom numbering type
- ATOM_NUMBERS - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.AtomNumberingType
- ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Deprecated.in 6.2.0 use atomNumberingType parameter instead.
- ATOM_NUMBERS_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Displays atom numbers.
- ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"atomPropertiesVisible"
. - ATOM_PROPERTIES_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
- ATOM_PROPERTY_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Coloring by mapping atom based property values to the surface.
- 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
- atomA - Variable in class chemaxon.marvin.space.monitor.DihedralControl
- atomAndBondColors(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Set the atom and bond colors.
- atomB - Variable in class chemaxon.marvin.space.monitor.DihedralControl
- 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.marvin.space.MolecularSurfaceComponent
- 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
- atomFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Atom font type.
- AtomIdentifier - Class in chemaxon.reaction
-
The identifier of an atom in the input of the reaction.
- AtomIdentifier(int, int) - Constructor for class chemaxon.reaction.AtomIdentifier
-
Initializes an atom identifier based on the input molecules of the reaction.
- AtomIdentifier(int, int, int) - Constructor for class chemaxon.reaction.AtomIdentifier
-
Initializes an atom identifier based on the input molecules of the reaction.
- 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.
- atomLabelSize(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the atom label font size.
- ATOMLIST - Static variable in class chemaxon.sss.search.MarkushFeature
-
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 - Variable in class com.chemaxon.search.MatchingOptions.Builder
- atomMapMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
-
Sets whether atom map numbers should be considered in search.
- atomMapMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
- atomMapping() - Method in interface chemaxon.marvin.alignment.MCSAlignmentResult
-
Array of atom - atom mapping.
- atomMapping() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Displays 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.
- atomNumber() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Displays atom numbers.
- atomNumberType(ImageExporter.AtomNumberingType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the type of atom numbering: Atom numbers or IUPAC numbering.
- AtomProperty - Class in chemaxon.marvin.space
-
The
AtomProperty
class provides access to chemical properties ofMolecule
atoms by atom index. - AtomProperty - Class in chemaxon.struc
-
Class for storing atom property enumerations.
- AtomProperty() - Constructor for class chemaxon.marvin.space.AtomProperty
- AtomProperty() - Constructor for class chemaxon.struc.AtomProperty
- AtomProperty.MoleculeAtomProperty - Class in chemaxon.marvin.space
- AtomProperty.Radical - Enum Class in chemaxon.struc
-
Enumeration of the supported radicals.
- AtomProperty.SmoleculeAtomProperty - Class in chemaxon.marvin.space
- 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 class chemaxon.struc.MoleculeGraph
-
Provides a list view of the atoms in the molecule.
- AtomSelection - Class in com.chemaxon.calculations.stereoanal.stereocenters
-
Selection which contains atom indexes.
- AtomSelection(int[], int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
-
Deprecated.
- AtomSelection(int, int[]) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtomSelection
-
Deprecated.
- 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.
- ATOMSIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Prefix of atom label font size parameter.
- 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 - Variable in class com.chemaxon.search.MatchingOptions.Builder
- atomTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
-
Sets whether atom types should be considered in search.
- atomTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
- AtomTyping - Enum Class in com.chemaxon.descriptors.alignment
-
Settings for shape associated atom typing.
- atomTypizer(EcfpAtomTypizers) - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
-
Set atom typizer to use.
- AtomValueChecker - Class in chemaxon.checkers
-
A descendant of
AtomChecker
detecting atoms with atom value. - AtomValueChecker() - Constructor for class chemaxon.checkers.AtomValueChecker
-
Default constructor.
- ATPROP_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Show atom properties flag.
- 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.
- AtropStereoCenter(AtomSelection, StereoConstants.StereoValue.AtropStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AtropStereoCenter
-
Deprecated.
- 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
- ATSYM_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Show atom symbols in 3D flag.
- 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)
. - ATTR_OPERATION - Static variable in class chemaxon.jchem.db.RegenerationChecker
- Au - Static variable in class chemaxon.core.ChemConst
- AUTO - Enum constant in enum class chemaxon.marvin.paint.constants.AnyBondStyle
-
Automatically decide whether Dashed or Solid rendering is used.
- AUTO_CHECK_STRUCTURE - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Automatic check for structures.
- AUTO_RESOLUTION_ENABLED - Static variable in class chemaxon.marvin.space.MolecularSurfaceComponent
- 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
-
Automatic ungroup bit in flags.
- autoGzip(InputStream) - Static method in class com.chemaxon.calculations.util.CmdlineUtils
-
Detect gzipped
InputStream
. - 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 - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- 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"
. - automaticSettingOfGridSize - Variable in class chemaxon.marvin.space.MolecularSurfaceComponent
- AverageLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.AverageLinkage
- 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.
- AxialStereoCenter(AtomSelection, StereoConstants.StereoValue.AxialStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.AxialStereoCenter
-
Deprecated.
- 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
- B_FACTOR_MODE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
- Ba - Static variable in class chemaxon.core.ChemConst
- BACKGROUND - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"background"
. - BACKGROUND_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
- BACKGROUND_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
- backgroundColor - Variable in class chemaxon.marvin.space.monitor.Label
- backgroundColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
- backgroundColorMode - Variable in class chemaxon.marvin.space.monitor.Label
- 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_AND_STICK - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.Rendering
- BALL_RADIUS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"ballRadius"
. - ballPrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
- ballRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
- ballRadius(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the ball radius in ball and stick mode.
- BALLRADIUS - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Ball radius for ball and stick mode.
- ballstick - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.renderingValues
- BALLSTICK - Enum constant in enum class chemaxon.marvin.paint.constants.RenderingStyle
-
Stick rendering style with balls at atoms
- BALLSTICK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.use
RenderingStyle
instead. - BALLSTICK_RENDERING_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.use
RenderingStyle
instead. - BASE64 - Static variable in class chemaxon.formats.MFileFormat
-
BASE64 encoded file.
- BaseColor16 - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
-
16 base colors defined with a palette, image data contains 2 bits/pixel
- BaseColor256 - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
-
256 colors defined with a palette, image data contains 2 bits/pixel
- BaseShapeComparatorParameter - Class in com.chemaxon.descriptors.alignment
- BaseShapeComparatorParameter(AlignmentProperties.FlexibilityMode, ShapeFunction, Optional<Integer>) - Constructor for class com.chemaxon.descriptors.alignment.BaseShapeComparatorParameter
- BASIC - Enum constant in enum class chemaxon.standardizer.actions.AromatizeAction.Type
-
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
- BemisMurckoClustering - Class in com.chemaxon.clustering.framework
-
Convenience utilities for using Bemis-Murcko clustering.
- bemismurckoloose - Enum constant in enum class chemaxon.marvin.calculations.StructuralFrameworksPlugin.FrameworkTypes
- bgColor(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the background color.
- bgColorAlpha(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the background color with alpha value.
- Bh - Static variable in class chemaxon.core.ChemConst
- Bi - Static variable in class chemaxon.core.ChemConst
- BIG_ENDIAN - Enum constant in enum class com.chemaxon.descriptors.common.BinaryVectors.Endianness
-
Decreasing numeric significance with increasing addresses/indices.
- BINARY_COMMONPART - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
-
Commonly set bits.
- BINARY_COMMONPART_NORMALIZED - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
-
Common set bit ratio.
- BINARY_DESCRIPTOR - Static variable in class chemaxon.descriptors.CDParameters
-
descriptor type constants
- BINARY_DICE - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
-
Dice's similarity measure.
- BINARY_EUCLIDEAN - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
-
Euclidean distance.
- BINARY_EUCLIDEAN_NORMALIZED - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
-
Normalized Euclidean distance.
- BINARY_TANIMOTO - Enum constant in enum class com.chemaxon.descriptors.metrics.BinaryMetrics
-
Tanimoto coefficient.
- 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.
- BinaryMetrics - Enum Class in com.chemaxon.descriptors.metrics
-
Simple metrics suitable for finite length binary vectors.
- 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.
- BinaryVectorComparator - Interface in com.chemaxon.descriptors.metrics
-
Basic functionality for finite binary vector based calculations.
- BinaryVectorComparator.Util - Class in com.chemaxon.descriptors.metrics
-
Simple consistency check utility.
- BinaryVectorDescriptor - Interface in com.chemaxon.descriptors.common
-
BinaryVectorDescriptor is a
Descriptor
which holds a fixed length binary fingerprint. - BinaryVectorMetricFactory<C> - Interface in com.chemaxon.descriptors.metrics
-
Represents available metrics for binary vector based descriptors.
- BinaryVectorMetricFactory.ToLinenote<C> - Class in com.chemaxon.descriptors.metrics
-
Utility for creating a default linenote.
- BinaryVectors - Class in com.chemaxon.descriptors.common
-
Utility methods related to bit string descriptors.
- BinaryVectors.Endianness - Enum Class in com.chemaxon.descriptors.common
-
Order of components in packed representations.
- 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.
- bitsPerPattern(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
-
Set bits per pattern.
- Bk - Static variable in class chemaxon.core.ChemConst
- BlackWhite - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
-
Black and white colors defined with a palette, image data contains 1 bit/pixel
- BlackWhiteGray - Enum constant in enum class chemaxon.marvin.io.image.exporter.PngExporter.BitPixelValues
-
Black, white, light, and dark gray colors defined with a palette, image data contains 2 bits/pixel
- BLUE - Static variable in class chemaxon.marvin.plugin.CalculatorPlugin
-
Constant storing the blue rgb value (the basic pKa result color).
- Bold - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
- 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"
. - BOLD_BOND_WIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Prefix of bold bond width parameter.
- BoldItalic - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
- BoldItalicUnderline - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
- BoldUnderline - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontStyle
- bond - Variable in class chemaxon.marvin.space.monitor.DihedralControl
- 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_DRAW_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
- BOND_DRAW_TYPE_STICK - Static variable in class chemaxon.marvin.space.MoleculeComponent
- BOND_DRAW_TYPE_WIRE - Static variable in class chemaxon.marvin.space.MoleculeComponent
- BOND_FACING - Static variable in class chemaxon.marvin.space.MoleculeComponent
- BOND_HASH_SPACING - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"bondHashSpacing"
. - BOND_HASH_SPACING - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Prefix of bondHashSpacing parameter.
- 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 - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Prefix of bond length parameter.
- BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"bondLengthVisible"
. - BOND_LENGTH_VISIBLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Show bond lengths.
- 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.
- bondCount(int) - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
-
Set bond count to consider.
- bondDistance - Variable in class chemaxon.marvin.space.MoleculeComponent
- bondFacing - Variable in class chemaxon.marvin.space.MoleculeComponent
- bondHashSpacing() - Method in class chemaxon.marvin.io.image.ImageExporter
- bondHashSpacing(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
The spacing of the hash in hashed bonds in C-C bond length units.
- 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.
- BONDLEN_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Show bond lengths flag.
- bondlength() - Method in class chemaxon.struc.Molecule
-
Calculate the regular bond length for the unified structure.
- bondlength() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the regular bond length.
- 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
-
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.
- bondRadius - Variable in class chemaxon.marvin.space.MoleculeComponent
- bonds() - Method in class chemaxon.struc.MolAtom
-
Provides a list view of the connected bonds of the atom.
- bonds() - Method in class chemaxon.struc.MoleculeGraph
-
Provides a 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.
- bondSlicePrecision - Variable in class chemaxon.marvin.space.MoleculeComponent
- 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)
- bondTypeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
- bondTypeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
-
Sets whether bond types should be considered in search.
- bondTypeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
- bondweights(double[], CTransform3D) - Method in class chemaxon.struc.MolAtom
-
Calculates the average of the bond unit vectors pointing out of this atom.
- bondWidth - Variable in class chemaxon.marvin.space.MoleculeComponent
- bondWidth(double) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the width of the double bond.
- BONDWIDTH - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Prefix of bond width parameter.
- BOOL - Static variable in class chemaxon.marvin.util.OptionDescriptor
-
Boolean option.
- BOOLEAN - Enum constant in enum class com.chemaxon.apidiscovery.ParameterWrapper.ParameterType
-
A boolean parameter (primitive type).
- 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"
. - BORDER_MODE_BRIGHTER_FOREGROUND - Static variable in class chemaxon.marvin.space.monitor.Label
- BORDER_MODE_FOREGROUND_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
- BORDER_MODE_NONE - Static variable in class chemaxon.marvin.space.monitor.Label
- BORDER_MODE_OWN_COLOR - Static variable in class chemaxon.marvin.space.monitor.Label
- borderColor - Variable in class chemaxon.marvin.space.monitor.Label
- borderColorChanged - Variable in class chemaxon.marvin.space.monitor.Label
- borderColorMode - Variable in class chemaxon.marvin.space.monitor.Label
- BOTH - Static variable in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Deprecated.
- Bottom - Enum constant in enum class chemaxon.formats.documents.jchemoffice.PropertyTablePosition
- BottomCenter - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontAlignment
- BottomLeft - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontAlignment
- BottomRight - Enum constant in enum class chemaxon.formats.documents.jchemoffice.FontAlignment
- boundingBox - Variable in class chemaxon.marvin.space.GraphicComponent
-
The smallest box containing the graphic component.
- BoundingBox - Class in chemaxon.marvin.space
-
Class for representing a bounding box of any component in the 3D space.
- BoundingBox() - Constructor for class chemaxon.marvin.space.BoundingBox
-
Creates a new instance of BoundingBox but does not set anything.
- BoundingBox(float, float, float, float, float, float) - Constructor for class chemaxon.marvin.space.BoundingBox
-
Creates a bounding box with the given coordinates, computes the center and radius of the box.
- 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.MolConverter.Builder
-
Builds the MolConverter.
- build() - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- build() - Method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder
-
Builds an unmodifiable export option.
- build() - Method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder
-
Builds an unmodifiable export option.
- build() - Method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder
-
Builds an unmodifiable export option.
- build() - Method in class chemaxon.marvin.io.image.exporter.JpegExporter.Builder
-
Builds an unmodifiable export option.
- build() - Method in class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder
-
Builds an unmodifiable export option.
- build() - Method in class chemaxon.marvin.io.image.exporter.PngExporter.Builder
-
Builds an unmodifiable export option.
- build() - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Builds an unmodifiable export option.
- 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 interface com.chemaxon.apidiscovery.interfaces.ParameterBuilder
-
Constructs an immutable instance of T.
- build() - Method in class com.chemaxon.clustering.common.IDBasedClusterBuilder
-
Build immutable clustering representation.
- build() - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
-
Build the immutable clustering representation.
- build() - Method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
- build() - Method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
- build() - Method in class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
-
Build a new instance of MaccsParameters.
- build() - Method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
- build() - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
- build() - Method in class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
- build() - Method in class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
- build() - Method in class com.chemaxon.search.MatchingOptions.Builder
-
Creates a search options object with the settings specified by this builder instance.
- build() - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
- build(IDBasedAssignerBuilder) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
-
Build an immutable snapshot of the clustering.
- build(DescriptorGenerator<D>, DescriptorComparator<D>) - Method in class com.chemaxon.clustering.common.MolInputBuilder
-
Build immutable input descriptor.
- buildButtonBar() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
- buildContentPanel() - Method in class chemaxon.marvin.uif.dialog.LicenseDialog
- builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.EmfExporter
-
Creates a builder for this class.
- builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.PdfExporter
-
Creates a builder for this class.
- builder() - Static method in class chemaxon.marvin.io.formats.vectgraphics.SvgExporter
-
Creates a builder for this class.
- builder() - Static method in class chemaxon.marvin.io.image.exporter.JpegExporter
-
Creates a builder for this class.
- builder() - Static method in class chemaxon.marvin.io.image.exporter.MsbmpExporter
-
Creates a builder for this class.
- builder() - Static method in class chemaxon.marvin.io.image.exporter.PngExporter
-
Creates a builder for this class.
- 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.MolConverter.Builder
-
Constructs an empty Builder object.
- Builder() - Constructor for class chemaxon.marvin.calculations.HlbPlugin.Builder
- Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.EmfExporter.Builder
- Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.PdfExporter.Builder
- Builder() - Constructor for class chemaxon.marvin.io.formats.vectgraphics.SvgExporter.Builder
- Builder() - Constructor for class chemaxon.marvin.io.image.exporter.JpegExporter.Builder
- Builder() - Constructor for class chemaxon.marvin.io.image.exporter.MsbmpExporter.Builder
- Builder() - Constructor for class chemaxon.marvin.io.image.exporter.PngExporter.Builder
- Builder() - Constructor for class chemaxon.marvin.io.image.ImageExporter.Builder
- Builder() - Constructor for class chemaxon.naming.document.annotate.DocumentAnnotatorOptions.Builder
- Builder() - Constructor for class chemaxon.standardizer.StandardizerActionFactory.Builder
- Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
-
Constructor with default settings.
- Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
-
Constructor with default settings.
- Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
-
Constructor mandated by descriptors API contracts.
- Builder() - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
-
Constructor with default settings.
- Builder() - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
-
Instantiate builder with default values.
- Builder() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
-
Constructor with default settings.
- Builder() - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
-
Constructor with default settings.
- Builder() - Constructor for class com.chemaxon.search.MatchingOptions.Builder
-
Creates a Builder object with the default settings.
- Builder() - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Creates a Builder object with the default settings.
- Builder(double, double) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
-
Instantiate with weights.
- Builder(CfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.Builder
-
Constructor based on a parameter object.
- Builder(EcfpParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.Builder
-
Constructor based on a parameter object.
- Builder(MaccsParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.Builder
-
Constructor mandated by descriptors API contracts.
- Builder(PfParameters) - Constructor for class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.Builder
-
Constructor based on a parameter object.
- Builder(TverskyParameters) - Constructor for class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
-
Instantiate builder based on an actual parameter instance.
- Builder(BvParameters) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters.Builder
-
Construct to represent the state of a parameter object instance.
- Builder(FvParameters) - Constructor for class com.chemaxon.descriptors.vectors.floats.FvParameters.Builder
-
Construct to represent the state of a parameter object instance.
- Builder(MatchingOptions) - Constructor for class com.chemaxon.search.MatchingOptions.Builder
-
Creates a Builder object containing the settings of the given search options object.
- Builder(McsSearchOptions) - Constructor for class com.chemaxon.search.mcs.McsSearchOptions.Builder
-
Creates a Builder object containing the settings of the given search options object.
- builderClass() - Element in annotation interface com.chemaxon.apidiscovery.annotations.BuilderClass
-
Associated builder class for this immutable object.
- BuilderClass - Annotation Interface in com.chemaxon.apidiscovery.annotations
-
This annotation gives information about the associated
ParameterBuilder
for this class. - 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. - BUILT_IN_CHAIN_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Coloring by built-in chain colors.
- BUILT_IN_CPK_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Coloring by built-in cpk colors.
- BUILT_IN_RAINBOW_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Coloring by built-in rainbow colors.
- BUILT_IN_RESIDUE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Coloring by built-in residue colors.
- BUILT_IN_SECONDARY_STRUCTURE_MAPPING - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Coloring by built-in secondary structure colors.
- BUTTON_MENUBAR - Static variable in class chemaxon.marvin.sketch.SketchParameterConstants
-
Identifier of parameter:
"buttonmenubar"
. - BvGenerator - Interface in com.chemaxon.descriptors.vectors.binary
-
Generator for generic binary vector descriptors.
- BvParameters - Class in com.chemaxon.descriptors.vectors.binary
-
Parameters for generic binary vector descriptor.
- BvParameters() - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters
-
Construct with default values.
- BvParameters(BvParameters.Builder) - Constructor for class com.chemaxon.descriptors.vectors.binary.BvParameters
-
Constructor based on a builder.
- BvParameters.Builder - Class in com.chemaxon.descriptors.vectors.binary
-
Builder for BvParameters.
- BvParameters.ConstructBvGenerator - Interface in com.chemaxon.descriptors.vectors.binary
-
Interface representing BvGenerator implementation constructor
- BvParameters.StringFormat - Enum Class in com.chemaxon.descriptors.vectors.binary
-
Fingerprint textual representation.
- BYTE - Static variable in class chemaxon.naming.document.DocumentToStructure
-
For internal usage only.
- BYTES_IN_INT - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
-
Number of bytes in an int.
- BYTES_IN_LONG - Static variable in class com.chemaxon.descriptors.common.BinaryVectors
-
Number of bytes in a long.
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_REGISTRATION_SENSITIVITY_EXCEPTION - Static variable in class chemaxon.jchem.db.CacheRegistrationUtil
-
Error sensitivity - exception.
- CACHE_REGISTRATION_SENSITIVITY_LOG - Static variable in class chemaxon.jchem.db.CacheRegistrationUtil
-
Error sensitivity - log
- CACHE_REGISTRATION_SENSITIVITY_NONE - Static variable in class chemaxon.jchem.db.CacheRegistrationUtil
-
Error sensitivity - none.
- CACHE_REMOVAL_METHOD_LOADTIME - Enum constant in enum class chemaxon.jchem.db.cache.CacheManager.CacheRemovalMethodImplementation
- CACHE_REMOVAL_METHOD_LRU - Enum constant in enum class chemaxon.jchem.db.cache.CacheManager.CacheRemovalMethodImplementation
- 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.
- CacheManager - Enum Class in chemaxon.jchem.db.cache
-
Singleton for managing cache-related functions.
- CacheManager.CacheRemovalMethodImplementation - Enum Class in chemaxon.jchem.db.cache
-
For internal use only.
- cacheMemory - Variable in class chemaxon.struc.MoleculeGraph
- CacheRegistrationUtil - Class in chemaxon.jchem.db
-
Utility class for cache registration.
- CacheRegistrationUtil(ConnectionHandler) - Constructor for class chemaxon.jchem.db.CacheRegistrationUtil
- 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.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.
- calcDissimilarity(MDReader, MDReader) - Method in class chemaxon.descriptors.MDHitEvaluator
-
Precalculates dissimilarity values.
- calcDividingPoint(DPoint3, DPoint3, double) - Static method in class chemaxon.marvin.util.CleanUtil
-
Calculates the division point of a segment with a given ratio.
- calcExpTime() - Method in class chemaxon.jchem.file.ProgressWriter
-
Recalculates expected time.
- 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
- calcMetricDistribution(int, int, float, float, int, float[]) - Method in class chemaxon.descriptors.MDHitEvaluator
-
Retrieves the distribution of the given metric from the dissimilarity values calculated by a previous call to
calcDissimilarity()
. - calcMetricDistribution(int, int, float, float, int, float[], MDReader, MDReader) - Method in class chemaxon.descriptors.MDHitEvaluator
-
Retrieves the distribution of the given metric from the dissimilarity values calculated by a screen using the given two molecular descriptor readers.
- calcMinDist() - Method in class chemaxon.marvin.alignment.MinMaxDistance
-
Calculates the minimum distance between two atoms in the molecule.
- calcMolFormula() - Method in class chemaxon.util.MolHandler
-
Calculates the molecular formula of the molecule.
- calcMolWeight() - Method in class chemaxon.util.MolHandler
-
Calculates the molecular weight of the molecule.
- calcMolWeightInDouble() - Method in class chemaxon.util.MolHandler
-
Calculates the molecular weight of 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, SubProgressObserver) - Method in class chemaxon.marvin.alignment.AtropIsomerDetector
-
Run the atropisomer calculation.
- calculate(Molecule, SubProgressObserver, 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.
- calculateBinaryVectorDissimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
-
Calculate represented dissimilarity score from binary vector parameters.
- calculateBinaryVectorDissimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
- calculateBinaryVectorSimilarity(int, int, int, int) - Method in interface com.chemaxon.descriptors.metrics.BinaryVectorComparator
-
Calculate represented similarity score from binary vector parameters.
- calculateBinaryVectorSimilarity(int, int, int, int) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters
- 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.
- calculateCosAFromScalarMul(MolBond, MolBond) - Static method in class chemaxon.checkers.StructureCheckerHelper
-
Calculate the cosines value of the angle between the bonds from the scalar multiplication of the bonds.
- calculateDarkness() - Method in interface com.chemaxon.descriptors.common.BinaryVectorDescriptor
-
Calculate the darkness of this fingerprint.
- calculateDissimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
- calculateDissimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
-
Compare two descriptors in serialized form.
- calculateDissimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
-
Compare two descriptors.
- calculateDissimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
- calculateDissimilarityMatrix(DissimilarityInput, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
-
Distance matrix calculation.
- calculateFloatVectorDissimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
-
Calculate dissimilarity.
- calculateFloatVectorSimilarity(float[], float[]) - Method in interface com.chemaxon.descriptors.metrics.FloatVectorComparator
-
Deprecated.In various cases (euclid, euclid sqr, manhattan) this has no practical interpretation
- 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.
- calculateSimilarity(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
- calculateSimilarity(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
-
Compare two descriptors in serialized form.
- calculateSimilarity(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
-
Compare two descriptors.
- calculateSimilarity(T, T) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
- 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.
- CALCULATIONS_PACK - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: Calculations Pack
- 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>) - 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
- CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin
-
Deprecated, for removal: This API element is subject to removal in a future version.This class has been moved to a new package, import and use it from its new location:
CalculatorPluginDisplay
- CalculatorPluginDisplay<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.gui
-
Common base class for calculator plugin displays.
- CalculatorPluginDisplay() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginDisplay
-
Deprecated.
- CalculatorPluginDisplay() - Constructor for class com.chemaxon.calculations.gui.CalculatorPluginDisplay
- CalculatorPluginOutput<P extends CalculatorPlugin> - Class in chemaxon.marvin.plugin
-
Deprecated, for removal: This API element is subject to removal in a future version.This class has been moved to a new package, import and use it from its new location:
CalculatorPluginOutput
- CalculatorPluginOutput<P extends CalculatorPlugin> - Class in com.chemaxon.calculations.cli
-
Class providing plugin output in table form.
- CalculatorPluginOutput() - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Deprecated.
- CalculatorPluginOutput() - Constructor for class com.chemaxon.calculations.cli.CalculatorPluginOutput
-
Default constructor.
- CalculatorPluginOutput(CalculatorPlugin) - Constructor for class chemaxon.marvin.plugin.CalculatorPluginOutput
-
Deprecated.
- 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
- calcWidth() - Method in class chemaxon.struc.MoleculeGraph
-
Calculates the molecule width.
- call() - Method in class chemaxon.marvin.plugin.concurrent.PluginWorkUnit
-
Performs the calculation and returns the result returned by
PluginWorkUnit.getResult()
. - call() - Method in class chemaxon.marvin.plugin.concurrent.ReusablePluginWorkUnit
-
Performs the calculation and returns the result returned by
ReusablePluginWorkUnit.getResult()
. - callback(String, Object) - Method in interface chemaxon.jep.ChemContext
-
Implements
CallbackIface
. - callback(String, Object) - Method in class chemaxon.jep.ChemJEP
-
Delegates
CallbackIface.callback(String, Object)
to the context. - callback(String, Object) - Method in class chemaxon.jep.context.AtomContext
-
Implements
CallbackIface
. - callback(String, Object) - Method in class chemaxon.jep.context.MolContext
-
Implements
CallbackIface
. - callback(String, Object) - Method in class chemaxon.jep.context.ReactionContext
-
Implements
CallbackIface
. - callback(String, Object) - Method in class chemaxon.marvin.space.GraphicScene
- callback(String, Object) - Method in class chemaxon.marvin.space.MolecularSurfaceComponent
- callback(String, Object) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Callback function to make avoiding direct calls easier.
- 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.Line can be in the given format.
- CAN_BE - Static variable in class chemaxon.formats.recognizer.PDBRecognizer
-
Deprecated.Line can be in the given format.
- canBe1LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
-
Deprecated.Tests whether a string can be one-letter-abbreviated peptide name.
A valid name contains only uppercase letters. - canBe3LetterPeptide(String) - Static method in class chemaxon.formats.recognizer.PeptideRecognizer
-
Deprecated.Tests whether a string can be three-letter-abbreviated peptide name.
- 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.Tests whether a string can be SMARTS.
- canBeSMILES(String) - Static method in class chemaxon.formats.recognizer.SMILESRecognizer
-
Deprecated.Tests whether a string can be SMILES.
- cancel() - Method in interface chemaxon.checkers.runner.CheckerRunner
-
Stops the background thread
- cancel() - Method in class chemaxon.jchem.db.Importer
-
Stops the importing progress.
- 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
- CancelObserver - Interface in com.chemaxon.calculations.common
-
Callback to propagate cancel requests into long running tasks.
- canHandle(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory
-
Returns true if this factory can handle the given xml.
- CANONICAL - Enum constant in enum class chemaxon.standardizer.actions.TautomerizeAction.TautomerForm
- 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.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.as of release 5.5, replaced by
Ring.carboaromaticRingCount()
- CARBON_VIS_INCHAIN - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility is switched on in chain.
- CARBON_VIS_INCHAIN_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
String constant for switching on carbon-visibility in chain.
- CARBON_VIS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility mask.
- CARBON_VIS_OFF - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility is switched off.
- CARBON_VIS_OFF_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
String constant for switching off carbon-visibility.
- CARBON_VIS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility offset.
- CARBON_VIS_ON - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Carbon-visibility is switched on.
- CARBON_VIS_ON_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
String constant for switching on carbon-visibility.
- CARBON_VIS_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Array of carbon-visibility styles.
- carbonDisplay(ImageExporter.CarbonDisplay) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Show the atom labels on carbon atoms.
- 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.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.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.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.as of release 5.5, replaced by
Ring.carboRings(int)
- CardLayoutArrangement - Enum Class in chemaxon.formats.documents.jchemoffice
- CARTRIDGE - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: JChem Cartridge
- CATIONIC_TYPE - Static variable in class chemaxon.marvin.space.PharmacophorePoint
- 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"
. - CELL_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
- CellOrComponentId - Class in chemaxon.marvin.space
-
Class to identify cells and components.
- CellOrComponentId(int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
-
Creates a cell id.
- CellOrComponentId(int, int) - Constructor for class chemaxon.marvin.space.CellOrComponentId
-
Creates an id.
- 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
- center - Variable in class chemaxon.marvin.space.monitor.Control
- center - Variable in class chemaxon.marvin.space.monitor.DihedralControl
- centerx() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the x coordinate of the center of the box.
- centery() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the y coordinate of the center of the box.
- centerz() - Method in class chemaxon.marvin.space.BoundingBox
-
Returns the z coordinate of the center of the box.
- 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. - CFGenerator(int) - Constructor for class chemaxon.descriptors.CFGenerator
-
Deprecated.since 5.4
- 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.
- Cfp - Interface in com.chemaxon.descriptors.fingerprints.cfp
-
Folded fixed length bit string representation of the CFP descriptor.
- 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.
- CfpComparator - Interface in com.chemaxon.descriptors.fingerprints.cfp
-
Comparator for
Cfp
descriptor representation. - CfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
-
Calculates CFP (fixed length folded binary vector representation) descriptors.
- CfpParameters - Class in com.chemaxon.descriptors.fingerprints.cfp
-
CFP parameters class.
- CfpParameters() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
-
Constructor using the default settings.
- CfpParameters.Builder - Class in com.chemaxon.descriptors.fingerprints.cfp
-
Builder class for the immutable parameter object.
- CfpParameters.ConstructCfpGenerator - Interface in com.chemaxon.descriptors.fingerprints.cfp
-
Interface representing CFP generator constructor.
- CfpTableReader - Class in com.chemaxon.descriptors.fingerprints.cfp
-
MDTable reader for CFP.
- CfpTableReader() - Constructor for class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
- CfpTableReader.Factory - Interface in com.chemaxon.descriptors.fingerprints.cfp
-
Factory class.
- CHAIN - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.CarbonDisplay
- 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.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.as of release 5.5, replaced by
Ring.chainBondCount()
- chainOf(StandardizerWrapper...) - Static method in class com.chemaxon.overlap.io.StandardizerWrappers
-
Create a chained wrapper.
- 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.
- changeColorMapperColors(int) - Method in class chemaxon.marvin.space.SurfaceColoring
-
Switches to another built-in color palette and leaves minimum, maximum and cutoff values unchanged.
- 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).
- charAt(int) - Method in class chemaxon.struc.graphics.MTextDocument
-
Gets a character of the document.
- CHARGE_FONT - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Sets the circled charge's font.
- CHARGE_FONT_SIZE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Sets the circled charge's font.
- 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_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Charge Plugin Group
- CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"chargeWithCircle"
. - CHARGE_WITH_CIRCLE - Static variable in class chemaxon.marvin.io.image.ImageExportParamConstants
-
Show charge symbols in a circle.
- CHARGE_WITH_CIRCLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
- CHARGE_WITH_CIRCLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
- CHARGED_H - Static variable in class chemaxon.struc.MolAtom
-
Include charged Hydrogen atom(s).
- chargeFont(String) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Font type in circled charge display.
- chargeMatching - Variable in class com.chemaxon.search.MatchingOptions.Builder
- chargeMatching(boolean) - Method in class com.chemaxon.search.MatchingOptions.Builder
-
Sets whether formal charges of atoms should be considered in search.
- chargeMatching(boolean) - Method in class com.chemaxon.search.mcs.McsSearchOptions.Builder
- 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 - 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.
- checkBitCounts(int, int, int, int) - Static method in class com.chemaxon.descriptors.metrics.BinaryVectorComparator.Util
-
Check that descriptor comparison parameters are consistent.
- 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.
- checkChemTermColValue(Object) - Static method in class chemaxon.jchem.db.UpdateHandler
- checkConsistency() - Method in class chemaxon.struc.Molecule
-
Deprecated.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.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.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
- CHECKERCONFIG_XML - Static variable in class chemaxon.checkers.StructureCheckerFactory
-
Deprecated.Chemaxon's default checker configuration file name
- 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
- checkError() - Method in class chemaxon.util.ErrorHandler
-
Throws the exception stored in the object.
- 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 - checkException() - Method in class chemaxon.jchem.db.JChemSearch
- checkException() - Method in class chemaxon.util.ErrorHandler
-
Throws the exception stored in the object.
- 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.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?
- CHEM_CURATOR_COMPOUND - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: ChemCurator Compound
- CHEM_CURATOR_FULL - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: ChemCurator Full
- 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.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.clustering - package chemaxon.clustering
-
Provides classes for clustering.
- chemaxon.clustering.adapter - package chemaxon.clustering.adapter
- chemaxon.clustering.libmcs - package chemaxon.clustering.libmcs
- chemaxon.clustering.libmcs.adapter - package chemaxon.clustering.libmcs.adapter
-
Adapter to expose
LibraryMcs
clustering through the (com.chemaxon.clustering
) API. - chemaxon.common.util - package chemaxon.common.util
- 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
-
Classes for virtual screening using Molecular 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.documents.jchemexcel - package chemaxon.formats.documents.jchemexcel
- chemaxon.formats.documents.jchemoffice - package chemaxon.formats.documents.jchemoffice
- chemaxon.formats.recognizer - package chemaxon.formats.recognizer
-
Provides classes to recognize files of various file formats.
- chemaxon.jchem.db - package chemaxon.jchem.db
-
Provides classes for database operations.
- chemaxon.jchem.db.cache - package chemaxon.jchem.db.cache
- chemaxon.jchem.file - package chemaxon.jchem.file
- 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.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.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.io.formats.vectgraphics - package chemaxon.marvin.io.formats.vectgraphics
- chemaxon.marvin.io.image - package chemaxon.marvin.io.image
- chemaxon.marvin.io.image.exporter - package chemaxon.marvin.io.image.exporter
- chemaxon.marvin.modules.datatransfer - package chemaxon.marvin.modules.datatransfer
-
Since Marvin 5.3 this package contains the clipboard handler infrastructure in Marvin.
- chemaxon.marvin.modules.reaction - package chemaxon.marvin.modules.reaction
- chemaxon.marvin.paint - package chemaxon.marvin.paint
-
Defines display options constants.
- chemaxon.marvin.paint.constants - package chemaxon.marvin.paint.constants
- 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.space - package chemaxon.marvin.space
-
Contains the core classes of MarvinSpace including the graphic canvas and the basic visualizer classes.
- chemaxon.marvin.space.monitor - package chemaxon.marvin.space.monitor
-
Classes that represent measurement and changing of coordinates according to measurements in MarvinSpace.
- chemaxon.marvin.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.util.codeassist - package chemaxon.marvin.util.codeassist
- 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.pharmacophore - package chemaxon.pharmacophore
-
Classes for pharmacophore point perception, pharmacophore fingerprint generation and pharmacophore dissimilarity calculations.
- chemaxon.reaction - package chemaxon.reaction
-
Classes for reaction processing related tasks.
- chemaxon.sss - package chemaxon.sss
-
Contains packages for structure search and screening.
- chemaxon.sss.formula - package chemaxon.sss.formula
- chemaxon.sss.screen - package chemaxon.sss.screen
-
Classes for screeening.
- chemaxon.sss.search - package chemaxon.sss.search
-
Provides structural search capabilities.
- 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.util - package chemaxon.util
-
Provides general utility classes.
- chemaxon.util.concurrent.marvin - package chemaxon.util.concurrent.marvin
- chemaxon.util.iterator - package chemaxon.util.iterator
-
Provides iterator classes for molecules and their components.
- ChemConst - Class in chemaxon.core
- ChemConst() - Constructor for class chemaxon.core.ChemConst
- ChemContext - Interface in chemaxon.jep
-
Interface of expression evaluation contexts.
- CHEMICAL_ATOM_TYPES - Enum constant in enum class com.chemaxon.descriptors.alignment.AtomTyping
- 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 - Class in chemaxon.jep
-
Expression parser and evaluator for chemical expressions.
- ChemJEP() - Constructor for class chemaxon.jep.ChemJEP
-
Constructor.
- ChemJEP(Class) - Constructor for class chemaxon.jep.ChemJEP
-
Constructor.
- CHEMLOCATOR_PERSONAL - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: ChemLocator Personal
- CHEMLOCATOR_SERVER - Static variable in class chemaxon.license.LicenseManager
-
Identifier of product: ChemLocator Server
- chemTermColValues - Variable in class chemaxon.jchem.db.UpdateHandler.RowData
- chiral_all - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
- CHIRAL_ALL - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
- CHIRAL_ALL_POSSIBLE - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
- chiral_allPossible - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
- CHIRAL_FLAG - Enum constant in enum class chemaxon.checkers.StructureCheckerErrorType
-
Error type represents molecules marked with "absolute stereo" flag.
- chiral_off - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
- CHIRAL_OFF - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
- chiral_selected - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.chiralValues
- CHIRAL_SELECTED - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.ChiralityDisplayOption
- chiralCenterCount() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Calculates the number of chiral centers.
- chiralCenterCount() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated.as of release 5.5, replaced by
Stereochemistry.chiralCenterCount()
- chiralCenterCount() - Method in class chemaxon.marvin.calculations.StereoisomerPlugin
-
Deprecated.Calculates the number of tetrahedral stereogenic centers.
- chiralCenters() - Method in class chemaxon.calculations.stereo.Stereochemistry
-
Determines the chiral center atoms.
- chiralCenters() - Method in class chemaxon.calculations.TopologyAnalyser
-
Deprecated.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"
. - chiralityDisplay(ImageExporter.ChiralityDisplayOption) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the chirality display option.
- 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.If substituents located on the same side of the reference plane.
- 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.
- CisTransStereoCenter(AtomSelection, StereoConstants.StereoValue.CisTransStereo, List<AttachedData>) - Constructor for class com.chemaxon.calculations.stereoanal.stereocenters.CisTransStereoCenter
-
Deprecated.
- 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
- CLASS_NOT_FOUND_ERROR - Static variable in class chemaxon.util.ErrorHandler
- className - Variable in class chemaxon.standardizer.StandardizerActionFactory.StandardizerClassDescriptor
- clean(boolean, String) - Method in class chemaxon.util.MolHandler
-
Calculates 2D coordinates.
- clean(int) - Method in class chemaxon.formats.MolConverter.Builder
-
Enables cleaning.
- clean(int) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- clean(int, String) - Method in class chemaxon.formats.MolConverter.Builder
-
Enables cleaning.
- clean(int, String) - Method in class chemaxon.formats.MolConverter.Options
-
Deprecated.
- clean(int, String) - Method in class chemaxon.struc.MoleculeGraph
-
Deprecated.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.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"
. - cleanResults() - Method in class chemaxon.jchem.db.JChemSearch
-
Cleans stored search results.
- cleanup() - Method in class chemaxon.marvin.space.GraphicComponent
- cleanup() - Method in class chemaxon.marvin.space.PharmacophoreArrow
- cleanup() - Method in class chemaxon.marvin.space.PharmacophorePoint
- cleanup(long) - Method in class chemaxon.reaction.ConcurrentReactorProcessor
-
Cancels work currently executed, awaits termination of associated worker threads and releases any resource this processor has reserved.
- 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.
- clear() - Method in class chemaxon.jchem.file.ProgressWriter
-
Clears texts except main text.
- 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.marvin.space.BoundingBox
-
Clears all previously set coordinate from the box.
- clear() - Method in class chemaxon.marvin.space.monitor.Monitor
-
Deletes all items from selectedItems.
- clear() - Method in class chemaxon.pharmacophore.PMap
-
Sets every feature for every atom to
false
- 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
- clearAllCellStyle() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Clears all the previously set cell style of the property columns
- clearAllColumnWidth() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Clears all the previously set width of the property columns
- clearAssigned() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
- clearCache() - Method in enum class chemaxon.jchem.db.cache.CacheManager
-
Clears the cache that stores fingerprints and structures.
- 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
- clearClipboard() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Clears the clipboard by creating an empty Transferable and placing it on the clipboard.
- clearClipboardConditionally() - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Clears the clipboard, if
ClipboardHandler.isClearClipboardBeforeExport()
is true. - 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.
- clearFeatures(int) - Method in class chemaxon.pharmacophore.PMap
-
Clears all features corresponding to the given atom index.
- 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.
- 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.
- clearPropertyColumnNames() - Method in class chemaxon.formats.documents.jchemexcel.StructureToJC4XL
-
Clears the display name list of properties
- clearQProps() - Method in class chemaxon.struc.MolAtom
-
Clears query props.
- clearSavedAtomIndices() - Method in class chemaxon.struc.sgroup.SuperatomSgroup
- clearSelection(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Sets all components and parts of components to be unselected in the given cell.
- clearSelections() - Method in class chemaxon.marvin.space.GraphicCell
-
Sets all components and parts of components to be unselected.
- clearSets() - Method in class chemaxon.struc.MDocument
-
Clears the atomSets and the bondSets.
- 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
- ClipboardHandler - Class in chemaxon.marvin.modules.datatransfer
-
Facade of the Clipboard handling in Marvin.
- clipboardOperation - Variable in class chemaxon.marvin.modules.datatransfer.MarvinTransferable
-
Clipboard operation type.
- clipSurface(BoundingBox) - Method in class chemaxon.marvin.space.SurfaceComponent
-
The bounding box of the surface can be used to determine 6 clipping planes and clip (do not draw) parts lying outside of the box.
- clone() - Method in class chemaxon.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.MDSet
-
Clones the object.
- 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.
- clone() - Method in class chemaxon.pharmacophore.PMap
-
Clones this PMap object.
- clone() - Method in class chemaxon.sss.search.JChemSearchOptions
-
Makes an identical copy of this SearchObject.
- 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.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.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.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.MPolyline
- 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.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).
- clone() - Method in class chemaxon.util.HitColoringAndAlignmentOptions
-
Makes an identical copy of the Options
- 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.JChemSearchOptions
-
Copies parameters to
other
. - 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.JChemSearchOptions
- 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 - cloneLeavingGroups(SuperatomSgroup) - Method in class chemaxon.struc.sgroup.SuperatomSgroup
-
Deprecated.As of Marvin 6.2, no replacement.
Not supported feature. - 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.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.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.MObjectProp
-
Clones the object.
- cloneProp() - Method in class chemaxon.struc.prop.MStringProp
-
Clones the object.
- cloneResult - Variable in class chemaxon.descriptors.MDReader
-
indicates if mdSet is cloned or not in
next()
- 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.descriptors.GenerateMD
-
Closes the generator, all output files or database connection.
- close() - Method in class chemaxon.descriptors.MDArrayReader
-
Closes the reader
- close() - Method in class chemaxon.descriptors.MDDBReader
-
Closes down the descriptor stream.
- close() - Method in class chemaxon.descriptors.MDDBWriter
-
Closes down the descriptor output stream.
- close() - Method in class chemaxon.descriptors.MDFileReader
-
Closes the reader.
- close() - Method in class chemaxon.descriptors.MDFileWriter
-
Closes the stream, after that no more operations are permitted.
- close() - Method in class chemaxon.descriptors.MDReader
-
Closes down the descriptor stream.
- close() - Method in class chemaxon.descriptors.MDSimilarityResultWriter
-
Closes output.
- close() - Method in class chemaxon.descriptors.MDWriter
-
Closes down the descriptor output stream.
- close() - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentReader
-
Closes the office document stream.
- close() - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentTemplateWriter
-
Clear up resources collected during the report generation process.
- close() - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentWriter
-
Closes the office Document stream.
- 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.jchem.db.DatabaseProperties
-
Should be called only if the use of prepared statements are enabled with
DatabaseProperties.setUsePreparedStatement(boolean)
. - close() - Method in class chemaxon.jchem.db.UpdateHandler
-
Closes the handler (required to call).
- close() - Method in class chemaxon.jchem.file.ProgressWriter
-
Indicate that the operation is complete.
- close() - Method in class chemaxon.marvin.io.formats.AbstractMRecordReader
-
Interrupts parsing.
- close() - Method in class chemaxon.marvin.io.formats.MoleculeImporter
- 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 class chemaxon.util.ConnectionHandler
-
Closes the connection to the database.
- close() - Method in class com.chemaxon.calculations.cli.CalculatorPluginOutput
-
Closes the output.
- close() - Method in interface com.chemaxon.calculations.common.ProgressObserver
-
Equivalent to
ProgressObserver.done()
. - close() - Method in interface com.chemaxon.calculations.io.CloseableIterator
- close() - Method in class com.chemaxon.calculations.io.MemoizingIterator
- 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<T> - Interface in com.chemaxon.calculations.io
-
Closeable iterator.
- CloseableIterators - Class in com.chemaxon.calculations.io
-
Utility class.
- 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.
- cluster(double[][], LanceWilliamsMerge, SubProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
-
Invoke clustering.
- cluster(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
-
A spec for a clusterId.
- cluster(LegacyLibraryMcsParameters, Iterator<Molecule>) - Static method in class chemaxon.clustering.adapter.LegacyLibraryMcsAdapter
-
Deprecated.Launch clustering.
- cluster(LegacyLibraryMcsParameters, Iterator<Molecule>) - Static method in class chemaxon.clustering.libmcs.adapter.LegacyLibraryMcsAdapter
-
Launch clustering.
- cluster(DissimilarityInput, LanceWilliamsMerge, ProgressObserver) - Static method in class com.chemaxon.clustering.wards.LanceWilliamsAlgorithm
-
Invoke clustering.
- Cluster<T> - Interface in com.chemaxon.clustering.common
-
Cluster represents a group of structures.
- ClusterEnumerator(MGraph, boolean) - Constructor for class chemaxon.clustering.libmcs.LibraryMcs.ClusterEnumerator
- ClusterEnumerator(MGraph, boolean, boolean) - Constructor for class chemaxon.clustering.libmcs.LibraryMcs.ClusterEnumerator
- clusterLevel(T) - Method in interface com.chemaxon.clustering.common.LevelAssigner
-
Level associated to a hierarchic cluster.
- clusterLevelFunction() - Method in interface com.chemaxon.clustering.common.LevelAssigner
-
CLuster level association.
- clusterOf(int) - Method in class com.chemaxon.clustering.common.IDBasedHierarchicClusterBuidler
-
Look up immediate parent of a structure present in the clustering.
- clusterOf(T) - Method in interface com.chemaxon.clustering.common.HierarchicClustering
-
Identify the lowest level cluster containing the given item.
- clusterOf(T) - Method in interface com.chemaxon.clustering.common.SingleLevelClustering
-
Identify the cluster containing the given item.
- clusters() - Method in interface com.chemaxon.clustering.common.HierarchicCluster
-
Access further grouping of the represented elements.
- clusters() - Method in interface com.chemaxon.clustering.common.IDBasedHierarchicCluster
- clusters() - Method in interface com.chemaxon.clustering.common.SingleLevelClustering
-
Represented cluster.
- Cm - Static variable in class chemaxon.core.ChemConst
- CmdlineUtils - Class in com.chemaxon.calculations.util
-
Command line related utilities.
- 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
- CodeAssistConfiguration() - Constructor for class chemaxon.marvin.util.codeassist.CodeAssistFactory.CodeAssistConfiguration
- CodeAssistFactory - Class in chemaxon.marvin.util.codeassist
-
Manages the creation of Chemical Terms related components, such as the Code Assist text field, toolbars, favorite and macro handling components, and validation response component.
- CodeAssistFactory.CodeAssistConfiguration - Class in chemaxon.marvin.util.codeassist
-
Helper class for
CodeAssistFactory
to set upCodeAssist
- codeHIsotopeMass(int, int) - Static method in class chemaxon.marvin.io.formats.mdl.MolfileUtil
-
Add mass number information to the given code.
- coeffQuery(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
-
Set query coefficient.
- coeffTarget(double) - Method in class com.chemaxon.descriptors.metrics.TverskyParameters.Builder
-
Set target coefficient.
- 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
- collectStatisitcs(ConnectionHandler, String) - Method in class chemaxon.jchem.db.TableStatistics
- color - Variable in class chemaxon.marvin.space.GraphicComponent
- color - Variable in class chemaxon.marvin.space.MoleculeComponent
- color - Variable in class chemaxon.marvin.space.SurfaceComponent
- 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, Molecule, int[], HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
-
Performs hit coloring on the specified structure.
- color(Molecule, Molecule, HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
-
Performs hit coloring on the specified structure.
- 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_MAPPER_BLUE_TO_GREEN - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in blue-cyan-green palette will be used.
- COLOR_MAPPER_BLUE_TO_RED - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in blue-lightgray-red palette will be used.
- COLOR_MAPPER_FIRE - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in "fire" palette will be used.
- COLOR_MAPPER_GREEN_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in green-cyan-blue palette will be used.
- COLOR_MAPPER_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in rainbow palette will be used.
- COLOR_MAPPER_RED_TO_BLUE - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in red-lightgray-blue palette will be used.
- COLOR_MAPPER_REVERSE_RAINBOW - Static variable in class chemaxon.marvin.space.SurfaceColoring
-
Built-in reverse rainbow palette will be used.
- COLOR_SCHEME - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"colorScheme"
. - COLOR_SCHEMES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Array of color schemes strings.
- color3 - Variable in class chemaxon.marvin.space.SurfaceComponent
- 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
- colorHit(Molecule, Molecule, int[], HitColoringAndAlignmentOptions) - Static method in class chemaxon.util.HitDisplayUtil
-
Returns the colored copy of the specified target structure, the original target is kept unchanged.
- coloring(boolean) - Method in class chemaxon.marvin.space.SurfaceComponent
- coloring(ImageExporter.Coloring) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Sets the coloring scheme.
- 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.
- COLORS_MASK - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Color scheme mask in display option flags.
- COLORS_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Color scheme offset in display option flags.
- colorType - Variable in class chemaxon.marvin.space.MoleculeComponent
- COLS - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"cols"
. - com.chemaxon.apidiscovery - package com.chemaxon.apidiscovery
-
API Discovery framework.
- com.chemaxon.apidiscovery.annotations - package com.chemaxon.apidiscovery.annotations
-
Annotations used by the API Discovery framework.
- com.chemaxon.apidiscovery.interfaces - package com.chemaxon.apidiscovery.interfaces
-
Interfaces introduced for the API Discovery framework.
- com.chemaxon.apidiscovery.util - package com.chemaxon.apidiscovery.util
-
Various utilities.
- com.chemaxon.calculations.cli - package com.chemaxon.calculations.cli
- com.chemaxon.calculations.common - package com.chemaxon.calculations.common
-
Common components of Calculator APIs.
- com.chemaxon.calculations.elemanal - package com.chemaxon.calculations.elemanal
-
API of the elemental analysis functionality.
- com.chemaxon.calculations.gui - package com.chemaxon.calculations.gui
- com.chemaxon.calculations.io - package com.chemaxon.calculations.io
- 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.calculations.util - package com.chemaxon.calculations.util
-
Various utilities used in calculations, descriptors, clustering and overlap analysis.
- com.chemaxon.clustering.common - package com.chemaxon.clustering.common
-
Common components of clustering related APIs.
- com.chemaxon.clustering.framework - package com.chemaxon.clustering.framework
-
Hierarchic structural framework based clustering.
- com.chemaxon.clustering.singlelinkage - package com.chemaxon.clustering.singlelinkage
-
Single linkage clustering algorithm.
- com.chemaxon.clustering.sphex - package com.chemaxon.clustering.sphex
-
Sphere exclusion clustering algorithm.
- com.chemaxon.clustering.util - package com.chemaxon.clustering.util
-
Clustering related utilities.
- com.chemaxon.clustering.wards - package com.chemaxon.clustering.wards
-
Ward's minimum variance implemented as a generic agglomerative hierarchical clustering algorithm.
- com.chemaxon.common.annotations - package com.chemaxon.common.annotations
- com.chemaxon.descriptors.alignment - package com.chemaxon.descriptors.alignment
-
3D flexible alignment based molecular shape similarity calculation.
- com.chemaxon.descriptors.common - package com.chemaxon.descriptors.common
-
Unguarded descriptor handling.
- com.chemaxon.descriptors.db - package com.chemaxon.descriptors.db
-
Interfaces for database import/export.
- com.chemaxon.descriptors.fingerprints.cfp - package com.chemaxon.descriptors.fingerprints.cfp
-
API of the Chemaxon hashed fingerprint family molecular descriptors.
- com.chemaxon.descriptors.fingerprints.ecfp - package com.chemaxon.descriptors.fingerprints.ecfp
-
API of the ECFP fingerprint family molecular descriptors.
- com.chemaxon.descriptors.fingerprints.maccs - package com.chemaxon.descriptors.fingerprints.maccs
-
ChemAxon implementation of the MACCS 166 bit fingerprints.
- com.chemaxon.descriptors.fingerprints.pf2d - package com.chemaxon.descriptors.fingerprints.pf2d
-
API of the 2D pharmacophore fingerprint family molecular descriptors.
- com.chemaxon.descriptors.metrics - package com.chemaxon.descriptors.metrics
-
Common descriptor comparison metrics.
- com.chemaxon.descriptors.vectors.binary - package com.chemaxon.descriptors.vectors.binary
-
Generic binary vector descriptors.
- com.chemaxon.descriptors.vectors.floats - package com.chemaxon.descriptors.vectors.floats
-
Generic floating point vector descriptors.
- com.chemaxon.mapper - package com.chemaxon.mapper
- com.chemaxon.overlap.io - package com.chemaxon.overlap.io
- 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.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.
- Common - Class in chemaxon.clustering
-
Common superclass for JKlustor tools.
- Common() - Constructor for class chemaxon.clustering.Common
- compare(byte[], byte[]) - Method in class com.chemaxon.descriptors.alignment.AbstractShapeComparator
- compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
- compare(byte[], byte[]) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
-
Compare two descriptors in serialized form.
- compare(int, int, MDSet) - Method in class chemaxon.descriptors.MDSimilarity
-
Compares a target descriptor against all queries added prior to the call of this method using the given metric of the given descriptor.
- compare(MDReader) - Method in class chemaxon.descriptors.MDSimilarity
-
Compares a list of target descriptor sets (read by a molecular descriptor reader) against all queries added prior to the call of this method the same way as
compareQueries( MolecularDescriptor target )
but for each target. - compare(MDSet) - Method in class chemaxon.descriptors.MDSimilarity
-
Compares a target descriptor set (for instance from a database) against all queries added prior to the call of this method.
- compare(StructureFixer, StructureFixer) - Method in class chemaxon.fixers.FixerPriorityComparator
- compare(D, D) - Method in interface com.chemaxon.descriptors.common.DescriptorComparator
-
Compare two descriptors.
- compare(T, T) - Method in interface com.chemaxon.descriptors.alignment.ShapeComparator
- Compare - Class in chemaxon.clustering
-
Compares two sets of objects (like compound libraries) using diversity and dissimilarity calculations.
- Compare() - Constructor for class chemaxon.clustering.Compare
- 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(AtomIdentifier) - Method in class chemaxon.reaction.AtomIdentifier
- compareTo(GroupDefinition) - Method in class chemaxon.standardizer.advancedactions.GroupDefinition
- compareTo(Object) - Method in class com.chemaxon.calculations.gui.PluginFactory.PluginRecord
- comparisonContextFactory() - Method in interface com.chemaxon.descriptors.common.DescriptorGenerator
-
Get an unguarded context factory.
- comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpGenerator
- comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpGenerator
- comparisonContextFactory() - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfGenerator
- comparisonLinenote() - Method in interface com.chemaxon.descriptors.metrics.MetricFactory
-
Gets the string based parameterization description.
- ComparisonResult - Interface in com.chemaxon.descriptors.common
-
Result of a descriptor comparison.
- compatible(Guarded, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat
-
Ensure the guard object based compatibility of two objects.
- compatibleWithGuard(Object, String, Guarded) - Static method in class com.chemaxon.descriptors.common.Guarded.EnsureThat
-
Ensure the guard object based compatibility of two objects.
- 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, Class) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP
object. - compile(String, Class, SymbolTable) - Method in class chemaxon.jep.Evaluator
-
Compiles the expression, creates
ChemJEP
object. - COMPLETE - Enum constant in enum class com.chemaxon.mapper.Mapper.MappingStyle
-
All atoms will be mapped
- CompleteLinkage() - Constructor for class com.chemaxon.clustering.wards.LanceWilliamsMerges.CompleteLinkage
- component - Variable in class chemaxon.marvin.space.monitor.Control
- COMPONENT - Enum constant in enum class chemaxon.struc.SgroupType
- COMPONENT_RANGE - Static variable in class chemaxon.marvin.space.GraphicScene
- COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
- COMPONENT_TYPE_ATOM - Static variable in class chemaxon.marvin.space.MoleculeComponent
- COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
- COMPONENT_TYPE_BOND - Static variable in class chemaxon.marvin.space.MoleculeComponent
- COMPONENT_TYPE_ENTIRE - Static variable in class chemaxon.marvin.space.GraphicComponent
-
Indicates if the entire component is selected by picking.
- COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
- COMPONENT_TYPE_MOLECULE - Static variable in class chemaxon.marvin.space.MoleculeComponent
- COMPONENT_TYPE_RESIDUE - Static variable in class chemaxon.marvin.space.MacroMoleculeComponent
- componentBecameSelected() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns true if a component became selected previously.
- componentBecameSelected(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if a component became selected previously in the given cell.
- componentBecameUnselected() - Method in class chemaxon.marvin.space.GraphicCell
-
Returns true if a component became unselected previously.
- componentBecameUnselected(int) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if a component became unselected previously in the given cell.
- 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.
- ComponentElement - Class in chemaxon.marvin.space
-
Class to identify parts of GraphicComponents mainly during selection.
- ComponentElement(ComponentElement) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Copies the given
ComponentElement
. - ComponentElement(GraphicComponent, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of
ComponentElement
of a simple (not structured)GraphicComponent
. - ComponentElement(GraphicComponent, int, int, int) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of
ComponentElement
of a complex (structured)GraphicComponent
. - ComponentElement(GraphicComponent, int, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of
ComponentElement
. - ComponentElement(GraphicComponent, int, Integer) - Constructor for class chemaxon.marvin.space.ComponentElement
-
Creates a new instance of
ComponentElement
. - componentHidden(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Hides windows if the parent frame is hidden.
- componentMoved(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Does nothing.
- componentResized(ComponentEvent) - Method in class chemaxon.marvin.beans.MarvinPane
-
Does nothing.
- 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.
- COMPOSITE - Static variable in class chemaxon.jchem.db.DatabaseConstants
- COMPOSITE_DRIVER - Static variable in class chemaxon.jchem.db.DatabaseConstants
-
JDBC driver for Composite database
- COMPOSITE_TYPE_NAME - Static variable in class chemaxon.jchem.db.DatabaseConstants
- COMPOSITE_URL_EXAMPLE - Static variable in class chemaxon.jchem.db.DatabaseConstants
-
JDBC URL example for Composite database
- COMPOSITE_URL_TEMPLATE - Static variable in class chemaxon.jchem.db.DatabaseConstants
-
JDBC URL template for Composite database
- 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.io.MemoizingIterator
- computeNext() - Method in class com.chemaxon.calculations.stereoisomers.StereoisomerEnumeration
- computeSurface(MacroMoleculeComponent.MoleculeVisualizer) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Activates the container cell of the
MoleculeVisualizer
, and computes its Connolly surface. - computeSurface(String) - Method in class chemaxon.marvin.space.MSpaceEasy
-
Computes the given type of surface in the active cell of the viewer.
- ConcurrentReactorProcessor - Class in chemaxon.reaction
-
Executes a chemical reaction: creates products from reactants with reaction center data.
- ConcurrentReactorProcessor() - Constructor for class chemaxon.reaction.ConcurrentReactorProcessor
- 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.
- ConditionalRuleOperators - Enum Class in chemaxon.formats.documents.jchemoffice
- ConditionRule - Class in chemaxon.formats.documents.jchemoffice
- ConditionRule() - Constructor for class chemaxon.formats.documents.jchemoffice.ConditionRule
- ConditionRule(ConditionalRuleOperators, double) - Constructor for class chemaxon.formats.documents.jchemoffice.ConditionRule
- ConditionRule(ConditionalRuleOperators, String) - Constructor for class chemaxon.formats.documents.jchemoffice.ConditionRule
- 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
. - CONFIRM_TRANSFER - Static variable in class chemaxon.marvin.view.ViewParameterConstants
-
Identifier of parameter:
"confirmTransfer"
. - CONFORMATION_PLUGIN_GROUP - Static variable in class chemaxon.license.LicenseManager
-
Identifier of plugin: Conformation Plugin Group
- ConformerPlugin - Class in chemaxon.marvin.calculations
-
Plugin class for conformer calculation.
- ConformerPlugin() - Constructor for class chemaxon.marvin.calculations.ConformerPlugin
-
Constructor.
- CONJUGATED - Static variable in class chemaxon.struc.MolBond
-
Conjugation state of the bond.
- 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.
- ConnectionHandler - Class in chemaxon.util
-
A JavaBean for connecting to relational databases using JDBC.
- ConnectionHandler() - Constructor for class chemaxon.util.ConnectionHandler
-
Creates new ConnectionHandler Connection will automatically be non-commitable (see
ConnectionHandler.isCommitable()
) to preserve compatibility with previous versions. - ConnectionHandler(boolean) - Constructor for class chemaxon.util.ConnectionHandler
-
Creates new ConnectionHandler
- ConnectionHandler(ConnectionHandler) - Constructor for class chemaxon.util.ConnectionHandler
-
Creates new ConnectionHandler based on the settings of an other ConnectionHandler.
- ConnectionHandler(ConnectionHandler, boolean) - Constructor for class chemaxon.util.ConnectionHandler
-
Creates new ConnectionHandler based on the settings of an other ConnectionHandler.
- ConnectionHandler(Connection, String) - Constructor for class chemaxon.util.ConnectionHandler
-
Creates a new ConnectionHandler and sets the connection to an externally created Connection (e.g.
- ConnectionHandler(Connection, String, boolean) - Constructor for class chemaxon.util.ConnectionHandler
-
Creates a new ConnectionHandler and sets the connection to an externally created Connection (e.g.
- 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.
- connectToDatabase() - Method in class chemaxon.util.ConnectionHandler
-
Connects to the database.
- 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
- constant - Variable in class chemaxon.marvin.services.ServiceArgument
-
field indicates constant argument
- constructBvGenerator(BvParameters) - Method in interface com.chemaxon.descriptors.vectors.binary.BvParameters.ConstructBvGenerator
-
Construct new instance
- constructCfpGenerator(CfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpParameters.ConstructCfpGenerator
-
Constructor invocation.
- constructEcfpGenerator(EcfpParameters) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters.ConstructEcfpGenerator
-
Constructor invocation.
- constructMaccsGenerator(MaccsParameters) - Method in interface com.chemaxon.descriptors.fingerprints.maccs.MaccsParameters.ConstructMaccsGenerator
-
Constructor invocation.
- constructPfGenerator(PfParameters) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfParameters.ConstructPfGenerator
-
Constructor invocation.
- containerFrame - Variable in class chemaxon.marvin.space.MSpaceEasy
- contains(float, float, float) - Method in class chemaxon.marvin.space.BoundingBox
-
Tells whether the given location is inside the box.
- contains(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.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.
- containsAllAtomsOf(Sgroup) - Method in class chemaxon.struc.Sgroup
-
Checks if the S-group contains the atoms of another S-group.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MAtomSetPoint
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MChemicalStruct
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MEFlowBasePoint
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.graphics.MPolyline
-
Checks if the atom set contains the specified atom object.
- containsAtom(MolAtom) - Method in class chemaxon.struc.MObject
-
Checks if the object contains the specified atom reference.
- containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicCell
-
Tells whether the component is in the cell.
- containsComponent(GraphicComponent) - Method in class chemaxon.marvin.space.GraphicScene
-
Returns true if the component exists in the scene.
- containsCoordinateBond(MoleculeGraph) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Decides whether a molecule graph contains coordinate bonds.
- containsHydrogens() - Method in class chemaxon.util.MolHandler
-
True if the molecule contains explicit Hydrogen atoms, false otherwise.
- containsLadderTypePolymer() - Method in class chemaxon.struc.sgroup.RepeatingUnitSgroup
-
Decides whether the structure of this sgroup contains a ladder-type repeating unit.
- containsMulticenterSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Decides whether a molecule contains Multicenter S-groups.
- containsOnlyOne(Class) - Method in class chemaxon.struc.MDocument
-
Tests whether the document contains only one object of the specified class.
- containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.graphics.MRoundedRectangle
- containsPoint(DPoint3, CTransform3D) - Method in class chemaxon.struc.MObject
- containsPropertyKey(String) - Method in class chemaxon.struc.MolAtom
-
Returns true if this atom has a mapping for the specified property key.
- containsPropertyKey(String) - Method in class chemaxon.struc.MolBond
-
Returns true if this bond has a mapping for the specified property key.
- containsPseudoAtom(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Returns
true
if molecule contains pseudo atom. - containsSRUSgroup(Molecule) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Decides whether a molecule contains SRU S-groups.
- 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
- control - Variable in class chemaxon.marvin.space.monitor.DihedralMonitor
- control - Variable in class chemaxon.marvin.space.monitor.Monitor
- control(int) - Method in class chemaxon.marvin.space.monitor.Control
-
Does control on z event.
- control(int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
-
One part of the molecule being in one of the end of the torsion bond will be rotated around the bond.
- control(int) - Method in class chemaxon.marvin.space.monitor.DihedralMonitor
-
Passes the control event to the control.
- control(int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
-
Changes the location say translates the component of the control in the global coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
-
Changes the orientation that is rotates the component of the control in the global coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
-
Changes the location say translates the component of the control in its local coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
-
Changes the orientation say rotates the component of the control in its local coordinate system.
- control(int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Causes the monitor's controll to take action with 1 parameter.
- control(int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
-
Resizes the component in z direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.Control
-
Does control on x-y events.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.DihedralControl
-
Does nothing.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalLocationControl
-
Changes the location say translates the component of the control in the global coordinate system.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.GlobalOrientationControl
-
Changes the orientation say rotates the component of the control in the global coordinate system.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalLocationControl
-
Changes the location say translates the component of the control in its local coordinate system.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.LocalOrientationControl
-
Changes the orientation say rotates the component of the control in its local coordinate system.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.PositionMonitor
-
Causes the monitor's controll to take action with 2 parameters.
- control(int, int) - Method in class chemaxon.marvin.space.monitor.ResizeControl
-
Resizes the component in x, y direction uniformly which means that it will either increase or decrease its size with one unit or do nothing if the given value was positive, negative or zero.
- Control - Class in chemaxon.marvin.space.monitor
-
Transformation on a
GraphicComponent
that changes the coordinates, and not just the view. - Control() - Constructor for class chemaxon.marvin.space.monitor.Control
-
Creates a new instance of Control
- ConversionOptions - Class in chemaxon.formats.documents.jchemoffice
- ConversionOptions() - Constructor for class chemaxon.formats.documents.jchemoffice.ConversionOptions
- ConversionOptions(boolean) - Constructor for class chemaxon.formats.documents.jchemoffice.ConversionOptions
- 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(double[][]) - Static method in class chemaxon.marvin.alignment.AlignRigidEasy
- convert(TransferDataImporter) - Static method in class chemaxon.marvin.modules.datatransfer.ClipboardHandler
-
Convert transfer data available on clipboard in one of the requested flavors.
- 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<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.DefaultStructureCheckerResult
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.MetalloceneCheckerResult
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in class chemaxon.checkers.result.SgroupCheckerResult
- convert(Molecule, Map<String, Map<? extends Object, ? extends Object>>) - Method in interface chemaxon.checkers.result.StructureCheckerResult
-
This method converts the entities contained in this result according to the convertData.
- convert(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
- convertAll(ImageExporter) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
-
Converts the rendering settings of all molecule structures in the given document to the format given in the imageWriter parameter
- convertAll(ImageExporter, IConversionOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
-
Converts the rendering settings of all molecule structures in the given document to the format given in the imageWriter parameter
- convertAll(String) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
-
Converts the rendering settings of all molecule structures in the given document to the format given in the moleculeImageSettingsFormat parameter
- convertAll(String, IConversionOptions) - Method in interface chemaxon.formats.documents.jchemoffice.IDocumentConverter
-
Converts the rendering settings of all molecule structures in the given document to the format given in the moleculeImageSettingsFormat parameter
- 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
-
Convert explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert explicit Hydrogen atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert explicit Hydrogen atoms attached to the specified atoms of the molecule to implicit.
- convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert explicit Hydrogen atoms attached to the specified atoms of a molecule to implicit.
- convertExplicitLonePairsToImplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Converts explicit lone pairs from a molecule to implicit.
- convertForAppletParameter(String) - Static method in class chemaxon.util.HTMLTools
-
Converts a string to a format that can be used as a value of an applet parameter in an HTML page.
- convertForJavaScript(String) - Static method in class chemaxon.util.HTMLTools
-
Converts a string to a format that can be used as a value of JavaScript variable in an HTML page.
- convertImplicitHToExplicit(MoleculeGraph) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit Hydrogen atoms of the molecule to explicit.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
- convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit Hydrogen atoms of the specified atoms in a molecule to explicit.
- convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]) - Static method in class chemaxon.calculations.hydrogenize.Hydrogenize
-
Convert implicit lone pairs of the atoms of a molecule to explicit.
- 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
- 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
-
Convert key of 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.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.MDocument.Prop
-
Deprecated.As of release 5.7, replaced by
MolExporter.convertToString(MDocument, String, int)
- convertToString(String, int) - Method in class chemaxon.struc.MProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
. - convertToString(String, int) - Method in class chemaxon.struc.prop.MBooleanProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
. - convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleArrayProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MDoubleProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MHashProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MHCoords3DProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerArrayProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MIntegerProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MListProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MMoleculeProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
. - convertToString(String, int) - Method in class chemaxon.struc.prop.MObjectProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- convertToString(String, int) - Method in class chemaxon.struc.prop.MStringProp
-
Deprecated.As of Marvin 5.7, replaced by
MPropHandler.convertToString(MProp, String)
- 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
- coordBondStyle(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Coordinate bond display style.
- coordBondStyleAtMulticenter(ImageExporter.LineType) - Method in class chemaxon.marvin.io.image.ImageExporter.Builder
-
Coordinate bond display style when it connects to a multicenter atom.
- COORDDEP - Static variable in class chemaxon.struc.MProp
-
Coordinate dependent property.
- COORDINATE - Static variable in class chemaxon.struc.MolBond
-
Coordinate bond flag.
- COORDINATE_BOND_ARROW_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_AT_MULTICENTER_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_AT_MULTICENTER_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_AT_MULTICENTER_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_HASHED_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_SOLID_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_STYLE - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"coordinateBondStyle"
. - COORDINATE_BOND_STYLE_AT_MULTICENTER - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Identifier of parameter:
"coordinateBondStyleAtMulticenter"
. - COORDINATE_BOND_STYLE_FLAG - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_STYLE_OFFSET - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- COORDINATE_BOND_STYLES - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
Deprecated.
- CoordinateBondOnMulticenterStyle - Enum Class in chemaxon.marvin.paint.constants
-
Holds the values for the possible rendering styles for Coordinate bonds connected to Multicenter atoms.
- CoordinateBondStyle - Enum Class in chemaxon.marvin.paint.constants
-
Holds the values for the possible rendering styles for Coordinate bonds.
- 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.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.
- COPY_AS_IMAGE_EMF - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated.
- COPY_AS_OLE - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated.
- COPY_AS_TEXT - Static variable in interface chemaxon.marvin.util.CopyOptConstants
-
Deprecated.
- COPY_OPTIONS - Static variable in class chemaxon.marvin.common.ParameterConstants
-
Deprecated.since 5.3.3 has no sense
- copyFrom(ISettings) - Method in interface chemaxon.formats.documents.jchemoffice.ISettings
-
Copies the entire settings from another settings instance
- copyFrom(ISettings) - Method in class chemaxon.formats.documents.jchemoffice.ReportSettings
- CopyOptConstants - Interface in chemaxon.marvin.util
-
Deprecated.since 5.2.1 the whole copy-paste engine was refactored. The constants defined in this interface either non exists in the new implementation or its value has changed. See the constants own description for details.
- copyProperties(MBracket) - Method in class chemaxon.struc.graphics.MBracket
-
Copies line properties to another line object.
- copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MEFlow
- copyProperties(MPolyline) - Method in class chemaxon.struc.graphics.MPolyline
-
Copies line properties to another line object.
- correctCornersRadius(double, double) - Method in class chemaxon.struc.graphics.MRoundedRectangle
- count() - Method in class chemaxon.descriptors.MDSimilarityResultWriter
-
Increments the counter of the results processed.
- 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.
- countNumberOfClusters(HierarchicClustering<?, ? extends HierarchicCluster<?>>) - Static method in class com.chemaxon.clustering.util.Util
-
Count the number of clusters in a clustering.
- countOrderedComponentSgroups() - Method in class chemaxon.struc.Molecule
-
Counts the ordered component S-groups.
- countRecords(MProgressMonitor, int, Runnable, int) - Method in class chemaxon.marvin.view.MDocStorage
-
Counts the total number of records and sets the size of the document storage.
- countRecordsInFraction(double, int, MProgressMonitor) - Method in class chemaxon.marvin.view.MDocStorage
-
Deprecated.
- COVALENT_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.
- cpk - Enum constant in enum class chemaxon.marvin.io.image.ImageExportParamConstants.coloringValues
- CPK - Enum constant in enum class chemaxon.marvin.io.image.ImageExporter.Coloring
- CPK_SCHEME - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
CPK color scheme in display option flags.
- CPK_SCHEME_S - Static variable in interface chemaxon.marvin.paint.DispOptConsts
-
CPK color scheme.
- Cr - Static variable in class chemaxon.core.ChemConst
- crdMolRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
- crdSafeRefresh() - Method in class chemaxon.marvin.alignment.AlignmentMolecule
- create() - Method in class com.chemaxon.apidiscovery.CreatorWrapper
-
Invoke creator method.
- 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.
- 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.CustomMatcherFactory
-
Creates a custom matcher for atom and bond pairs of the given query and target structures.
- create(String) - Static method in class chemaxon.descriptors.MDHypothesisCreator
-
Creates a hypothesis of the given type.
- 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.util.DotfileUtil
-
Opens a dotfile for writing.
- create(String, int, int) - Static method in class chemaxon.descriptors.SimilarityCalculatorFactory
-
Creates a similarity calculator object according to the user defined parameters.
- create(String, PSymbols) - Static method in class chemaxon.pharmacophore.PMap
-
Creates a PMap object from a pharmacophore point list string.
- create(String, String) - Static method in class chemaxon.marvin.plugin.CalculatorPlugin
-
Loads a plugin, first tries to load it from CLASSPATH, then from JAR.
- CREATE_OR_REPLACE_RESULT_TABLE - Static variable in class chemaxon.jchem.db.JChemSearch
-
Constant for the generation of result tables.
- createAnalysis(String) - Static method in class com.chemaxon.calculations.elemanal.MolecularFormulas
-
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.
- createBracket(Sgroup, DPoint3[], int) - Static method in class chemaxon.marvin.util.CleanUtil
- createChemicalTermsTextPane() - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane. - createChemicalTermsTextPane(boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space. - createChemicalTermsTextPane(boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space. - createChemicalTermsTextPane(CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane. - createChemicalTermsTextPane(CodeAssistFactory.CodeAssistConfiguration) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane
instance with code assist capabilities. - createChemicalTermsTextPane(String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane. - createChemicalTermsTextPane(String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space - createChemicalTermsTextPane(String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(String, boolean, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(String, boolean, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space - createChemicalTermsTextPane(String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space.
Default help text will be shown in empty textpane. - createChemicalTermsTextPane(String, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars.
Available function list will be shown when typing ctrl-space - createChemicalTermsTextPane(String, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(String, String, boolean, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(String, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities.
Default toolbar configuration will be used for toolbars. - createChemicalTermsTextPane(String, String, boolean, String) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities. - createChemicalTermsTextPane(String, String, boolean, String, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities. - createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities. - createChemicalTermsTextPane(String, String, boolean, String, boolean, CodeAssistDataProvider.Context, boolean) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Creates a
JTextPane
instance with code assist capabilities. - createChemicalTermsTextPane(String, String, boolean, String, CodeAssistDataProvider.Context) - Static method in class chemaxon.marvin.util.codeassist.CodeAssistFactory
-
Deprecated.use
CodeAssistFactory.createChemicalTermsTextPane(CodeAssistConfiguration)
Creates aJTextPane
instance with code assist capabilities. - 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.
- createDocumentConverter(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentConverter
method instantiates a class which implements theIDocumentConverter
interface. - createDocumentOLEConverter(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentOLEConverter
method instantiates a class which implements theIDocumentConverter
interface. - createDocumentOLEConverter(DocumentType, String, SupportedOLETypes) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentOLEConverter
method instantiates a class which implements theIDocumentConverter
interface. - createDocumentReader(DocumentType, InputStream) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentReader
method instantiates a class which implements theIDocumentReader
interface. - createDocumentReader(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentReader
method instantiates a class which implements theIDocumentReader
interface. - createDocumentTemplateWriter(DocumentType, InputStream, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentWriter
method instantiates a class which implements theIDocumentTemplateWriter
interface. - createDocumentTemplateWriter(DocumentType, String, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentTemplateWriter
method instantiates a class which implements theIDocumentTemplateWriter
interface. - createDocumentWriter(DocumentType, InputStream, OutputStream) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentWriter
method instantiates a class which implements theIDocumentWriter
interface. - createDocumentWriter(DocumentType, OutputStream) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentWriter
method instantiates a class which implements theIDocumentWriter
interface. - createDocumentWriter(DocumentType, String) - Static method in class chemaxon.formats.documents.jchemoffice.DocumentHandlerFactory
-
The static
createDocumentWriter
method instantiates a class which implements theIDocumentWriter
interface. - 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 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.
- createFeatureMap(Molecule) - Method in class chemaxon.pharmacophore.PMapper
-
Creates the feature ID -> atom index BitSet HashMap for the given target molecule.
- createForgivingNullObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
-
Deprecated.Use
ProgressObservers.nullProgressObserver()
instead. - createGData() - Method in class chemaxon.marvin.space.SurfaceComponent
- 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
- createImage(Buffer, int, int) - Method in class chemaxon.marvin.space.GraphicScene
- createImageExporterParameter(Properties, String, MDocument) - Static method in class chemaxon.util.ImageExportUtil
-
Creates the Image Exporter parameter String based on the values in the Properties object.
- createImportMod(MolInputStream) - Static method in class chemaxon.marvin.io.MRecordImporter
-
Creates an importer for the specified molecule input stream.
- createImportMod(String) - Static method in class chemaxon.marvin.io.MRecordImporter
-
Creates an importer for the specified molecule format.
- createImportModule() - Method in class chemaxon.formats.MFileFormat
-
Creates the molecule import module.
- 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.
- createLabels(MDSet) - Method in class chemaxon.descriptors.MDSimilarityResultWriter
-
Creates labels.
- createLicenseManagerPanel() - Static method in class chemaxon.license.LicenseManager
-
Creates the main panel which is used for end-user license managing.
- createMD(String) - Method in class chemaxon.jchem.db.MDTableHandler
-
Creates an MolecularDescriptor based on settings stored in the database
- createMDSet(String[]) - Method in class chemaxon.jchem.db.MDTableHandler
-
Creates an MDSet based on settings stored in the database
- createMDSetComponent(int, String, String) - Method in class chemaxon.descriptors.MDReader
-
Creates and sets the given component of the internal
MDSet
object of the given type and specified parameter settings. - createMDTable(String, String, String, String) - Method in class chemaxon.descriptors.GenerateMD
-
Creates a database table to store the
MolecularDescriptor
s generated. - createMDTable(String, String, String, String) - Method in class chemaxon.jchem.db.MDTableHandler
-
Creates a Molecular Descriptor Table.
- createMDTable(String, String, String, String, boolean) - Method in class chemaxon.jchem.db.MDTableHandler
-
Creates a Molecular Descriptor Table.
- createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.beans.MarvinPane
-
Deprecated.as of Marvin 3.3.1, replaced by SwingUtil.createMenu
- createMenu(ResourceBundle, String) - Static method in class chemaxon.marvin.util.SwingUtil
-
Utility method to create a menu with a label specified as a resource.
- createMenu(ResourceBundle, String, boolean) - Static method in class chemaxon.marvin.util.SwingUtil
-
Creates a menu with a label specified as a resource.
- createMenuItem(ResourceBundle, String) - 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
-
Creates a target molecule object for import.
- createMol() - Method in class chemaxon.marvin.io.formats.mdl.MolImport
-
Creates a new target molecule object.
- createMol() - Method in class chemaxon.marvin.io.MolImportModule
-
Creates a new target molecule object for the import.
- createMol() - Method in class chemaxon.marvin.io.MRecordImporter
-
Creates an empty target molecule for import.
- 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 interface chemaxon.formats.documents.jchemoffice.IMoleculeData
-
Creates a Molecule content for the MoleculeData
- 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. - createNeighbourBonds(Molecule, MolBond, boolean) - Static method in class chemaxon.checkers.StructureCheckerHelper
- 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.
- createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpParameters
-
Construct a builder for this parameter class, initialized to default.
- createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpParameters
-
Construct a builder for this parameter class, initialized to default.
- createNewBuilder() - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfParameters
-
Construct a builder for this parameter class, initialized to default.
- createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.binary.BvParameters
-
Construct a builder for this parameter class, initialized to default.
- createNewBuilder() - Static method in class com.chemaxon.descriptors.vectors.floats.FvParameters
-
Construct a builder for this parameter class, initialized to default.
- createNewCell() - Method in class chemaxon.marvin.space.GraphicScene
-
Sets an empty cell to be the active cell.
- createNewReader(String) - Static method in class com.chemaxon.descriptors.db.MDTableReader
-
Create an MDTableReader from the xml configuration string.
- createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader
-
Create a PfTableReader from the xml configuration string.
- createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader
-
Create a PfTableReader from the xml configuration string.
- createNewReader(String) - Static method in class com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader
-
Create a PfTableReader from the xml configuration string.
- createNext() - Method in class chemaxon.struc.graphics.MTextAttributes
-
Creates identical attributes for the next section.
- createNoCancelObserver() - Static method in class com.chemaxon.calculations.common.ProgressObservers
-
Deprecated.
- createNullObserver(String) - Static method in class com.chemaxon.calculations.common.ProgressObservers
-
Deprecated.
- createParameterPanel() - Method in class com.chemaxon.calculations.gui.CalculatorPluginDisplay
-
Creates the parameter panel.
- createPartialMappingMatcher() - Method in interface com.chemaxon.search.CustomMatcherFactory
- createPropertyTable(ConnectionHandler) - Static method in class chemaxon.jchem.db.DatabaseProperties
-
Creates a new property table for storing JChem's settings.
- createPropertyTable(ConnectionHandler, int) - Static method in class chemaxon.jchem.db.DatabaseProperties
-
Creates a new property table for storing JChem's settings.
- 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.
- createReader(String) - Method in interface com.chemaxon.descriptors.db.MDReaderFactory
-
Generates reader object.
- createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.cfp.CfpTableReader.Factory
- createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.ecfp.EcfpTableReader.Factory
- createReader(String) - Method in interface com.chemaxon.descriptors.fingerprints.pf2d.PfTableReader.Factory
- createRecognizer() - Method in class chemaxon.formats.MFileFormat
-
Creates a recognizer module.
- createRecognizer(String) - Method in class chemaxon.formats.MFileFormat
-
Deprecated.as of Marvin 2014.07.21.0 use
MFileFormat.createRecognizer()
instead - 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 a