private synchronized void singleMapping() { SingleMappingHandler mcs; mcs = new SingleMappingHandler(getQuery(), getTarget(), atomMatcher); clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); }
private synchronized void singleMapping() { SingleMappingHandler mcs; mcs = new SingleMappingHandler(getQuery(), getTarget(), isMatchRings()); clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); }
private synchronized void singleMapping() { SingleMappingHandler mcs; mcs = new SingleMappingHandler(getQuery(), getTarget(), isMatchRings()); clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); }
private synchronized void vfLibMCSAlgorithm() { VF2MCS mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new VF2MCS((IQueryAtomContainer) getQuery(), getTarget(), atomMatcher, bondMatcher); } else { mcs = new VF2MCS(getQuery(), getTarget(), atomMatcher, bondMatcher); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); }
private synchronized boolean cdkMCSAlgorithm() { CDKMCSHandler mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new CDKMCSHandler(getQuery(), getTarget(), atomMatcher, bondMatcher); } else { mcs = new CDKMCSHandler(getQuery(), getTarget(), atomMatcher, bondMatcher); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); return mcs.isTimeout(); }
private synchronized void vfLibMCSAlgorithm() { VF2MCS mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new VF2MCS((IQueryAtomContainer) getQuery(), getTarget()); } else { mcs = new VF2MCS(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType()); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); }
private synchronized boolean substructureAlgorithm() throws CDKException { if (DEBUG) { System.out.println("Check substructureAlgorithm"); } Substructure mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new Substructure((IQueryAtomContainer) getQuery(), getTarget(), atomMatcher, bondMatcher, true); } else { mcs = new Substructure(getQuery(), getTarget(), atomMatcher, bondMatcher, true); } clearMaps(); if (mcs.isSubgraph()) { getMCSList().addAll(mcs.getAllAtomMapping()); } return mcs.isSubgraph(); }
private synchronized void vfLibMCSAlgorithm() { VF2MCS mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new VF2MCS((IQueryAtomContainer) getQuery(), getTarget()); } else { mcs = new VF2MCS(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType()); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); }
private synchronized boolean cdkMCSAlgorithm() { CDKMCSHandler mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new CDKMCSHandler(getQuery(), getTarget()); } else { mcs = new CDKMCSHandler(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType()); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); return mcs.isTimeout(); }
private synchronized boolean cdkMCSAlgorithm() { CDKMCSHandler mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new CDKMCSHandler(getQuery(), getTarget()); } else { mcs = new CDKMCSHandler(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType()); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); return mcs.isTimeout(); }
private synchronized boolean mcsPlusAlgorithm() { MCSPlusHandler mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new MCSPlusHandler((IQueryAtomContainer) getQuery(), getTarget()); } else { mcs = new MCSPlusHandler(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType()); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); return mcs.isTimeout(); }
private synchronized boolean mcsPlusAlgorithm() { MCSPlusHandler mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new MCSPlusHandler((IQueryAtomContainer) getQuery(), getTarget()); } else { mcs = new MCSPlusHandler(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType()); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); return mcs.isTimeout(); }
private synchronized boolean substructureAlgorithm() throws CDKException { Substructure mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new Substructure((IQueryAtomContainer) getQuery(), getTarget(), true); } else { mcs = new Substructure(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType(), true); } clearMaps(); if (mcs.isSubgraph()) { getMCSList().addAll(mcs.getAllAtomMapping()); } return mcs.isSubgraph(); }
private synchronized boolean substructureAlgorithm() throws CDKException { Substructure mcs; if (getQuery() instanceof IQueryAtomContainer) { mcs = new Substructure((IQueryAtomContainer) getQuery(), getTarget(), true); } else { mcs = new Substructure(getQuery(), getTarget(), isMatchBonds(), isMatchRings(), isMatchAtomType(), true); } clearMaps(); if (mcs.isSubgraph()) { getMCSList().addAll(mcs.getAllAtomMapping()); } return mcs.isSubgraph(); }
private synchronized boolean mcsPlusAlgorithm() throws CDKException { IResults mcs; int expectedMaxGraphmatch = expectedMaxGraphmatch(getQuery(), getTarget()); if (getQuery() instanceof IQueryAtomContainer) { if (DEBUG) { System.out.println("org.openscience.smsd.algorithm.mcsplus2.MCSPlusMapper"); } mcs = new org.openscience.smsd.algorithm.mcsplus2.MCSPlusMapper((IQueryAtomContainer) getQuery(), getTarget(), atomMatcher, bondMatcher); } else if (expectedMaxGraphmatch < 3) { if (DEBUG) { System.out.println("org.openscience.smsd.algorithm.mcsplus1.MCSPlusMapper"); } mcs = new org.openscience.smsd.algorithm.mcsplus1.MCSPlusMapper(getQuery(), getTarget(), atomMatcher, bondMatcher); } else if (expectedMaxGraphmatch > 3) { if (DEBUG) { System.out.println("org.openscience.smsd.algorithm.mcsplus.MCSPlusMapper"); } mcs = new org.openscience.smsd.algorithm.mcsplus.MCSPlusMapper(getQuery(), getTarget(), atomMatcher, bondMatcher); } else { if (DEBUG) { System.out.println("org.openscience.smsd.algorithm.mcsplus2.MCSPlusMapper"); } mcs = new org.openscience.smsd.algorithm.mcsplus2.MCSPlusMapper(getQuery(), getTarget(), atomMatcher, bondMatcher); } clearMaps(); getMCSList().addAll(mcs.getAllAtomMapping()); return false; }