/** * Constructor for VF Substructure Algorithm * * Please call before calling substructure search * * if (super.isMatchRings()) { try { * MoleculeInitializer.initializeMolecule(super.getQuery()); * MoleculeInitializer.initializeMolecule(super.getTarget()); } catch * (CDKException ex) { } } * * @param query * @param target * @param shouldMatchBonds Match bond types (i.e. double to double etc) * @param matchRings Match ring atoms and ring size * @param findAllSubgraph report all subgraphs * @param matchAtomType * @throws CDKException */ public Substructure( IAtomContainer query, IAtomContainer target, AtomMatcher am, BondMatcher bm, boolean findAllSubgraph) throws CDKException { super(query, target, am, bm); super.setSubgraph(findSubgraphs(findAllSubgraph)); }
/** * Initialize query and target molecules. * * Note: Here its assumed that hydrogens are implicit and user has called * these two methods percieveAtomTypesAndConfigureAtoms and * CDKAromicityDetector before initializing calling this method. * * @param query query molecule * @param target target molecule This is the algorithm factory and entry * port for all the MCS algorithm in the Isomorphism supported algorithm * {@link org.openscience.smsd.interfaces.Algorithm} types: <OL> <lI>0: * Default, * <lI>1: MCSPlus, <lI>2: VFLibMCS, <lI>3: CDKMCS </OL> * @param algorithmType * {@link org.openscience.smsd.interfaces.Algorithm} */ public Isomorphism( IQueryAtomContainer query, IAtomContainer target, Algorithm algorithmType) { super(query, target); this.algorithmType = algorithmType; mcsBuilder(query, target); super.setSubgraph(isSubgraph()); }
/** * Initialize query and target molecules. * * Note: Here its assumed that hydrogens are implicit and user has called * these two methods percieveAtomTypesAndConfigureAtoms and * CDKAromicityDetector before initializing calling this method. * * @param query query molecule * @param target target molecule This is the algorithm factory and entry * port for all the MCS algorithm in the Isomorphism supported algorithm * {@link org.openscience.smsd.interfaces.Algorithm} types: <OL> <lI>0: * Default, * <lI>1: MCSPlus, <lI>2: VFLibMCS, <lI>3: CDKMCS </OL> * @param algorithmType * {@link org.openscience.smsd.interfaces.Algorithm} */ public Isomorphism( IQueryAtomContainer query, IAtomContainer target, Algorithm algorithmType) { super(query, target); this.algorithmType = algorithmType; mcsBuilder(query, target); super.setSubgraph(isSubgraph()); }
/** * Constructor for VF Substructure Algorithm * * @param query * @param target * @param findAllSubgraphFlag report all subgraphs * @throws CDKException */ public Substructure( IQueryAtomContainer query, IAtomContainer target, boolean findAllSubgraphFlag) throws CDKException { super(query, target, AtomMatcher.forQuery(), BondMatcher.forQuery()); super.setSubgraph(findSubgraphs(findAllSubgraphFlag)); }
this.algorithmType = algorithmType; mcsBuilder(super.getQuery(), super.getTarget()); super.setSubgraph(isSubgraph());
this.algorithmType = algorithmType; mcsBuilder(super.getQuery(), super.getTarget()); super.setSubgraph(isSubgraph());
super.setSubgraph(isSubgraph());
super.setSubgraph(isSubgraph());