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Also reuse connectedBond info for hydrogens, sulphurs, and phosphors
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@egonw
egonw committed Nov 15, 2015
1 parent ea2f2f8 commit e45f2b7
Showing 1 changed file with 23 additions and 23 deletions.
46 changes: 23 additions & 23 deletions base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
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Original file line number Diff line number Diff line change
Expand Up @@ -130,15 +130,15 @@ private IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom,
if ("C".equals(atom.getSymbol())) {
type = perceiveCarbons(atomContainer, atom, searcher, connectedBonds);
} else if ("H".equals(atom.getSymbol())) {
type = perceiveHydrogens(atomContainer, atom);
type = perceiveHydrogens(atomContainer, atom, connectedBonds);
} else if ("O".equals(atom.getSymbol())) {
type = perceiveOxygens(atomContainer, atom, searcher, connectedBonds);
} else if ("N".equals(atom.getSymbol())) {
type = perceiveNitrogens(atomContainer, atom, searcher, connectedBonds);
} else if ("S".equals(atom.getSymbol())) {
type = perceiveSulphurs(atomContainer, atom, searcher, connectedBonds);
} else if ("P".equals(atom.getSymbol())) {
type = perceivePhosphors(atomContainer, atom);
type = perceivePhosphors(atomContainer, atom, connectedBonds);
} else if ("Si".equals(atom.getSymbol())) {
type = perceiveSilicon(atomContainer, atom);
} else if ("Li".equals(atom.getSymbol())) {
Expand Down Expand Up @@ -1199,7 +1199,7 @@ private IAtomType perceiveMercury(IAtomContainer atomContainer, IAtom atom) thro
private IAtomType perceiveSulphurs(IAtomContainer atomContainer, IAtom atom,
RingSearch searcher, List<IBond> connectedBonds) throws CDKException {
if (connectedBonds == null) connectedBonds = atomContainer.getConnectedBondsList(atom);
IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
IBond.Order maxBondOrder = getMaximumBondOrder(connectedBonds);
int neighborcount = connectedBonds.size();
if (hasOneSingleElectron(atomContainer, atom)) {
// no idea how to deal with this yet
Expand Down Expand Up @@ -1322,72 +1322,72 @@ && countAttachedSingleBonds(connectedBonds, atom) == 2) {
return null;
}

private IAtomType perceivePhosphors(IAtomContainer atomContainer, IAtom atom) throws CDKException {
List<IBond> neighbors = atomContainer.getConnectedBondsList(atom);
int neighborcount = neighbors.size();
IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
private IAtomType perceivePhosphors(IAtomContainer atomContainer, IAtom atom, List<IBond> connectedBonds) throws CDKException {
if (connectedBonds == null) connectedBonds = atomContainer.getConnectedBondsList(atom);
int neighborcount = connectedBonds.size();
IBond.Order maxBondOrder = getMaximumBondOrder(connectedBonds);
if (countSingleElectrons(atomContainer, atom) == 3) {
IAtomType type = getAtomType("P.se.3");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
} else if (hasOneSingleElectron(atomContainer, atom)) {
// no idea how to deal with this yet
return null;
} else if (neighborcount == 0) {
if (atom.getFormalCharge() == null || atom.getFormalCharge().intValue() == 0) {
IAtomType type = getAtomType("P.ine");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
}
} else if (neighborcount == 1) {
if (atom.getFormalCharge() == null || atom.getFormalCharge().intValue() == 0) {
IAtomType type = getAtomType("P.ide");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
}
} else if (neighborcount == 3) {
int doubleBonds = countAttachedDoubleBonds(neighbors, atom);
int doubleBonds = countAttachedDoubleBonds(connectedBonds, atom);
if (atom.getFormalCharge() != null && atom.getFormalCharge().intValue() == 1) {
IAtomType type = getAtomType("P.anium");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
} else if (doubleBonds == 1) {
IAtomType type = getAtomType("P.ate");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
} else {
IAtomType type = getAtomType("P.ine");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
}
} else if (neighborcount == 2) {
if (maxBondOrder == CDKConstants.BONDORDER_DOUBLE) {
if (atom.getFormalCharge() != null && atom.getFormalCharge().intValue() == 1) {
IAtomType type = getAtomType("P.sp1.plus");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
} else {
IAtomType type = getAtomType("P.irane");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
}
} else if (maxBondOrder == CDKConstants.BONDORDER_SINGLE) {
IAtomType type = getAtomType("P.ine");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
}
} else if (neighborcount == 4) {
// count the number of double bonded oxygens
int doubleBonds = countAttachedDoubleBonds(neighbors, atom);
int doubleBonds = countAttachedDoubleBonds(connectedBonds, atom);
if (atom.getFormalCharge() == 1 && doubleBonds == 0) {
IAtomType type = getAtomType("P.ate.charged");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
} else if (doubleBonds == 1) {
IAtomType type = getAtomType("P.ate");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
}
} else if (neighborcount == 5) {
if (atom.getFormalCharge() == null || atom.getFormalCharge().intValue() == 0) {
IAtomType type = getAtomType("P.ane");
if (isAcceptable(atom, atomContainer, type, neighbors)) return type;
if (isAcceptable(atom, atomContainer, type, connectedBonds)) return type;
}
}
return null;
}

private IAtomType perceiveHydrogens(IAtomContainer atomContainer, IAtom atom) throws CDKException {
List<IBond> connectedBonds = atomContainer.getConnectedBondsList(atom);
private IAtomType perceiveHydrogens(IAtomContainer atomContainer, IAtom atom, List<IBond> connectedBonds) throws CDKException {
if (connectedBonds == null) connectedBonds = atomContainer.getConnectedBondsList(atom);
int neighborcount = connectedBonds.size();
if (hasOneSingleElectron(atomContainer, atom)) {
if ((atom.getFormalCharge() == CDKConstants.UNSET || atom.getFormalCharge() == 0) && neighborcount == 0) {
Expand Down

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