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Class cleanup
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@johnmay
johnmay committed Jan 10, 2019
1 parent dfd6f28 commit b407027
Showing 1 changed file with 73 additions and 64 deletions.
137 changes: 73 additions & 64 deletions tool/charges/src/main/java/org/openscience/cdk/charges/Polarizability.java
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Original file line number Diff line number Diff line change
Expand Up @@ -60,9 +60,7 @@ public Polarizability() {}
private void addExplicitHydrogens(IAtomContainer container) {
try {
CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher.getInstance(container.getBuilder());
Iterator<IAtom> atoms = container.atoms().iterator();
while (atoms.hasNext()) {
IAtom atom = atoms.next();
for (IAtom atom : container.atoms()) {
IAtomType type = matcher.findMatchingAtomType(container, atom);
AtomTypeManipulator.configure(atom, type);
}
Expand Down Expand Up @@ -125,7 +123,7 @@ public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContaine
acH = atomContainer;
}

List<IAtom> startAtom = new ArrayList<IAtom>(1);
List<IAtom> startAtom = new ArrayList<>(1);
startAtom.add(0, atom);
double bond;

Expand Down Expand Up @@ -167,7 +165,7 @@ public double calculateGHEffectiveAtomPolarizability(IAtomContainer atomContaine
acH = atomContainer;
}

List<IAtom> startAtom = new ArrayList<IAtom>(1);
List<IAtom> startAtom = new ArrayList<>(1);
startAtom.add(0, atom);
double bond;

Expand Down Expand Up @@ -215,70 +213,81 @@ private double getKJPolarizabilityFactor(IAtomContainer atomContainer, IAtom ato
double polarizabilitiyFactor = 0;
String AtomSymbol;
AtomSymbol = atom.getSymbol();
if (AtomSymbol.equals("H")) {
polarizabilitiyFactor = 0.387;
} else if (AtomSymbol.equals("C")) {
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
polarizabilitiyFactor = 1.230;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 1.064;/* 1.064 */
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
polarizabilitiyFactor = 1.382;
switch (AtomSymbol) {
case "H":
polarizabilitiyFactor = 0.387;
break;
case "C":
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
polarizabilitiyFactor = 1.230;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 1.064;/* 1.064 */
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
polarizabilitiyFactor = 1.382;
} else {
polarizabilitiyFactor = 1.37;
}
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.TRIPLE
|| atomContainer.getMaximumBondOrder(atom) == IBond.Order.QUADRUPLE) {
polarizabilitiyFactor = 1.279;
}
break;
case "N":
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() < 0) {
polarizabilitiyFactor = 1.090;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 1.094;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
polarizabilitiyFactor = 1.030;
} else {
polarizabilitiyFactor = 1.37;
polarizabilitiyFactor = 0.852;
}
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.TRIPLE
|| atomContainer.getMaximumBondOrder(atom) == IBond.Order.QUADRUPLE) {
polarizabilitiyFactor = 1.279;
}
} else if (AtomSymbol.equals("N")) {
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() < 0) {
polarizabilitiyFactor = 1.090;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 1.094;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
polarizabilitiyFactor = 1.030;
} else {
polarizabilitiyFactor = 0.852;
}
} else if (AtomSymbol.equals("O")) {
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == -1) {
polarizabilitiyFactor = 1.791;
} else if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == 1) {
polarizabilitiyFactor = 0.422;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 0.664;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
polarizabilitiyFactor = 0.460;
}
} else if (AtomSymbol.equals("P")) {
if (atomContainer.getConnectedBondsCount(atom) == 4
break;
case "O":
if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == -1) {
polarizabilitiyFactor = 1.791;
} else if (atom.getCharge() != CDKConstants.UNSET && atom.getCharge() == 1) {
polarizabilitiyFactor = 0.422;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 0.664;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
polarizabilitiyFactor = 0.460;
}
break;
case "P":
if (atomContainer.getConnectedBondsCount(atom) == 4
&& atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
polarizabilitiyFactor = 0;
}
} else if (AtomSymbol.equals("S")) {
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
polarizabilitiyFactor = 3.38;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 3.20;/* 3.19 */
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
polarizabilitiyFactor = 3.51;
polarizabilitiyFactor = 0;
}
break;
case "S":
if (atom.getFlag(CDKConstants.ISAROMATIC)) {
polarizabilitiyFactor = 3.38;
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.SINGLE) {
polarizabilitiyFactor = 3.20;/* 3.19 */
} else if (atomContainer.getMaximumBondOrder(atom) == IBond.Order.DOUBLE) {
if (getNumberOfHydrogen(atomContainer, atom) == 0) {
polarizabilitiyFactor = 3.51;
} else {
polarizabilitiyFactor = 3.50;
}
} else {
polarizabilitiyFactor = 3.50;
polarizabilitiyFactor = 3.42;
}
} else {
polarizabilitiyFactor = 3.42;
}
} else if (AtomSymbol.equals("F")) {
polarizabilitiyFactor = 0.296;
} else if (AtomSymbol.equals("Cl")) {
polarizabilitiyFactor = 2.343;
} else if (AtomSymbol.equals("Br")) {
polarizabilitiyFactor = 3.5;
} else if (AtomSymbol.equals("I")) {
polarizabilitiyFactor = 5.79;
break;
case "F":
polarizabilitiyFactor = 0.296;
break;
case "Cl":
polarizabilitiyFactor = 2.343;
break;
case "Br":
polarizabilitiyFactor = 3.5;
break;
case "I":
polarizabilitiyFactor = 5.79;
break;
}
return polarizabilitiyFactor;
}
Expand Down

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