/** * {@inheritDoc} * * @return */ @Override public synchronized AtomAtomMapping getFirstAtomMapping() { return getMCSList().isEmpty() ? new AtomAtomMapping(getQuery(), getTarget()) : getMCSList().iterator().next(); }
/** * {@inheritDoc} * * @return */ @Override public synchronized AtomAtomMapping getFirstAtomMapping() { return getMCSList().isEmpty() ? new AtomAtomMapping(getQuery(), getTarget()) : getMCSList().iterator().next(); }
/** * @return the allBondMCS */ public synchronized List<Map<IBond, IBond>> getAllBondMaps() { if (!getMCSList().isEmpty()) { return makeBondMapsOfAtomMaps(getQuery(), getTarget(), getMCSList()); } return new ArrayList<>(); }
/** * {@inheritDoc} * * @return */ @Override public synchronized AtomAtomMapping getFirstAtomMapping() { return getMCSList().isEmpty() ? new AtomAtomMapping(getQuery(), getTarget()) : getMCSList().iterator().next(); }
/** * @return the allBondMCS */ public synchronized List<Map<IBond, IBond>> getAllBondMaps() { if (!getMCSList().isEmpty()) { return makeBondMapsOfAtomMaps(getQuery(), getTarget(), getMCSList()); } return new ArrayList<>(); }
/** * @return the allBondMCS */ public synchronized List<Map<IBond, IBond>> getAllBondMaps() { if (!getMCSList().isEmpty()) { return makeBondMapsOfAtomMaps(getQuery(), getTarget(), getMCSList()); } return new ArrayList<>(); }
synchronized void printMatch(BaseMapping isomorphism) { int overlap = isomorphism.getFirstAtomMapping().isEmpty() ? 0 : isomorphism.getFirstAtomMapping().getCount(); try { System.out.println("Q: " + isomorphism.getQuery().getID() + " T: " + isomorphism.getTarget().getID() + " atoms: " + isomorphism.getQuery().getAtomCount() + " atoms: " + isomorphism.getTarget().getAtomCount() + " overlaps: " + overlap + " mcs " + isomorphism.getFirstAtomMapping().getCommonFragmentAsSMILES()); } catch (CloneNotSupportedException | CDKException ex) { LOGGER.error(Level.SEVERE, "Print MCS ", ex.getMessage()); } }
boolean flag = false; IAtomContainer reactant = getQuery(); IAtomContainer product = getTarget(); int stereoMisMatchScore = 0; if (getMappingCount() > 0) {
boolean flag = false; IAtomContainer reactant = getQuery(); IAtomContainer product = getTarget(); int stereoMisMatchScore = 0; if (getMappingCount() > 0) {
boolean flag = false; IAtomContainer reactant = getQuery(); IAtomContainer product = getTarget(); int stereoMisMatchScore = 0; if (getMappingCount() > 0) {
super(query, target, am, bm); this.algorithmType = algorithmType; mcsBuilder(super.getQuery(), super.getTarget()); super.setSubgraph(isSubgraph());
super(query, target, AtomMatcher.forQuery(), BondMatcher.forQuery()); this.algorithmType = algorithmType; mcsBuilder(super.getQuery(), super.getTarget()); super.setSubgraph(isSubgraph());
outputHandler.writeTargetMol(smsd.getTarget());