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dkatzel-ncatsdkatzel-ncats
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changed several places from atom.getSymbol().equals("a string") to "a string".equals(atom.getSymbol()) 
1 parent a592307 commit b3baaea

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14 files changed

+47
-43
lines changed

14 files changed

+47
-43
lines changed

‎base/atomtype/src/main/java/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -78,7 +78,7 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
7878
for (int j = 0; j <= attachedAtoms.size() - 1; j++) {
7979
IAtom attached = (IAtom) attachedAtoms.get(j);
8080
IBond b = atomContainer.getBond(atom, attached);
81-
if (attached.getSymbol().equals("H")) NumHAtoms++;
81+
if ("H".equals(attached.getSymbol())) NumHAtoms++;
8282

8383
if (atom.getFlag(CDKConstants.ISAROMATIC) && attached.getFlag(CDKConstants.ISAROMATIC)) {
8484

‎base/atomtype/src/main/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -142,7 +142,7 @@ private boolean isCarbonyl(IAtomContainer atomContainer, IAtom atom) {
142142
if (neighbors.size() != 1) return false;
143143
IBond neighbor = neighbors.get(0);
144144
IAtom neighborAtom = neighbor.getOther(atom);
145-
if (neighborAtom.getSymbol().equals("C")) {
145+
if ("C".equals(neighborAtom.getSymbol())) {
146146
if (neighbor.getOrder() == IBond.Order.SINGLE) {
147147
if (countAttachedBonds(atomContainer, neighborAtom, IBond.Order.DOUBLE, "O") == 1) return true;
148148
} else if (neighbor.getOrder() == IBond.Order.DOUBLE) {
@@ -171,7 +171,7 @@ private int countAttachedBonds(IAtomContainer container, IAtom atom, IBond.Order
171171
if (bond.getAtomCount() == 2 && bond.contains(atom)) {
172172
if (symbol != null) {
173173
IAtom neighbor = bond.getOther(atom);
174-
if (neighbor.getSymbol().equals(symbol)) {
174+
if (symbol.equals(neighbor.getSymbol())) {
175175
doubleBondedAtoms++;
176176
}
177177
} else {

‎base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -1025,7 +1025,7 @@ private boolean isAmide(IAtom atom, IAtomContainer atomContainer, List<IBond> co
10251025
if (connectedBonds.size() < 1) return false;
10261026
for (IBond bond : connectedBonds) {
10271027
IAtom neighbor = bond.getOther(atom);
1028-
if (neighbor.getSymbol().equals("C")) {
1028+
if ("C".equals(neighbor.getSymbol())) {
10291029
if (countAttachedDoubleBonds(atomContainer.getConnectedBondsList(neighbor), neighbor, "O") == 1) return true;
10301030
}
10311031
}
@@ -1036,7 +1036,7 @@ private boolean isThioAmide(IAtom atom, IAtomContainer atomContainer, List<IBond
10361036
if (connectedBonds.size() < 1) return false;
10371037
for (IBond bond : connectedBonds) {
10381038
IAtom neighbor = bond.getOther(atom);
1039-
if (neighbor.getSymbol().equals("C")) {
1039+
if ("C".equals(neighbor.getSymbol())) {
10401040
if (countAttachedDoubleBonds(atomContainer.getConnectedBondsList(neighbor), neighbor, "S") == 1) return true;
10411041
}
10421042
}
@@ -1047,7 +1047,7 @@ private int countExplicitHydrogens(IAtom atom, List<IBond> connectedBonds) {
10471047
int count = 0;
10481048
for (IBond bond : connectedBonds) {
10491049
IAtom aAtom = bond.getOther(atom);
1050-
if (aAtom.getSymbol().equals("H")) {
1050+
if ("H".equals(aAtom.getSymbol())) {
10511051
count++;
10521052
}
10531053
}
@@ -1063,7 +1063,7 @@ private int countExplicitHydrogens(IAtom atom, List<IBond> connectedBonds) {
10631063
private List<IBond> heavyBonds(final List<IBond> bonds) {
10641064
final List<IBond> heavy = new ArrayList<IBond>(bonds.size());
10651065
for (final IBond bond : bonds) {
1066-
if (!(bond.getBegin().getSymbol().equals("H") && bond.getEnd().getSymbol().equals("H"))) {
1066+
if (!("H".equals(bond.getBegin().getSymbol()) && "H".equals(bond.getEnd().getSymbol()))) {
10671067
heavy.add(bond);
10681068
}
10691069
}
@@ -2458,7 +2458,7 @@ private int countAttachedBonds(List<IBond> connectedBonds, IAtom atom, IBond.Ord
24582458
if (bond.getAtomCount() == 2) {
24592459
if (symbol != null) {
24602460
// if other atom is of the given element (by its symbol)
2461-
if (bond.getOther(atom).getSymbol().equals(symbol)) {
2461+
if (symbol.equals(bond.getOther(atom).getSymbol())) {
24622462
doubleBondedAtoms++;
24632463
}
24642464
} else {

‎base/dict/src/main/java/org/openscience/cdk/dict/CDKDictionaryReferences.java‎

Lines changed: 15 additions & 12 deletions
Original file line numberDiff line numberDiff line change
@@ -91,18 +91,21 @@ private static void makeReferencesExplicitForElement(IElement element) {
9191
element.setProperty(prefix + ":field:symbol", "chemical:atomSymbol");
9292
element.setProperty(prefix + ":field:atomicNumber", "chemical:atomicNumber");
9393

94-
if (element.getSymbol().equals("C")) {
95-
element.setProperty(prefix + ":self:" + selfCounter++, "element:carbon");
96-
} else if (element.getSymbol().equals("N")) {
97-
element.setProperty(prefix + ":self:" + selfCounter++, "element:nitrogen");
98-
} else if (element.getSymbol().equals("O")) {
99-
element.setProperty(prefix + ":self:" + selfCounter++, "element:oxygen");
100-
} else if (element.getSymbol().equals("H")) {
101-
element.setProperty(prefix + ":self:" + selfCounter++, "element:hydrogen");
102-
} else if (element.getSymbol().equals("S")) {
103-
element.setProperty(prefix + ":self:" + selfCounter++, "element:sulphur");
104-
} else if (element.getSymbol().equals("P")) {
105-
element.setProperty(prefix + ":self:" + selfCounter++, "element:phosphorus");
94+
String symbol = element.getSymbol();
95+
if(symbol !=null) {
96+
if (symbol.equals("C")) {
97+
element.setProperty(prefix + ":self:" + selfCounter++, "element:carbon");
98+
} else if (symbol.equals("N")) {
99+
element.setProperty(prefix + ":self:" + selfCounter++, "element:nitrogen");
100+
} else if (symbol.equals("O")) {
101+
element.setProperty(prefix + ":self:" + selfCounter++, "element:oxygen");
102+
} else if (symbol.equals("H")) {
103+
element.setProperty(prefix + ":self:" + selfCounter++, "element:hydrogen");
104+
} else if (symbol.equals("S")) {
105+
element.setProperty(prefix + ":self:" + selfCounter++, "element:sulphur");
106+
} else if (symbol.equals("P")) {
107+
element.setProperty(prefix + ":self:" + selfCounter++, "element:phosphorus");
108+
}
106109
}
107110
}
108111

‎base/standard/src/main/java/org/openscience/cdk/geometry/BondTools.java‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -217,8 +217,8 @@ private static boolean isEndOfDoubleBond(IAtomContainer container, IAtom atom, I
217217

218218
if (container.getBond(atom, parent) != null) {
219219
if (container.getBond(atom, parent).getOrder() == Order.DOUBLE
220-
&& (lengthAtom == 3 || (lengthAtom == 2 && atom.getSymbol().equals("N")))
221-
&& (lengthParent == 3 || (lengthParent == 2 && parent.getSymbol().equals("N")))) {
220+
&& (lengthAtom == 3 || (lengthAtom == 2 && "N".equals(atom.getSymbol())))
221+
&& (lengthParent == 3 || (lengthParent == 2 && "N".equals(parent.getSymbol())))) {
222222
List<IAtom> atoms = container.getConnectedAtomsList(atom);
223223
IAtom one = null;
224224
IAtom two = null;
@@ -230,9 +230,9 @@ private static boolean isEndOfDoubleBond(IAtomContainer container, IAtom atom, I
230230
}
231231
}
232232
String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
233-
if ((one != null && two == null && atom.getSymbol().equals("N") && Math.abs(giveAngleBothMethods(
233+
if ((one != null && two == null && "N".equals(atom.getSymbol()) && Math.abs(giveAngleBothMethods(
234234
parent, atom, one, true)) > Math.PI / 10)
235-
|| (!atom.getSymbol().equals("N") && one != null && two != null && !morgannumbers[container
235+
|| (!"N".equals(atom.getSymbol()) && one != null && two != null && !morgannumbers[container
236236
.indexOf(one)].equals(morgannumbers[container.indexOf(two)]))) {
237237
return (true);
238238
} else {
@@ -264,7 +264,7 @@ private static boolean isStartOfDoubleBond(IAtomContainer container, IAtom a, IA
264264

265265
int lengthAtom = container.getConnectedAtomsList(a).size() + hcount;
266266

267-
if (lengthAtom != 3 && (lengthAtom != 2 && !(a.getSymbol().equals("N")))) {
267+
if (lengthAtom != 3 && (lengthAtom != 2 && !"N".equals(a.getSymbol()))) {
268268
return (false);
269269
}
270270
List<IAtom> atoms = container.getConnectedAtomsList(a);
@@ -286,11 +286,11 @@ && isEndOfDoubleBond(container, atom, a, doubleBondConfiguration)) {
286286
}
287287
String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
288288
if (one != null
289-
&& ((!a.getSymbol().equals("N")
289+
&& ((!"N".equals(a.getSymbol())
290290
&& two != null
291291
&& !morgannumbers[container.indexOf(one)].equals(morgannumbers[container
292292
.indexOf(two)]) && doubleBond && doubleBondConfiguration[container.indexOf(container.getBond(
293-
a, nextAtom))]) || (doubleBond && a.getSymbol().equals("N") && Math.abs(giveAngleBothMethods(
293+
a, nextAtom))]) || (doubleBond && "N".equals(a.getSymbol()) && Math.abs(giveAngleBothMethods(
294294
nextAtom, a, parent, true)) > Math.PI / 10))) {
295295
return (true);
296296
} else {
@@ -559,7 +559,7 @@ public static void makeUpDownBonds(IAtomContainer container) {
559559
up++;
560560
} else if (stereo == IBond.Stereo.DOWN) {
561561
down++;
562-
} else if (stereo == IBond.Stereo.NONE && conAtom.getSymbol().equals("H")) {
562+
} else if (stereo == IBond.Stereo.NONE && "H".equals(conAtom.getSymbol())) {
563563
h = conAtom;
564564
hs++;
565565
} else {

‎base/standard/src/main/java/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -618,7 +618,7 @@ public static void convertImplicitToExplicitHydrogens(IAtomContainer atomContain
618618
Map<IAtom, IAtom> hNeighbor = Maps.newHashMapWithExpectedSize(atomContainer.getAtomCount());
619619

620620
for (IAtom atom : atomContainer.atoms()) {
621-
if (!atom.getSymbol().equals("H")) {
621+
if (!"H".equals(atom.getSymbol())) {
622622
Integer hCount = atom.getImplicitHydrogenCount();
623623
if (hCount != null) {
624624
for (int i = 0; i < hCount; i++) {
@@ -748,7 +748,7 @@ public static IAtomContainer removeNonChiralHydrogens(IAtomContainer org) {
748748
if (bondStereo != null && bondStereo != IBond.Stereo.NONE) addToRemove = false;
749749
IAtom neighboursNeighbour = bond.getOther(neighbour);
750750
// remove in any case if the hetero atom is connected to more than one hydrogen
751-
if (neighboursNeighbour.getSymbol().equals("H") && !neighboursNeighbour.equals(atom)) {
751+
if ("H".equals(neighboursNeighbour.getSymbol()) && !neighboursNeighbour.equals(atom)) {
752752
addToRemove = true;
753753
break;
754754
}
@@ -1183,7 +1183,7 @@ private static boolean suppressibleHydrogen(final IAtomContainer container, fina
11831183
if (atom.getImplicitHydrogenCount() != null && atom.getImplicitHydrogenCount() != 0) return false;
11841184
// molecule hydrogen
11851185
List<IAtom> neighbors = container.getConnectedAtomsList(atom);
1186-
if (neighbors.size() == 1 && (neighbors.get(0).getSymbol().equals("H") ||
1186+
if (neighbors.size() == 1 && ("H".equals(neighbors.get(0).getSymbol()) ||
11871187
neighbors.get(0) instanceof IPseudoAtom)) return false;
11881188
// what about bridging hydrogens?
11891189
// hydrogens with atom-atom mapping?
@@ -1595,7 +1595,7 @@ public static IBond.Order getMaximumBondOrder(IAtomContainer container) {
15951595
public static List<IAtom> getHeavyAtoms(IAtomContainer container) {
15961596
List<IAtom> newAc = new ArrayList<IAtom>();
15971597
for (int f = 0; f < container.getAtomCount(); f++) {
1598-
if (!container.getAtom(f).getSymbol().equals("H")) {
1598+
if (!"H".equals(container.getAtom(f).getSymbol())) {
15991599
newAc.add(container.getAtom(f));
16001600
}
16011601
}

‎base/test-core/src/test/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTestFileReposTest.java‎

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -38,6 +38,7 @@
3838

3939
import java.io.InputStream;
4040
import java.util.List;
41+
import java.util.Objects;
4142

4243
/**
4344
* This class tests the matching of atom types defined in the
@@ -172,7 +173,7 @@ private TestResults testFile(String dir, String filename, ISimpleChemObjectReade
172173
} else
173174
// OK, the matcher did find something. Now, let's see of the
174175
// atom type properties are consistent with those of the atom
175-
if (!atom.getSymbol().equals(matched.getSymbol())) {
176+
if (!Objects.equals(atom.getSymbol(),matched.getSymbol())) {
176177
// OK, OK, that's very basic indeed, but why not
177178
results.failed++;
178179
System.out.println("Symbol does not match: " + results.tested + " in file " + filename);

‎base/valencycheck/src/main/java/org/openscience/cdk/tools/SaturationChecker.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -273,9 +273,9 @@ public void newSaturate(IAtomContainer atomContainer) throws CDKException {
273273
boolean succeeded = newSaturate(bonds, atomContainer);
274274
for (int i = 0; i < bonds.length; i++) {
275275
if (bonds[i].getOrder() == IBond.Order.DOUBLE && bonds[i].getFlag(CDKConstants.ISAROMATIC)
276-
&& (bonds[i].getBegin().getSymbol().equals("N") && bonds[i].getEnd().getSymbol().equals("N"))) {
276+
&& ("N".equals(bonds[i].getBegin().getSymbol()) && "N".equals(bonds[i].getEnd().getSymbol()))) {
277277
int atomtohandle = 0;
278-
if (bonds[i].getBegin().getSymbol().equals("N")) atomtohandle = 1;
278+
if ("N".equals(bonds[i].getBegin().getSymbol())) atomtohandle = 1;
279279
List<IBond> bondstohandle = atomContainer.getConnectedBondsList(bonds[i].getAtom(atomtohandle));
280280
for (int k = 0; k < bondstohandle.size(); k++) {
281281
IBond bond = bondstohandle.get(k);
@@ -611,7 +611,7 @@ public int calculateNumberOfImplicitHydrogens(IAtom atom, double bondOrderSum, d
611611
int missingHydrogen = 0;
612612
if (atom instanceof IPseudoAtom) {
613613
// don't figure it out... it simply does not lack H's
614-
} else if (atom.getAtomicNumber() != null && atom.getAtomicNumber() == 1 || atom.getSymbol().equals("H")) {
614+
} else if (atom.getAtomicNumber() != null && atom.getAtomicNumber() == 1 || "H".equals(atom.getSymbol())) {
615615
missingHydrogen = (int) (1 - bondOrderSum - singleElectronSum - atom.getFormalCharge());
616616
} else {
617617
logger.info("Calculating number of missing hydrogen atoms");

‎misc/extra/src/main/java/org/openscience/cdk/tools/AtomTypeTools.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -229,7 +229,7 @@ else if (smile.equals(BENZENE_SMI))
229229

230230
int ncount = 0;
231231
for (int i = 0; i < ring.getAtomCount(); i++) {
232-
if (ring.getAtom(i).getSymbol().equals("N")) {
232+
if ("N".equals(ring.getAtom(i).getSymbol())) {
233233
ncount = ncount + 1;
234234
}
235235
}

‎storage/ctab/src/main/java/org/openscience/cdk/io/MDLV2000Writer.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -473,7 +473,7 @@ public void writeMolecule(IAtomContainer container) throws Exception {
473473

474474
// firstly check if it's a numbered R group
475475
Matcher matcher = NUMERED_R_GROUP.matcher(label);
476-
if (pseudoAtom.getSymbol().equals("R") && !label.isEmpty() && matcher.matches()) {
476+
if ("R".equals(pseudoAtom.getSymbol()) && !label.isEmpty() && matcher.matches()) {
477477

478478
line.append("R# ");
479479
if (rgroups == null) {

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