- add(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds all atoms and electronContainers of a given atomcontainer to this
container.
- addAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds an atom to this container.
- addBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a Bond to this AtomContainer.
- addBond(int, int, IBond.Order, IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a bond to this container.
- addBond(int, int, IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a bond to this container.
- addElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a ElectronContainer to this AtomContainer.
- addListener(IChemObjectListener) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Use this to add yourself to this IChemObject as a listener.
- addLonePair(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a lone pair to this AtomContainer.
- addLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a LonePair to this Atom.
- addProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Sets the properties of this object.
- addSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a single electron to this AtomContainer.
- addSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Adds a LonePair to this Atom.
- addStereoElement(IStereoElement) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
Add a symbol to this QueryAtom
- addSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Add a symbol to this QueryAtom
- apply(int[]) - Method in class org.openscience.cdk.isomorphism.ComponentGrouping
-
Does the mapping respected the component grouping specified by the
query.
- areRootAtomsDefined() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Checks validity of RGroupQuery.
- areRootAtomsDefined() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- areSubstituentsDefined() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Checks validity of the RGroupQuery.
- areSubstituentsDefined() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- atLeast(int) - Method in class org.openscience.cdk.isomorphism.Mappings
-
Efficiently determine if there are at least 'n' matches
- atomCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Number of atoms contained by this object.
- atomCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Number of atoms contained by this object.
- atomicNumber - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The atomic number for this element giving their position in the periodic table.
- AtomMatcher - Class in org.openscience.cdk.isomorphism
-
Defines compatibility checking of atoms for (subgraph)-isomorphism mapping.
- AtomMatcher() - Constructor for class org.openscience.cdk.isomorphism.AtomMatcher
-
- atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Internal array of atoms.
- atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an Iterable for looping over all atoms in this container.
- atoms - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
A list of atoms participating in this query bond.
- atoms() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the Iterator to atoms making up this query bond.
- charge - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The partial charge of the atom.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Clones this AtomContainer object and its content.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Clones this query bond object, including clones of the atoms between which the
query bond is defined.
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- clone() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
- compare(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Compares a query bond with this query bond.
- ComponentGrouping - Class in org.openscience.cdk.isomorphism
-
A predicate for verifying component level grouping in query/target structure
matching.
- ComponentGrouping(IAtomContainer, IAtomContainer) - Constructor for class org.openscience.cdk.isomorphism.ComponentGrouping
-
Create a predicate to match components for the provided query and target.
- ComponentGrouping(int[], int[]) - Constructor for class org.openscience.cdk.isomorphism.ComponentGrouping
-
Create a predicate to match components for the provided query (grouping)
and target (connected components).
- contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given atom object.
- contains(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given bond object.
- contains(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given LonePair object.
- contains(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given SingleElectron object.
- contains(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
True, if the AtomContainer contains the given ElectronContainer object.
- contains(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns true if the given atom participates in this query bond.
- count() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Convenience method to count the number mappings.
- countUnique() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Convenience method to count the number of unique atom mappings.
- createAnyAtomAnyBondContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with wildcard atoms and wildcard bonds.
- createAnyAtomContainer(IAtomContainer, boolean) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with AnyAtoms / Aromatic Atoms and OrderQueryBonds / AromaticQueryBonds.
- createAnyAtomForPseudoAtomQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's and
OrderQueryBond's.
- createBasicQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's, AromaticQueryBond's and
OrderQueryBond's.
- createSymbolAndBondOrderQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolQueryAtom's and OrderQueryBond's.
- createSymbolAndChargeQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
Creates a QueryAtomContainer with SymbolAncChargeQueryAtom's and
OrderQueryBond's.
- createSymbolChargeIDQueryContainer(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainerCreator
-
- CTFileQueryBond - Class in org.openscience.cdk.isomorphism.matchers
-
Captures query bond types defined in the CTFile.
- CTFileQueryBond(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
-
- CTFileQueryBond.Type - Enum in org.openscience.cdk.isomorphism.matchers
-
- filter(Predicate<int[]>) - Method in class org.openscience.cdk.isomorphism.Mappings
-
Filter the mappings and keep only those which match the provided
predicate (Guava).
- findIdentical(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Pattern
-
Create a pattern which can be used to find molecules which are the same
as the query structure.
- findIdentical(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
-
Create a pattern which can be used to find molecules which are the same
as the query structure.
- findIdentical(IAtomContainer, AtomMatcher, BondMatcher) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
-
Create a pattern which can be used to find molecules which are the same
as the query structure.
- findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Pattern
-
Create a pattern which can be used to find molecules which contain the
query structure.
- findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.Ullmann
-
Create a pattern which can be used to find molecules which contain the
query structure.
- findSubstructure(IAtomContainer) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
-
Create a pattern which can be used to find molecules which contain the
query structure.
- findSubstructure(IAtomContainer, AtomMatcher, BondMatcher) - Static method in class org.openscience.cdk.isomorphism.VentoFoggia
-
Create a pattern which can be used to find molecules which contain the
query structure.
- first() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Obtain the first match - if there is no first match an empty array is
returned.
- forAny() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher
-
Atoms are always compatible.
- forAny() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
-
All bonds are compatible.
- forElement() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher
-
Atoms are compatible if they are the same element.
- formalCharge - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The formal charge of the atom with CDKConstants.UNSET as default.
- formalNeighbourCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The formal number of neighbours this atom type can have with CDKConstants_UNSET
as default.
- forOrder() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
-
Bonds are compatible if they are both aromatic or their orders are equal.
- forQuery() - Static method in class org.openscience.cdk.isomorphism.AtomMatcher
-
Atoms are compatible if the second atom (
atom2) is accepted by
the
IQueryAtom,
atom1.
- forQuery() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
-
Bonds are compatible if the first
bond1 (an
IQueryBond)
matches the second,
bond2.
- forStrictOrder() - Static method in class org.openscience.cdk.isomorphism.BondMatcher
-
Bonds are compatible if they are both aromatic or their orders are equal
and they are non-aromatic.
- fractionalPoint3d - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
A 3 point specifying the location of this atom in a crystal unit cell.
- get2DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the geometric 2D center of the query bond.
- get3DCenter() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the geometric 3D center of the query bond.
- getAllConfigurations() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Produces all combinations of the root structure (scaffold) with the R-groups
substituted in valid ways, using each R-group's definitions and conditions.
- getAllConfigurations() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getAllRgroupQueryAtoms() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
Returns all R# type atoms (pseudo atoms) found in the root structure.
- getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- getAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns an Atom from this query bond.
- getAtomContainerCount() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Return the total number of atom containers (count the root plus all substituents).
- getAtomContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of Atoms in this Container.
- getAtomCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the number of Atoms in this Bond.
- getAtomicNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the atomic number of this element.
- getAtomNumber(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given atom in the atoms array.
- getAtomTypeName() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the id attribute of the AtomType object.
- getBegin() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- getBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- getBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the bond that connects the two given atoms.
- getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
- getBondCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of Bonds in this Container.
- getBondNumber(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of the bond between two given atoms in the
electronContainers array.
- getBondNumber(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given bond in the electronContainers array.
- getBondOrderSum() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the bondOrderSum attribute of the AtomType object.
- getBondOrderSum(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
- getBuilder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the partial charge of this atom.
- getConnectedAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- getConnectedAtoms(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- getConnectedAtomsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of atoms connected to the given atom.
- getConnectedAtomsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an ArrayList of all atoms connected to the given atom.
- getConnectedBondsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of Bonds for a given Atom.
- getConnectedBondsCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of connected atoms (degree) to the given atom.
- getConnectedBondsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an ArrayList of all Bonds connected to the given atom.
- getConnectedElectronContainersList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an ArrayList of all electronContainers connected to the given atom.
- getConnectedLonePairsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of LonePairs for a given Atom.
- getConnectedLonePairsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the array of lone pairs connected to an atom.
- getConnectedSingleElectronsCount(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the sum of the SingleElectron for a given Atom.
- getConnectedSingleElectronsList(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an array of all SingleElectron connected to the given atom.
- getContainer() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
- getContainer() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- getCovalentRadius() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the covalent radius for this AtomType.
- getElectronContainer(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the ElectronContainer at position number in the
container.
- getElectronContainerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of ElectronContainers in this Container.
- getElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the number of electrons in this bond
- getEnd() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- getExactMass() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the ExactMass attribute of the Isotope object.
- getFirstAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the atom at position 0 in the container.
- getFirstAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getFlag(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
- getFlags() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
- getFlagValue() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
- getFormalCharge() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the formal charge of this atom.
- getFormalNeighbourCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the formal neighbour count of this atom.
- getFractionalPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns a point specifying the location of this
atom in a Crystal unit cell.
- getGroup() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getHybridization() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the hybridization of this atom.
- getID() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns the identifier (ID) of this object.
- getImplicitHydrogenCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the hydrogen count of this atom.
- getIndex() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
- getIndex() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- getLastAtom() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the atom at the last position in the container.
- getListenerCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns the number of ChemObjectListeners registered with this object.
- getLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- getLonePairCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of LonePairs in this Container.
- getLonePairNumber(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given lone pair in the lone pair array.
- getMassNumber() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the atomic mass of this element.
- getMaxBondOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the MaxBondOrder attribute of the AtomType object.
- getMaximumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the maximum bond order that this atom currently has in the context
of this AtomContainer.
- getMinimumBondOrder(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the minimum bond order that this atom currently has in the context
of this AtomContainer.
- getNaturalAbundance() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the NaturalAbundance attribute of the Isotope object.
- getNotification() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- getOccurrence() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Returns the occurrence value.
- getOrder() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the query bond order of this query bond.
- getOther(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- getPoint2d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns a point specifying the location of this
atom in a 2D space.
- getPoint3d() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns a point specifying the location of this
atom in a 3D space.
- getProperties() - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns a Map with the IChemObject's properties.
- getProperty(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Returns a property for the IChemObject.
- getProperty(Object, Class<T>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
- getRequiredRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getRGroupDefinitions() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for the R-group definitions (substituents).
- getRGroupDefinitions() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRGroupNumber() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getRgroupQueryAtoms(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
Returns all R# type atoms (pseudo atoms) found in the root structure
for a certain provided RGgroup number.
- getRGroups() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- getRootAttachmentPoints() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
- getRootAttachmentPoints() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getRootStructure() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Getter for the root structure of this R-Group.
- getRootStructure() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getSecondAttachmentPoint() - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- getSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- getSingleElectronCount() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the number of the single electrons in this container,
- getSingleElectronNumber(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns the position of a given single electron in the single electron array.
- getStereo() - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Returns the stereo descriptor for this query bond.
- getStereoParity() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the stereo parity of this atom.
- getSubstituents() - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Return all the substituent atom containers, in other words the atom containers
defined in this RGroupQuery except for the root structure.
- getSubstituents() - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- getSymbol() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Returns the element symbol of this element.
- getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
Retrieve the Set of symbols
- getSymbolSet() - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Retrieve the Set of symbols
- getTitle() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- getType() - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
-
Getter for type
- getValency() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Gets the the exact electron valency of the AtomType object.
- growArraySize - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Amount by which the bond and atom arrays grow when elements are added and
the arrays are not large enough for that.
- remove(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes all atoms and electronContainers of a given atomcontainer from this
container.
- removeAllBonds() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes all Bonds from this container.
- removeAllElectronContainers() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes electronContainers from this container.
- removeAllElements() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes all atoms and bond from this container.
- removeAtom(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the given atom and all connected electronContainers from the
AtomContainer.
- removeAtom(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- removeAtomAndConnectedElectronContainers(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Deprecated.
- removeAtomOnly(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the atom at the given position from the AtomContainer.
- removeAtomOnly(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the given atom from the AtomContainer.
- removeBond(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the bond at the given position from the AtomContainer.
- removeBond(IAtom, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the bond that connects the two given atoms.
- removeBond(IBond) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the bond from this container.
- removeElectronContainer(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the bond at the given position from this container.
- removeElectronContainer(IElectronContainer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes this ElectronContainer from this container.
- removeListener(IChemObjectListener) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
- removeLonePair(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the lone pair at the given position from the AtomContainer.
- removeLonePair(ILonePair) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the lone pair from the AtomContainer.
- removeProperty(Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Removes a property for a IChemObject.
- removeSingleElectron(int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the single electron at the given position from the AtomContainer.
- removeSingleElectron(ISingleElectron) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Removes the single electron from the AtomContainer.
- removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
Remove a symbol from this QueryAtom
- removeSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Remove a symbol from this QueryAtom
- RGroup - Class in org.openscience.cdk.isomorphism.matchers
-
Represents a single substitute structure in an
RGroupList.
- RGroup() - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroup
-
- RGroupList - Class in org.openscience.cdk.isomorphism.matchers
-
Represents a list of Rgroup substitutes to be associated with some
RGroupQuery.
- RGroupList(int) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Default constructor.
- RGroupList(int, boolean, String, int) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Constructor with attributes given.
- RGroupQuery - Class in org.openscience.cdk.isomorphism.matchers
-
Represents information contained in a Symyx RGfile (R-group query file).
It contains a root structure (the scaffold if you like), a map with
R-group definitions (each of which can contain multiple substitutes) and
a map with attachment points.
- RGroupQuery(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- ROOT_LABEL - Static variable in class org.openscience.cdk.isomorphism.matchers.RGroup
-
Standard label/title to be used for the root atom container.
- setAtom(int, IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- setAtom(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets an atom in this query bond.
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
-
- setAtomAt(IAtom, int) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
-
- setAtomicNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the atomic number of this element.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBond
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.OrderQueryBondOrderOnly
-
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Sets the array of atoms of this AtomContainer.
- setAtoms(IAtom[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the array of atoms making up this query bond.
- setAtomTypeName(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the if attribute of the AtomType object.
- setBondOrderSum(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the the exact bond order sum attribute of the AtomType object.
- setBonds(IBond[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Sets the array of bonds of this AtomContainer.
- setCharge(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the partial charge of this atom.
- setCovalentRadius(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the covalent radius for this AtomType.
- setElectronCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the number of electrons in this bond
- setExactMass(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the ExactMass attribute of the Isotope object.
- setFirstAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setFlag(int, boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
- setFlags(boolean[]) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
- setFormalCharge(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the formal charge of this atom.
- setFormalNeighbourCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the formal neighbour count of this atom.
- setFractionalPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets a point specifying the location of this
atom in a Crystal unit cell.
- setGroup(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setHCount(int) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- setHybridization(IAtomType.Hybridization) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the hybridization of this atom.
- setID(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Sets the identifier (ID) of this object.
- setImplicitHydrogenCount(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the number of implicit hydrogen count of this atom.
- setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
- setIsAromatic(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
- setIsInRing(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
- setMassNumber(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the atomic mass of this element.
- setMaxBondOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the MaxBondOrder attribute of the AtomType object.
- setNaturalAbundance(Double) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the NaturalAbundance attribute of the Isotope object.
- setNotification(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
- setOccurrence(String) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Picky setter for occurrence fields.
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.InverseSymbolSetQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- setOperator(String) - Method in class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
- setOrder(IBond.Order) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the bond order of this query bond.
- setPoint2d(Point2d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets a point specifying the location of this
atom in a 2D space.
- setPoint3d(Point3d) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets a point specifying the location of this
atom in 3D space.
- setProperties(Map<Object, Object>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
- setProperty(Object, Object) - Method in class org.openscience.cdk.isomorphism.matchers.QueryChemObject
-
Sets a property for a IChemObject.
- setRequiredRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setRestH(boolean) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setRGroupDefinitions(Map<Integer, RGroupList>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for the R-group definitions (substituents).
- setRGroupDefinitions(Map<Integer, RGroupList>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRGroupNumber(int) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
Setter for rGroupNumber, checks for valid range.
- setRGroups(List<RGroup>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupList
-
- setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for root attachment points = bonds that connect R pseudo-atoms to the scaffold.
- setRootAttachmentPoints(Map<IAtom, Map<Integer, IBond>>) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setRootStructure(IAtomContainer) - Method in interface org.openscience.cdk.isomorphism.matchers.IRGroupQuery
-
Setter for the root structure of this R-Group.
- setRootStructure(IAtomContainer) - Method in class org.openscience.cdk.isomorphism.matchers.RGroupQuery
-
- setSecondAttachmentPoint(IAtom) - Method in class org.openscience.cdk.isomorphism.matchers.RGroup
-
- setStereo(IBond.Stereo) - Method in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
Sets the stereo descriptor for this query bond.
- setStereoElements(List<IStereoElement>) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
- setStereoParity(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the stereo parity for this atom.
- setSymbol(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the element symbol of this element.
- setTitle(String) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- setType(CTFileQueryBond.Type) - Method in class org.openscience.cdk.isomorphism.matchers.CTFileQueryBond
-
Getter for bond type
- setValency(Integer) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
Sets the the exact electron valency of the AtomType object.
- singleElectronCount - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Number of single electrons contained by this object.
- singleElectrons - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Internal array of single electrons.
- singleElectrons() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Returns an Iterable for looping over all single electrons in this container.
- stateChanged(IChemObjectChangeEvent) - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Called by objects to which this object has
registered as a listener.
- stereo - Variable in class org.openscience.cdk.isomorphism.matchers.QueryBond
-
A descriptor the stereochemical orientation of this query bond.
- stereochemistry() - Method in class org.openscience.cdk.isomorphism.Mappings
-
Filter the mappings for those which preserve stereochemistry specified in
the query.
- stereoElements - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
-
Internal list of atom parities.
- stereoElements() - Method in class org.openscience.cdk.isomorphism.matchers.QueryAtomContainer
- stereoParity - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
A stereo parity descriptor for the stereochemistry of this atom.
- symbol - Variable in class org.openscience.cdk.isomorphism.matchers.QueryAtom
-
The element symbol for this element as listed in the periodic table.
- SymbolAndChargeQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
- SymbolAndChargeQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- SymbolAndChargeQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolAndChargeQueryAtom
-
- SymbolChargeIDQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
- SymbolChargeIDQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- SymbolChargeIDQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolChargeIDQueryAtom
-
- SymbolQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
- SymbolQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- SymbolQueryAtom(IAtom) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolQueryAtom
-
- SymbolSetQueryAtom - Class in org.openscience.cdk.isomorphism.matchers
-
A QueryAtom that matches all symbols in this container.
- SymbolSetQueryAtom(IChemObjectBuilder) - Constructor for class org.openscience.cdk.isomorphism.matchers.SymbolSetQueryAtom
-
Constructor for the SymbolSetQueryAtom object