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johnmayjohnmay
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Overhaul hydrogen atom typing.
1 parent 3bcfe0d commit 8e3e2e9

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+102
-63
lines changed
  • descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular

1 file changed

+102
-63
lines changed

‎descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java‎

Lines changed: 102 additions & 63 deletions
Original file line numberDiff line numberDiff line change
@@ -1018,6 +1018,26 @@ private void calcGroup025_026_028_029_031_032_034_035_043_044(int i) {
10181018
}
10191019
}
10201020

1021+
private boolean isPyrroleLikeHetero(IAtom atom) {
1022+
if (!atom.isAromatic())
1023+
return false;
1024+
switch (atom.getAtomicNumber()) {
1025+
case 7:
1026+
case 15:
1027+
if (atom.getBondCount() == 3 && atom.getFormalCharge() == 0)
1028+
return true;
1029+
if (atom.getBondCount() == 2 && atom.getImplicitHydrogenCount() == 1)
1030+
return true;
1031+
if (atom.getBondCount() == 2 && atom.getFormalCharge() == -1)
1032+
return true;
1033+
return false;
1034+
case 8:
1035+
case 16:
1036+
return true;
1037+
}
1038+
return false;
1039+
}
1040+
10211041
private int getHAtomType(IAtom ai, List connectedAtoms) {
10221042
//ai is the atom connected to a H atoms.
10231043
//ai environment determines what is the H atom type
@@ -1053,76 +1073,95 @@ private int getHAtomType(IAtom ai, List connectedAtoms) {
10531073
return 51;
10541074
} // end if(ai.getSymbol().equals("C") && !ai.getFlag(CDKConstants.ISAROMATIC))
10551075

1056-
List bonds = atomContainer.getConnectedBondsList(ai);
1057-
int doublebondcount = 0;
1058-
int triplebondcount = 0;
1059-
String hybrid = "";
1060-
1061-
for (int j = 0; j <= bonds.size() - 1; j++) {
1062-
if (((IBond) bonds.get(j)).getOrder() == IBond.Order.DOUBLE)
1063-
doublebondcount++;
1064-
else if (((IBond) bonds.get(j)).getOrder() == IBond.Order.TRIPLE) triplebondcount++;
1065-
}
1076+
IAtomType.Hybridization hyb;
10661077

1067-
if (doublebondcount == 0 && triplebondcount == 0)
1068-
hybrid = "sp3";
1069-
else if (doublebondcount == 1 && triplebondcount == 0)
1070-
hybrid = "sp2";
1071-
else if (doublebondcount == 2 || triplebondcount == 1) hybrid = "sp";
1078+
int ndoub = 0;
1079+
int ntrip = 0;
10721080
int oxNum = 0;
10731081
int xCount = 0;
1074-
1075-
for (int j = 0; j <= ca.size() - 1; j++) {
1076-
//String s = ((IAtom)ca.get(j)).getSymbol();
1077-
// if (s.equals("F") || s.equals("O") || s.equals("Cl")
1078-
// || s.equals("Br") || s.equals("N") || s.equals("S"))
1079-
if (ap.getNormalizedElectronegativity(((IAtom) ca.get(j)).getSymbol()) > 1) {
1080-
java.util.List bonds2 = atomContainer.getConnectedBondsList(((IAtom) ca.get(j)));
1081-
boolean haveDouble = false;
1082-
for (int k = 0; k <= bonds2.size() - 1; k++) {
1083-
if (((IBond) bonds2.get(k)).getOrder() == IBond.Order.DOUBLE) {
1084-
haveDouble = true;
1085-
break;
1082+
boolean hasConjHetereo = false;
1083+
1084+
for (IBond bond : ai.bonds()) {
1085+
if (bond.getOrder() == IBond.Order.DOUBLE)
1086+
ndoub++;
1087+
else if (bond.getOrder() == IBond.Order.TRIPLE)
1088+
ntrip++;
1089+
final IAtom nbor = bond.getOther(ai);
1090+
if (isHetero(nbor)) {
1091+
if (bond.isAromatic()) {
1092+
if (bond.getOrder() == IBond.Order.SINGLE) {
1093+
if (!isPyrroleLikeHetero(nbor) && !hasConjHetereo) {
1094+
oxNum += 2;
1095+
hasConjHetereo = true;
1096+
} else
1097+
oxNum++;
1098+
} else if (!hasConjHetereo) {
1099+
hasConjHetereo = true;
1100+
oxNum += 2;
1101+
} else {
1102+
oxNum++;
10861103
}
1104+
} else
1105+
oxNum += bond.getOrder().numeric();
1106+
}
1107+
else if (nbor.getAtomicNumber() == 6) {
1108+
for (IBond bond2 : nbor.bonds()) {
1109+
IAtom nbor2 = bond2.getOther(nbor);
1110+
if (isHetero(nbor2))
1111+
xCount++;
10871112
}
1088-
if (haveDouble && ((IAtom) ca.get(j)).getSymbol().equals("N"))
1089-
oxNum += 2; // C-N bond order for pyridine type N's is considered to be 2
1090-
else
1091-
oxNum += BondManipulator
1092-
.destroyBondOrder(atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder());
10931113
}
1094-
java.util.List ca2 = atomContainer.getConnectedAtomsList(((IAtom) ca.get(j)));
1114+
}
10951115

1096-
for (int k = 0; k <= ca2.size() - 1; k++) {
1097-
String s2 = ((IAtom) ca2.get(k)).getSymbol();
1098-
if (!s2.equals("C")) xCount++;
1099-
}
1100-
}// end j loop
1101-
1102-
if (oxNum == 0) {
1103-
if (hybrid.equals("sp3")) {
1104-
if (xCount == 0)
1105-
return 46;
1106-
else if (xCount == 1)
1107-
return 52;
1108-
else if (xCount == 2)
1109-
return 53;
1110-
else if (xCount == 3)
1111-
return 54;
1112-
else if (xCount >= 4) return 55;
1113-
} else if (hybrid.equals("sp2")) {
1114-
return 47;
1115-
} else if (hybrid.equals("sp")) {
1116-
return 48;
1117-
}
1118-
} else if (oxNum == 1 && hybrid.equals("sp3"))
1119-
return 47;
1120-
else if (oxNum == 2 && hybrid.equals("sp3") || oxNum == 1 && hybrid.equals("sp2"))
1121-
return 48;
1122-
else if ((oxNum == 3 && hybrid.equals("sp3")) || (oxNum >= 2 && hybrid.equals("sp2"))
1123-
|| (oxNum >= 1 && hybrid.equals("sp"))) return 49;
1124-
1125-
return (0);
1116+
if (ndoub == 0 && ntrip == 0)
1117+
hyb = IAtomType.Hybridization.SP3;
1118+
else if (ndoub == 1 && ntrip == 0)
1119+
hyb = IAtomType.Hybridization.SP2;
1120+
else if (ndoub == 2 || ntrip == 1)
1121+
hyb = IAtomType.Hybridization.SP1;
1122+
else
1123+
return 0; // unknown
1124+
1125+
switch (hyb) {
1126+
case SP1:
1127+
if (oxNum == 0)
1128+
return 48;
1129+
if (oxNum == 1)
1130+
return 49;
1131+
break;
1132+
case SP2:
1133+
if (oxNum == 0)
1134+
return 47;
1135+
if (oxNum == 1)
1136+
return 48;
1137+
if (oxNum == 2 || oxNum == 3)
1138+
return 49;
1139+
break;
1140+
case SP3:
1141+
if (oxNum == 0) {
1142+
if (xCount == 0)
1143+
return 46;
1144+
else if (xCount == 1)
1145+
return 52;
1146+
else if (xCount == 2)
1147+
return 53;
1148+
else if (xCount == 3)
1149+
return 54;
1150+
else if (xCount == 4)
1151+
return 55;
1152+
}
1153+
if (oxNum == 1)
1154+
return 47;
1155+
if (oxNum == 2)
1156+
return 48;
1157+
if (oxNum == 3)
1158+
return 49;
1159+
break;
1160+
}
1161+
1162+
System.out.println("Fall through");
1163+
1164+
return 0;
11261165
}
11271166

11281167
private void calcGroup056_57(int i) {

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