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Replaced getSymbol in ALOGPDescriptor and HybridizationRatioDescriptor using regex replacement
1 parent 229e3b7 commit 08430e0

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2 files changed

+19
-17
lines changed

2 files changed

+19
-17
lines changed

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

Lines changed: 17 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -23,6 +23,7 @@
2323
import org.openscience.cdk.CDKConstants;
2424
import org.openscience.cdk.atomtype.EStateAtomTypeMatcher;
2525
import org.openscience.cdk.exception.CDKException;
26+
import org.openscience.cdk.interfaces.IElement;
2627
import org.openscience.cdk.interfaces.IAtom;
2728
import org.openscience.cdk.interfaces.IAtomContainer;
2829
import org.openscience.cdk.interfaces.IAtomType;
@@ -850,7 +851,7 @@ private void calcGroup024_027_030_033_042(int i) {
850851
} else
851852
throw new IllegalStateException();
852853

853-
if (ca0.getSymbol().equals("C") && ca1.getSymbol().equals("C")) {
854+
if (ca0.getAtomicNumber() == IElement.C && ca1.getAtomicNumber() == IElement.C) {
854855
frags[24]++;
855856
alogpfrag[i] = 24;
856857
return;
@@ -884,8 +885,8 @@ private void calcGroup024_027_030_033_042(int i) {
884885
alogpfrag[i] = 42;
885886
}
886887

887-
} else if (ca0.getSymbol().equals("C") && !ca1.getSymbol().equals("C")
888-
|| (!ca0.getSymbol().equals("C") && ca1.getSymbol().equals("C"))) {
888+
} else if (ca0.getAtomicNumber() == IElement.C && ca1.getAtomicNumber() != IElement.C
889+
|| (ca0.getAtomicNumber() != IElement.C && ca1.getAtomicNumber() == IElement.C)) {
889890

890891
if (haveDouble1 && haveDouble2) { // R--CH--X
891892
frags[27]++;
@@ -978,7 +979,7 @@ public int compare(IAtom a, IAtom b) {
978979

979980
if (!sameringatoms[0].getSymbol().equals("C") && !sameringatoms[1].getSymbol().equals("C")) {
980981
if (haveDouble1 && haveDouble2) { // X--CR--X
981-
if (nonringatom.getSymbol().equals("C")) {
982+
if (nonringatom.getAtomicNumber() == IElement.C) {
982983
frags[31]++;
983984
alogpfrag[i] = 31;
984985
} else { // X--CX--X
@@ -988,7 +989,7 @@ public int compare(IAtom a, IAtom b) {
988989

989990
} else {
990991

991-
if (nonringatom.getSymbol().equals("C")) { // X--CR..X
992+
if (nonringatom.getAtomicNumber() == IElement.C) { // X--CR..X
992993
frags[43]++;
993994
alogpfrag[i] = 43;
994995

@@ -1000,7 +1001,7 @@ public int compare(IAtom a, IAtom b) {
10001001
}
10011002
} else if (sameringatoms[0].getSymbol().equals("C") && sameringatoms[1].getSymbol().equals("C")) {
10021003

1003-
if (nonringatom.getSymbol().equals("C")) {// R--CR--R
1004+
if (nonringatom.getAtomicNumber() == IElement.C) {// R--CR--R
10041005
frags[25]++;
10051006
alogpfrag[i] = 25;
10061007
} else { // R--CX--R
@@ -1012,7 +1013,7 @@ public int compare(IAtom a, IAtom b) {
10121013
|| (!sameringatoms[0].getSymbol().equals("C") && sameringatoms[1].getSymbol().equals("C"))) {
10131014

10141015
if (haveDouble1 && haveDouble2) { // R--CR--X
1015-
if (nonringatom.getSymbol().equals("C")) {
1016+
if (nonringatom.getAtomicNumber() == IElement.C) {
10161017
frags[28]++;
10171018
alogpfrag[i] = 28;
10181019
} else { // R--CX--X
@@ -1022,7 +1023,7 @@ public int compare(IAtom a, IAtom b) {
10221023

10231024
} else {
10241025

1025-
if (nonringatom.getSymbol().equals("C")) { // R--CR..X
1026+
if (nonringatom.getAtomicNumber() == IElement.C) { // R--CR..X
10261027
frags[34]++;
10271028
alogpfrag[i] = 34;
10281029

@@ -1250,7 +1251,7 @@ private void calcGroup058_61(int i) {
12501251
// 62: O in O-
12511252
if (fragment[i].equals("SsOm")) {
12521253
IAtom ca0 = (IAtom) ca.get(0);
1253-
if (ca0.getSymbol().equals("N") && ca0.getFormalCharge() == 1) {
1254+
if (ca0.getAtomicNumber() == IElement.N && ca0.getFormalCharge() == 1) {
12541255
frags[61]++;
12551256
alogpfrag[i] = 61;
12561257
} else {
@@ -1260,7 +1261,7 @@ private void calcGroup058_61(int i) {
12601261

12611262
} else if (fragment[i].equals("SdO")) {
12621263
IAtom ca0 = (IAtom) ca.get(0);
1263-
if (ca0.getSymbol().equals("N") && ca0.getFormalCharge() == 1) {
1264+
if (ca0.getAtomicNumber() == IElement.N && ca0.getFormalCharge() == 1) {
12641265
frags[61]++;
12651266
alogpfrag[i] = 61;
12661267
} else {
@@ -1303,7 +1304,7 @@ private void calcGroup059_060_063(int i) {
13031304
}
13041305
}
13051306

1306-
if (ca0.getSymbol().equals("O") || ca1.getSymbol().equals("O")) {
1307+
if (ca0.getAtomicNumber() == IElement.O || ca1.getAtomicNumber() == IElement.O) {
13071308
frags[63]++;
13081309
alogpfrag[i] = 63;
13091310
} else {
@@ -1325,7 +1326,7 @@ private void calcGroup066_to_079(int i) {
13251326
int nAl = 0;
13261327
IAtom atom = atomContainer.getAtom(i);
13271328
IAtom ai = atom;
1328-
if (!ai.getSymbol().equals("N")) return;
1329+
if (ai.getAtomicNumber() != IElement.N) return;
13291330
List<IAtom> nbors = atomContainer.getConnectedAtomsList(atom);
13301331

13311332
int htype = 50; //H atom attached to a hetero atom
@@ -1355,7 +1356,7 @@ private void calcGroup066_to_079(int i) {
13551356
for (int k = 0; k <= ca2.size() - 1; k++) {
13561357
IAtom ca2k = (IAtom) ca2.get(k);
13571358
if (atomContainer.indexOf(ca2k) != i) {
1358-
if (!ca2k.getSymbol().equals("C")) {
1359+
if (ca2k.getAtomicNumber() != IElement.C) {
13591360
if (!ca2k.getFlag(CDKConstants.ISAROMATIC)
13601361
&& !((IAtom) nbors.get(j)).getFlag(CDKConstants.ISAROMATIC)
13611362
&& !ai.getFlag(CDKConstants.ISAROMATIC)) {
@@ -1380,7 +1381,7 @@ private void calcGroup066_to_079(int i) {
13801381
break;
13811382
}
13821383
}
1383-
if (ca0.getFlag(CDKConstants.ISAROMATIC) || !ca0.getSymbol().equals("C")) {
1384+
if (ca0.getFlag(CDKConstants.ISAROMATIC) || ca0.getAtomicNumber() != IElement.C) {
13841385
frags[69]++;
13851386
alogpfrag[i] = 69;
13861387
} else {
@@ -1453,7 +1454,7 @@ private void calcGroup066_to_079(int i) {
14531454

14541455
} else if (fragment[i].equals("StN")) {
14551456
IAtom ca0 = (IAtom) nbors.get(0);
1456-
if (ca0.getSymbol().equals("C")) { // R#N
1457+
if (ca0.getAtomicNumber() == IElement.C) { // R#N
14571458
frags[74]++;
14581459
alogpfrag[i] = 74;
14591460
}
@@ -1462,7 +1463,7 @@ private void calcGroup066_to_079(int i) {
14621463
if (fragment[i].equals("SdsN")) {
14631464
IAtom ca0 = nbors.get(0);
14641465
IAtom ca1 = nbors.get(1);
1465-
if (ca0.getSymbol().equals("O") && ca1.getSymbol().equals("O")) {
1466+
if (ca0.getAtomicNumber() == IElement.O && ca1.getAtomicNumber() == IElement.O) {
14661467
frags[76]++;
14671468
alogpfrag[i] = 76;
14681469
return;

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
2222
package org.openscience.cdk.qsar.descriptors.molecular;
2323

2424
import org.openscience.cdk.exception.CDKException;
25+
import org.openscience.cdk.interfaces.IElement;
2526
import org.openscience.cdk.interfaces.IAtom;
2627
import org.openscience.cdk.interfaces.IAtomContainer;
2728
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
@@ -122,7 +123,7 @@ public DescriptorValue calculate(IAtomContainer container) {
122123
int nsp2 = 0;
123124
int nsp3 = 0;
124125
for (IAtom atom : clone.atoms()) {
125-
if (!atom.getSymbol().equals("C")) continue;
126+
if (atom.getAtomicNumber() != IElement.C) continue;
126127
if (atom.getHybridization() == Hybridization.SP2)
127128
nsp2++;
128129
else if (atom.getHybridization() == Hybridization.SP3) nsp3++;

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