Uses of Interface
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer

Packages that use IQueryAtomContainer

Package	Description
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.pharmacophore
org.openscience.cdk.smsd
org.openscience.cdk.smsd.algorithm.matchers
org.openscience.cdk.smsd.algorithm.mcgregor
org.openscience.cdk.smsd.algorithm.mcsplus
org.openscience.cdk.smsd.algorithm.rgraph
org.openscience.cdk.smsd.algorithm.single
org.openscience.cdk.smsd.algorithm.vflib
org.openscience.cdk.smsd.algorithm.vflib.query
org.openscience.cdk.smsd.interfaces

Uses of IQueryAtomContainer in org.openscience.cdk.isomorphism.matchers

Classes in org.openscience.cdk.isomorphism.matchers that implement IQueryAtomContainer

Modifier and Type	Class and Description
class	QueryAtomContainer

Methods in org.openscience.cdk.isomorphism.matchers that return IQueryAtomContainer

Modifier and Type	Method and Description
IQueryAtomContainer	QueryAtomContainer.clone() Clones this AtomContainer object and its content.

Uses of IQueryAtomContainer in org.openscience.cdk.isomorphism.matchers.smarts

Constructors in org.openscience.cdk.isomorphism.matchers.smarts with parameters of type IQueryAtomContainer

Constructor and Description
RecursiveSmartsAtom(IQueryAtomContainer query) Creates a new instance

Uses of IQueryAtomContainer in org.openscience.cdk.pharmacophore

Classes in org.openscience.cdk.pharmacophore that implement IQueryAtomContainer

Modifier and Type	Class and Description
class	PharmacophoreQuery Represents a colleciton of pharmacophore groups and constraints.

Uses of IQueryAtomContainer in org.openscience.cdk.smsd

Methods in org.openscience.cdk.smsd with parameters of type IQueryAtomContainer

Modifier and Type	Method and Description
void	Isomorphism.init(IQueryAtomContainer reactant, IAtomContainer product) Deprecated.

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.algorithm.matchers

Constructors in org.openscience.cdk.smsd.algorithm.matchers with parameters of type IQueryAtomContainer

Constructor and Description
DefaultMCSPlusAtomMatcher(IQueryAtom smartQueryAtom, IQueryAtomContainer container) Deprecated. Constructor
DefaultVFAtomMatcher(IQueryAtom smartQueryAtom, IQueryAtomContainer container) Deprecated. Constructor

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.algorithm.mcgregor

Methods in org.openscience.cdk.smsd.algorithm.mcgregor with parameters of type IQueryAtomContainer

Modifier and Type	Method and Description
protected void	QueryProcessor.process(IQueryAtomContainer query, IAtomContainer target, List<Integer> unmappedAtomsMolA, List<Integer> mappedAtoms, int counter) Deprecated.

Constructors in org.openscience.cdk.smsd.algorithm.mcgregor with parameters of type IQueryAtomContainer

Constructor and Description
McGregor(IQueryAtomContainer source, IAtomContainer target, List<List<Integer>> mappings) Deprecated. Constructor for the McGregor algorithm.

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.algorithm.mcsplus

Methods in org.openscience.cdk.smsd.algorithm.mcsplus with parameters of type IQueryAtomContainer

Modifier and Type	Method and Description
void	MCSPlusHandler.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.algorithm.rgraph

Methods in org.openscience.cdk.smsd.algorithm.rgraph with parameters of type IQueryAtomContainer

Modifier and Type	Method and Description
void	CDKSubGraphHandler.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.
void	CDKMCSHandler.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.algorithm.single

Methods in org.openscience.cdk.smsd.algorithm.single with parameters of type IQueryAtomContainer

Modifier and Type	Method and Description
protected List<Map<IAtom,IAtom>>	SingleMapping.getOverLaps(IQueryAtomContainer source, IAtomContainer target, boolean removeHydrogen) Deprecated. Returns single mapping solutions.
void	SingleMappingHandler.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.algorithm.vflib

Methods in org.openscience.cdk.smsd.algorithm.vflib with parameters of type IQueryAtomContainer

Modifier and Type	Method and Description
void	VFlibTurboHandler.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.
void	VFlibSubStructureHandler.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.
void	VFlibMCSHandler.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.algorithm.vflib.query

Constructors in org.openscience.cdk.smsd.algorithm.vflib.query with parameters of type IQueryAtomContainer

Constructor and Description
QueryCompiler(IQueryAtomContainer molecule) Deprecated. Construct query object from the molecule

Uses of IQueryAtomContainer in org.openscience.cdk.smsd.interfaces

Methods in org.openscience.cdk.smsd.interfaces with parameters of type IQueryAtomContainer

Modifier and Type	Method and Description
abstract void	AbstractMCS.init(IQueryAtomContainer source, IAtomContainer target) Deprecated. initialize query and target molecules.
void	IMCSBase.set(IQueryAtomContainer source, IAtomContainer target) Deprecated. Initialise the query and target molecule.