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xperrylinnxperrylinn
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applied find and replace regex patterns from pervious patch to rest of qsarmolecular module. All test pass except in XLogDescriptor -- getAtmoicNumber is null
1 parent 142caf1 commit bf386e2

12 files changed

+69
-57
lines changed

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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -25,6 +25,7 @@
2525
import org.openscience.cdk.exception.CDKException;
2626
import org.openscience.cdk.graph.PathTools;
2727
import org.openscience.cdk.graph.matrix.AdjacencyMatrix;
28+
import org.openscience.cdk.interfaces.IElement;
2829
import org.openscience.cdk.interfaces.IAtom;
2930
import org.openscience.cdk.interfaces.IAtomContainer;
3031
import org.openscience.cdk.interfaces.IAtomType;
@@ -123,9 +124,9 @@ public DescriptorValue calculate(IAtomContainer container) {
123124

124125
for (int k = 0; k < 5; k++) {
125126
for (int i = 0; i < natom; i++) {
126-
if (molecule.getAtom(i).getSymbol().equals("H")) continue;
127+
if (molecule.getAtom(i).getAtomicNumber() == IElement.H) continue;
127128
for (int j = 0; j < natom; j++) {
128-
if (molecule.getAtom(j).getSymbol().equals("H")) continue;
129+
if (molecule.getAtom(j).getAtomicNumber() == IElement.H) continue;
129130
if (distancematrix[i][j] == k) {
130131
polarizabilitySum[k] += w[i] * w[j];
131132
} else

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

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,7 @@
2727
import org.openscience.cdk.graph.PathTools;
2828
import org.openscience.cdk.graph.matrix.AdjacencyMatrix;
2929
import org.openscience.cdk.interfaces.IAtomContainer;
30+
import org.openscience.cdk.interfaces.IElement;
3031
import org.openscience.cdk.interfaces.IBond;
3132
import org.openscience.cdk.interfaces.IBond.Order;
3233
import org.openscience.cdk.qsar.AbstractMolecularDescriptor;
@@ -344,7 +345,7 @@ public DescriptorValue calculate(IAtomContainer container) {
344345
// find number of heavy atoms
345346
int nheavy = 0;
346347
for (int i = 0; i < molecule.getAtomCount(); i++) {
347-
if (!molecule.getAtom(i).getSymbol().equals("H")) nheavy++;
348+
if (molecule.getAtom(i).getAtomicNumber() != IElement.H) nheavy++;
348349
}
349350

350351
if (nheavy == 0) return getDummyDescriptorValue(new CDKException("No heavy atoms in the molecule"));
@@ -355,7 +356,7 @@ public DescriptorValue calculate(IAtomContainer container) {
355356
counter = 0;
356357
try {
357358
for (int i = 0; i < molecule.getAtomCount(); i++) {
358-
if (molecule.getAtom(i).getSymbol().equals("H")) continue;
359+
if (molecule.getAtom(i).getAtomicNumber() == IElement.H) continue;
359360
diagvalue[counter] = Isotopes.getInstance().getMajorIsotope(molecule.getAtom(i).getSymbol())
360361
.getExactMass();
361362
counter++;
@@ -392,7 +393,7 @@ public DescriptorValue calculate(IAtomContainer container) {
392393
}
393394
counter = 0;
394395
for (int i = 0; i < molecule.getAtomCount(); i++) {
395-
if (molecule.getAtom(i).getSymbol().equals("H")) continue;
396+
if (molecule.getAtom(i).getAtomicNumber() == IElement.H) continue;
396397
diagvalue[counter] = molecule.getAtom(i).getCharge();
397398
counter++;
398399
}
@@ -409,7 +410,7 @@ public DescriptorValue calculate(IAtomContainer container) {
409410
Polarizability pol = new Polarizability();
410411
counter = 0;
411412
for (int i = 0; i < molecule.getAtomCount(); i++) {
412-
if (molecule.getAtom(i).getSymbol().equals("H")) continue;
413+
if (molecule.getAtom(i).getAtomicNumber() == IElement.H) continue;
413414
diagvalue[counter] = pol.calculateGHEffectiveAtomPolarizability(molecule, molecule.getAtom(i), false,
414415
topoDistance);
415416
counter++;

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -20,6 +20,7 @@
2020

2121
import org.openscience.cdk.exception.CDKException;
2222
import org.openscience.cdk.interfaces.IAtomContainer;
23+
import org.openscience.cdk.interfaces.IElement;
2324
import org.openscience.cdk.interfaces.IBond;
2425
import org.openscience.cdk.interfaces.IBond.Order;
2526
import org.openscience.cdk.qsar.AbstractMolecularDescriptor;
@@ -140,7 +141,7 @@ public DescriptorValue calculate(IAtomContainer container) {
140141
for (IBond bond : container.bonds()) {
141142
boolean hasHydrogen = false;
142143
for (int i = 0; i < bond.getAtomCount(); i++) {
143-
if (bond.getAtom(i).getSymbol().equals("H")) {
144+
if (bond.getAtom(i).getAtomicNumber() == IElement.H) {
144145
hasHydrogen = true;
145146
break;
146147
}

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

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,7 @@
2727
import org.openscience.cdk.config.Isotopes;
2828
import org.openscience.cdk.config.IsotopeFactory;
2929
import org.openscience.cdk.exception.CDKException;
30+
import org.openscience.cdk.interfaces.IElement;
3031
import org.openscience.cdk.interfaces.IAtom;
3132
import org.openscience.cdk.interfaces.IAtomContainer;
3233
import org.openscience.cdk.interfaces.IBond;
@@ -194,18 +195,18 @@ private static int getValenceElectronCount(IAtom atom) {
194195
* environments, -1 otherwise
195196
*/
196197
protected static double deltavSulphur(IAtom atom, IAtomContainer atomContainer) {
197-
if (!atom.getSymbol().equals("S")) return -1;
198+
if (atom.getAtomicNumber() != IElement.S) return -1;
198199

199200
// check whether it's a S in S-S
200201
List<IAtom> connected = atomContainer.getConnectedAtomsList(atom);
201202
for (IAtom connectedAtom : connected) {
202-
if (connectedAtom.getSymbol().equals("S")
203+
if (connectedAtom.getAtomicNumber() == IElement.S
203204
&& atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.SINGLE) return .89;
204205
}
205206

206207
int count = 0;
207208
for (IAtom connectedAtom : connected) {
208-
if (connectedAtom.getSymbol().equals("O")
209+
if (connectedAtom.getAtomicNumber() == IElement.O
209210
&& atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.DOUBLE) count++;
210211
}
211212
if (count == 1)
@@ -226,15 +227,15 @@ protected static double deltavSulphur(IAtom atom, IAtomContainer atomContainer)
226227
* -1 otherwise
227228
*/
228229
private static double deltavPhosphorous(IAtom atom, IAtomContainer atomContainer) {
229-
if (!atom.getSymbol().equals("P")) return -1;
230+
if (atom.getAtomicNumber() != IElement.P) return -1;
230231

231232
List<IAtom> connected = atomContainer.getConnectedAtomsList(atom);
232233
int conditions = 0;
233234

234235
if (connected.size() == 4) conditions++;
235236

236237
for (IAtom connectedAtom : connected) {
237-
if (connectedAtom.getSymbol().equals("O")
238+
if (connectedAtom.getAtomicNumber() == IElement.O
238239
&& atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.DOUBLE) conditions++;
239240
if (atomContainer.getBond(atom, connectedAtom).getOrder() == IBond.Order.SINGLE) conditions++;
240241
}

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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,6 +24,7 @@
2424
import org.openscience.cdk.qsar.DescriptorSpecification;
2525
import org.openscience.cdk.qsar.DescriptorValue;
2626
import org.openscience.cdk.qsar.IMolecularDescriptor;
27+
import org.openscience.cdk.interfaces.IElement;
2728
import org.openscience.cdk.qsar.result.DoubleResult;
2829
import org.openscience.cdk.qsar.result.IDescriptorResult;
2930
import org.openscience.cdk.tools.manipulator.AtomContainerManipulator;
@@ -120,10 +121,10 @@ public DescriptorValue calculate(IAtomContainer container) {
120121
int a = 0;
121122
double h = 0;
122123
for (int i = 0; i < container.getAtomCount(); i++) {
123-
if (!container.getAtom(i).getSymbol().equals("H")) {
124+
if (container.getAtom(i).getAtomicNumber() != IElement.H) {
124125
a++;
125126
}
126-
if (!container.getAtom(i).getSymbol().equals("H") && !container.getAtom(i).getSymbol().equals("C")) {
127+
if (container.getAtom(i).getAtomicNumber() != IElement.H && container.getAtom(i).getAtomicNumber() != IElement.C) {
127128
h++;
128129
}
129130
}

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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -27,6 +27,7 @@
2727
import org.openscience.cdk.exception.CDKException;
2828
import org.openscience.cdk.geometry.GeometryUtil;
2929
import org.openscience.cdk.interfaces.IAtomContainer;
30+
import org.openscience.cdk.interfaces.IElement;
3031
import org.openscience.cdk.interfaces.IBond;
3132
import org.openscience.cdk.qsar.AbstractMolecularDescriptor;
3233
import org.openscience.cdk.qsar.DescriptorSpecification;
@@ -220,7 +221,7 @@ public DescriptorValue calculate(IAtomContainer container) {
220221
return getDummyDescriptorValue(new CDKException("GravitationalIndex: Only handles 2 center bonds"));
221222
}
222223

223-
if (b.getBegin().getSymbol().equals("H") || b.getEnd().getSymbol().equals("H")) continue;
224+
if (b.getBegin().getAtomicNumber() == IElement.H || b.getEnd().getAtomicNumber() == IElement.H) continue;
224225

225226
mass1 = factory.getMajorIsotope(b.getBegin().getSymbol()).getMassNumber();
226227
mass2 = factory.getMajorIsotope(b.getEnd().getSymbol()).getMassNumber();
@@ -242,7 +243,7 @@ public DescriptorValue calculate(IAtomContainer container) {
242243
// all pairs
243244
ArrayList<Integer> x = new ArrayList<Integer>();
244245
for (int i = 0; i < container.getAtomCount(); i++) {
245-
if (!container.getAtom(i).getSymbol().equals("H")) x.add(i);
246+
if (container.getAtom(i).getAtomicNumber() != IElement.H) x.add(i);
246247
}
247248
int npair = x.size() * (x.size() - 1) / 2;
248249
pair[] p = new pair[npair];

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

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121

2222
import org.openscience.cdk.aromaticity.Aromaticity;
2323
import org.openscience.cdk.exception.CDKException;
24+
import org.openscience.cdk.interfaces.IElement;
2425
import org.openscience.cdk.interfaces.IAtom;
2526
import org.openscience.cdk.interfaces.IAtomContainer;
2627
import org.openscience.cdk.interfaces.IBond;
@@ -281,7 +282,7 @@ protected int getHydrogenSpecial(IAtom atom) {
281282
if (bondCount > 0) {
282283
IAtom neighbour = atom.bonds().iterator().next().getOther(atom);
283284
int numNeighbours = neighbour.getBondCount();
284-
if (neighbour.getSymbol().equals("C")) {
285+
if (neighbour.getAtomicNumber() == IElement.C) {
285286
if (carbonylConjugated(neighbour))
286287
toadd = 51;
287288
else {

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

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121
import org.openscience.cdk.CDKConstants;
2222
import org.openscience.cdk.aromaticity.Aromaticity;
2323
import org.openscience.cdk.exception.CDKException;
24+
import org.openscience.cdk.interfaces.IElement;
2425
import org.openscience.cdk.interfaces.IAtom;
2526
import org.openscience.cdk.interfaces.IAtomContainer;
2627
import org.openscience.cdk.interfaces.IBond;
@@ -178,7 +179,7 @@ public DescriptorValue calculate(IAtomContainer container) {
178179
if ((container.getMaximumBondOrder(container.getAtom(i)) != IBond.Order.SINGLE
179180
|| Math.abs(container.getAtom(i).getFormalCharge()) >= 1
180181
|| container.getAtom(i).getFlag(CDKConstants.ISAROMATIC)
181-
|| container.getAtom(i).getSymbol().equals("N") || container.getAtom(i).getSymbol().equals("O"))
182+
|| container.getAtom(i).getAtomicNumber() == IElement.N || container.getAtom(i).getAtomicNumber() == IElement.O)
182183
&& !container.getAtom(i).getFlag(CDKConstants.VISITED)) {
183184
//logger.debug("...... -> Accepted");
184185
startSphere = new ArrayList<IAtom>();
@@ -245,7 +246,7 @@ private void breadthFirstSearch(IAtomContainer container, List<IAtom> sphere, Li
245246
nextAtom = ((IBond) bond).getOther(atom);
246247
if ((container.getMaximumBondOrder(nextAtom) != IBond.Order.SINGLE
247248
|| Math.abs(nextAtom.getFormalCharge()) >= 1 || nextAtom.getFlag(CDKConstants.ISAROMATIC)
248-
|| nextAtom.getSymbol().equals("N") || nextAtom.getSymbol().equals("O"))
249+
|| nextAtom.getAtomicNumber() == IElement.N || nextAtom.getAtomicNumber() == IElement.O)
249250
& !nextAtom.getFlag(CDKConstants.VISITED)) {
250251
//logger.debug("BDS> AtomNr:"+container.indexOf(nextAtom)+" maxBondOrder:"+container.getMaximumBondOrder(nextAtom)+" Aromatic:"+nextAtom.getFlag(CDKConstants.ISAROMATIC)+" FormalCharge:"+nextAtom.getFormalCharge()+" Charge:"+nextAtom.getCharge()+" Flag:"+nextAtom.getFlag(CDKConstants.VISITED));
251252
path.add(nextAtom);

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

Lines changed: 5 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
2222
import org.openscience.cdk.exception.CDKException;
2323
import org.openscience.cdk.exception.NoSuchAtomException;
2424
import org.openscience.cdk.graph.SpanningTree;
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.IBond;
@@ -159,7 +160,7 @@ public DescriptorValue calculate(IAtomContainer ac) {
159160
for (IBond bond : ac.bonds()) {
160161
IAtom atom0 = bond.getBegin();
161162
IAtom atom1 = bond.getEnd();
162-
if (atom0.getSymbol().equals("H") || atom1.getSymbol().equals("H")) continue;
163+
if (atom0.getAtomicNumber() == IElement.H || atom1.getAtomicNumber() == IElement.H) continue;
163164
if (bond.getOrder() == Order.SINGLE) {
164165
if ((BondManipulator.isLowerOrder(ac.getMaximumBondOrder(atom0), IBond.Order.TRIPLE))
165166
&& (BondManipulator.isLowerOrder(ac.getMaximumBondOrder(atom1), IBond.Order.TRIPLE))) {
@@ -202,9 +203,9 @@ public DescriptorValue calculate(IAtomContainer ac) {
202203
*/
203204
private boolean isAmide(IAtom atom0, IAtom atom1, IAtomContainer ac) {
204205

205-
if (atom0.getSymbol().equals("C") && atom1.getSymbol().equals("N")) {
206+
if (atom0.getAtomicNumber() == IElement.C && atom1.getAtomicNumber() == IElement.N) {
206207
for (IAtom neighbor : ac.getConnectedAtomsList(atom0)) {
207-
if (neighbor.getSymbol().equals("O")
208+
if (neighbor.getAtomicNumber() == IElement.O
208209
&& ac.getBond(atom0, neighbor).getOrder() == Order.DOUBLE) {
209210
return true;
210211
}
@@ -217,7 +218,7 @@ private int getConnectedHCount(IAtomContainer atomContainer, IAtom atom) {
217218
List<IAtom> connectedAtoms = atomContainer.getConnectedAtomsList(atom);
218219
int n = 0;
219220
for (IAtom anAtom : connectedAtoms)
220-
if (anAtom.getSymbol().equals("H")) n++;
221+
if (anAtom.getAtomicNumber() == IElement.H) n++;
221222
return n;
222223
}
223224

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

Lines changed: 4 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -21,6 +21,7 @@
2121
import org.openscience.cdk.CDKConstants;
2222
import org.openscience.cdk.aromaticity.Aromaticity;
2323
import org.openscience.cdk.exception.CDKException;
24+
import org.openscience.cdk.interfaces.IElement;
2425
import org.openscience.cdk.interfaces.IAtom;
2526
import org.openscience.cdk.interfaces.IAtomContainer;
2627
import org.openscience.cdk.interfaces.IBond;
@@ -244,8 +245,8 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
244245

245246
// iterate over all atoms of ac
246247
for (IAtom atom : ac.atoms()) {
247-
if (atom.getSymbol().equals("N") || atom.getSymbol().equals("O") || atom.getSymbol().equals("S")
248-
|| atom.getSymbol().equals("P")) {
248+
if (atom.getAtomicNumber() == IElement.N || atom.getAtomicNumber() == IElement.O || atom.getAtomicNumber() == IElement.S
249+
|| atom.getAtomicNumber() == IElement.P) {
249250
int singleBondCount = 0;
250251
int doubleBondCount = 0;
251252
int tripleBondCount = 0;
@@ -272,7 +273,7 @@ else if (connectedBond.getOrder() == Order.DOUBLE)
272273

273274
// EXPLICIT hydrogens: count the number of hydrogen atoms
274275
for (int neighbourIndex = 0; neighbourIndex < numberOfNeighbours; neighbourIndex++)
275-
if (((IAtom) connectedAtoms.get(neighbourIndex)).getSymbol().equals("H")) hCount++;
276+
if (((IAtom) connectedAtoms.get(neighbourIndex)).getAtomicNumber() == IElement.H) hCount++;
276277
// IMPLICIT hydrogens: count the number of hydrogen atoms and adjust other atom profile properties
277278
Integer implicitHAtoms = atom.getImplicitHydrogenCount();
278279
if (implicitHAtoms == CDKConstants.UNSET) {

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