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Commit b407027

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johnmayjohnmay
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Class cleanup
1 parent dfd6f28 commit b407027

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+73
-64
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1 file changed

+73
-64
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‎tool/charges/src/main/java/org/openscience/cdk/charges/Polarizability.java‎

Lines changed: 73 additions & 64 deletions
Original file line numberDiff line numberDiff line change
@@ -60,9 +60,7 @@ public Polarizability() {}
6060
private void addExplicitHydrogens(IAtomContainer container) {
6161
try {
6262
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(container.getBuilder());
63-
Iterator<IAtom> atoms = container.atoms().iterator();
64-
while (atoms.hasNext()) {
65-
IAtom atom = atoms.next();
63+
for (IAtom atom : container.atoms()) {
6664
IAtomType type = matcher.findMatchingAtomType(container, atom);
6765
AtomTypeManipulator.configure(atom, type);
6866
}
@@ -125,7 +123,7 @@ public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContaine
125123
acH = atomContainer;
126124
}
127125

128-
List<IAtom> startAtom = new ArrayList<IAtom>(1);
126+
List<IAtom> startAtom = new ArrayList<>(1);
129127
startAtom.add(0, atom);
130128
double bond;
131129

@@ -167,7 +165,7 @@ public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContaine
167165
acH = atomContainer;
168166
}
169167

170-
List<IAtom> startAtom = new ArrayList<IAtom>(1);
168+
List<IAtom> startAtom = new ArrayList<>(1);
171169
startAtom.add(0, atom);
172170
double bond;
173171

@@ -215,70 +213,81 @@ private double getKJPolarizabilityFactor(IAtomContainer atomContainer, IAtom ato
215213
double polarizabilitiyFactor = 0;
216214
String AtomSymbol;
217215
AtomSymbol = atom.getSymbol();
218-
if (AtomSymbol.equals("H")) {
219-
polarizabilitiyFactor = 0.387;
220-
} else if (AtomSymbol.equals("C")) {
221-
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
222-
polarizabilitiyFactor = 1.230;
223-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
224-
polarizabilitiyFactor = 1.064;/* 1.064 */
225-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
226-
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
227-
polarizabilitiyFactor = 1.382;
216+
switch (AtomSymbol) {
217+
case "H":
218+
polarizabilitiyFactor = 0.387;
219+
break;
220+
case "C":
221+
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
222+
polarizabilitiyFactor = 1.230;
223+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
224+
polarizabilitiyFactor = 1.064;/* 1.064 */
225+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
226+
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
227+
polarizabilitiyFactor = 1.382;
228+
} else {
229+
polarizabilitiyFactor = 1.37;
230+
}
231+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.TRIPLE
232+
|| atomContainer.getMaximumBondOrder(atom) == IBond.Order.QUADRUPLE) {
233+
polarizabilitiyFactor = 1.279;
234+
}
235+
break;
236+
case "N":
237+
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() < 0) {
238+
polarizabilitiyFactor = 1.090;
239+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
240+
polarizabilitiyFactor = 1.094;
241+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
242+
polarizabilitiyFactor = 1.030;
228243
} else {
229-
polarizabilitiyFactor = 1.37;
244+
polarizabilitiyFactor = 0.852;
230245
}
231-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.TRIPLE
232-
|| atomContainer.getMaximumBondOrder(atom) == IBond.Order.QUADRUPLE) {
233-
polarizabilitiyFactor = 1.279;
234-
}
235-
} else if (AtomSymbol.equals("N")) {
236-
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() < 0) {
237-
polarizabilitiyFactor = 1.090;
238-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
239-
polarizabilitiyFactor = 1.094;
240-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
241-
polarizabilitiyFactor = 1.030;
242-
} else {
243-
polarizabilitiyFactor = 0.852;
244-
}
245-
} else if (AtomSymbol.equals("O")) {
246-
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == -1) {
247-
polarizabilitiyFactor = 1.791;
248-
} else if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == 1) {
249-
polarizabilitiyFactor = 0.422;
250-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
251-
polarizabilitiyFactor = 0.664;
252-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
253-
polarizabilitiyFactor = 0.460;
254-
}
255-
} else if (AtomSymbol.equals("P")) {
256-
if (atomContainer.getConnectedBondsCount(atom) == 4
246+
break;
247+
case "O":
248+
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == -1) {
249+
polarizabilitiyFactor = 1.791;
250+
} else if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == 1) {
251+
polarizabilitiyFactor = 0.422;
252+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
253+
polarizabilitiyFactor = 0.664;
254+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
255+
polarizabilitiyFactor = 0.460;
256+
}
257+
break;
258+
case "P":
259+
if (atomContainer.getConnectedBondsCount(atom) == 4
257260
&& atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
258-
polarizabilitiyFactor = 0;
259-
}
260-
} else if (AtomSymbol.equals("S")) {
261-
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
262-
polarizabilitiyFactor = 3.38;
263-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
264-
polarizabilitiyFactor = 3.20;/* 3.19 */
265-
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
266-
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
267-
polarizabilitiyFactor = 3.51;
261+
polarizabilitiyFactor = 0;
262+
}
263+
break;
264+
case "S":
265+
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
266+
polarizabilitiyFactor = 3.38;
267+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
268+
polarizabilitiyFactor = 3.20;/* 3.19 */
269+
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
270+
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
271+
polarizabilitiyFactor = 3.51;
272+
} else {
273+
polarizabilitiyFactor = 3.50;
274+
}
268275
} else {
269-
polarizabilitiyFactor = 3.50;
276+
polarizabilitiyFactor = 3.42;
270277
}
271-
} else {
272-
polarizabilitiyFactor = 3.42;
273-
}
274-
} else if (AtomSymbol.equals("F")) {
275-
polarizabilitiyFactor = 0.296;
276-
} else if (AtomSymbol.equals("Cl")) {
277-
polarizabilitiyFactor = 2.343;
278-
} else if (AtomSymbol.equals("Br")) {
279-
polarizabilitiyFactor = 3.5;
280-
} else if (AtomSymbol.equals("I")) {
281-
polarizabilitiyFactor = 5.79;
278+
break;
279+
case "F":
280+
polarizabilitiyFactor = 0.296;
281+
break;
282+
case "Cl":
283+
polarizabilitiyFactor = 2.343;
284+
break;
285+
case "Br":
286+
polarizabilitiyFactor = 3.5;
287+
break;
288+
case "I":
289+
polarizabilitiyFactor = 5.79;
290+
break;
282291
}
283292
return polarizabilitiyFactor;
284293
}

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