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Correct handling of halogens on hetero atoms.
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@johnmay
johnmay committed Feb 1, 2019
1 parent 9ca9a14 commit a192d17
Showing 1 changed file with 76 additions and 56 deletions.
132 changes: 76 additions & 56 deletions ...lecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -1520,20 +1520,25 @@ else if (bj.getOrder() == IBond.Order.TRIPLE) {
oxNum += atomContainer.getBond(ca0, ca2j).getOrder().numeric();
}

if (hybrid.equals("sp3") && oxNum == 1) {
frags[81]++;
alogpfrag[i] = 81;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[82]++;
alogpfrag[i] = 82;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[83]++;
alogpfrag[i] = 83;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[84]++;
alogpfrag[i] = 84;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4) || !ca0.getSymbol().equals("C")) {
if (ca0.getAtomicNumber() == 6) {
if (hybrid.equals("sp3") && oxNum == 1) {
frags[81]++;
alogpfrag[i] = 81;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[82]++;
alogpfrag[i] = 82;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[83]++;
alogpfrag[i] = 83;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[84]++;
alogpfrag[i] = 84;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4)) {
frags[85]++;
alogpfrag[i] = 85;
}
} else {
frags[85]++;
alogpfrag[i] = 85;
}
Expand Down Expand Up @@ -1591,20 +1596,25 @@ else if (bj.getOrder() == IBond.Order.TRIPLE) {
}
}

if (hybrid.equals("sp3") && oxNum == 1) {
frags[86]++;
alogpfrag[i] = 86;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[87]++;
alogpfrag[i] = 87;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[88]++;
alogpfrag[i] = 88;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[89]++;
alogpfrag[i] = 89;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4) || !ca0.getSymbol().equals("C")) {
if (ca0.getAtomicNumber() == 6) {
if (hybrid.equals("sp3") && oxNum == 1) {
frags[86]++;
alogpfrag[i] = 86;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[87]++;
alogpfrag[i] = 87;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[88]++;
alogpfrag[i] = 88;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[89]++;
alogpfrag[i] = 89;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4)) {
frags[90]++;
alogpfrag[i] = 90;
}
} else {
frags[90]++;
alogpfrag[i] = 90;
}
Expand Down Expand Up @@ -1663,20 +1673,25 @@ private void calcGroup091_to_095(int i) {

}

if (hybrid.equals("sp3") && oxNum == 1) {
frags[91]++;
alogpfrag[i] = 91;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[92]++;
alogpfrag[i] = 92;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[93]++;
alogpfrag[i] = 93;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[94]++;
alogpfrag[i] = 94;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4) || !ca0.getSymbol().equals("C")) {
if (ca0.getAtomicNumber() == 6) {
if (hybrid.equals("sp3") && oxNum == 1) {
frags[91]++;
alogpfrag[i] = 91;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[92]++;
alogpfrag[i] = 92;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[93]++;
alogpfrag[i] = 93;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[94]++;
alogpfrag[i] = 94;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4)) {
frags[95]++;
alogpfrag[i] = 95;
}
} else {
frags[95]++;
alogpfrag[i] = 95;
}
Expand Down Expand Up @@ -1735,20 +1750,25 @@ else if (bj.getOrder() == IBond.Order.TRIPLE) {

}

if (hybrid.equals("sp3") && oxNum == 1) {
frags[96]++;
alogpfrag[i] = 96;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[97]++;
alogpfrag[i] = 97;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[98]++;
alogpfrag[i] = 98;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[99]++;
alogpfrag[i] = 99;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4) || !ca0.getSymbol().equals("C")) {
if (ca0.getAtomicNumber() == 6) {
if (hybrid.equals("sp3") && oxNum == 1) {
frags[96]++;
alogpfrag[i] = 96;
} else if (hybrid.equals("sp3") && oxNum == 2) {
frags[97]++;
alogpfrag[i] = 97;
} else if (hybrid.equals("sp3") && oxNum == 3) {
frags[98]++;
alogpfrag[i] = 98;
} else if (hybrid.equals("sp2") && oxNum == 1) {
frags[99]++;
alogpfrag[i] = 99;
} else if ((hybrid.equals("sp2") && oxNum > 1) || (hybrid.equals("sp") && oxNum >= 1)
|| (hybrid.equals("sp3") && oxNum == 4)) {
frags[100]++;
alogpfrag[i] = 100;
}
} else {
frags[100]++;
alogpfrag[i] = 100;
}
Expand Down

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