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Replaced IBond.Order.ordinal() usages with IBond.Order.numeric()
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@johnmay @egonw
johnmay authored and egonw committed Nov 12, 2012
1 parent 8c34bfe commit 427fac6
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Showing 25 changed files with 142 additions and 192 deletions.
23 changes: 9 additions & 14 deletions src/main/org/openscience/cdk/AtomContainer.java
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Expand Up @@ -927,18 +927,13 @@ public double getBondOrderSum(IAtom atom)
double count = 0;
for (int i = 0; i < bondCount; i++)
{
if (bonds[i].contains(atom)) {
if (bonds[i].getOrder() == IBond.Order.SINGLE) {
count += 1;
} else if (bonds[i].getOrder() == IBond.Order.DOUBLE) {
count += 2;
} else if (bonds[i].getOrder() == IBond.Order.TRIPLE) {
count += 3;
} else if (bonds[i].getOrder() == IBond.Order.QUADRUPLE) {
count += 4;
}
}
}
if(bonds[i].contains(atom)) {
IBond.Order order = bonds[i].getOrder();
if(order != null){
count += order.numeric();
}
}
}
return count;
}

Expand All @@ -953,7 +948,7 @@ public Order getMaximumBondOrder(IAtom atom) {
IBond.Order max = IBond.Order.SINGLE;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom) &&
bonds[i].getOrder().ordinal() > max.ordinal()) {
bonds[i].getOrder().numeric() > max.numeric()) {
max = bonds[i].getOrder();
}
}
Expand All @@ -973,7 +968,7 @@ public Order getMinimumBondOrder(IAtom atom)
IBond.Order min = IBond.Order.QUADRUPLE;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom) &&
bonds[i].getOrder().ordinal() < min.ordinal()) {
bonds[i].getOrder().numeric() < min.numeric()) {
min = bonds[i].getOrder();
}
}
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19 changes: 7 additions & 12 deletions src/main/org/openscience/cdk/Ring.java
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Expand Up @@ -137,19 +137,14 @@ public IBond getNextBond(IBond bond, IAtom atom)
*/
public int getBondOrderSum()
{
int orderSum = 0;
for (int i = 0; i < getBondCount(); i++) {
if (getBond(i).getOrder() == IBond.Order.SINGLE) {
orderSum += 1;
} else if (getBond(i).getOrder() == IBond.Order.DOUBLE) {
orderSum += 2;
} else if (getBond(i).getOrder() == IBond.Order.TRIPLE) {
orderSum += 3;
} else if (getBond(i).getOrder() == IBond.Order.QUADRUPLE) {
orderSum += 4;
}
int sum = 0;
for (int i = 0; i < getBondCount(); i++) {
IBond.Order order = getBond(i).getOrder();
if(order != null) {
sum += order.numeric();
}
}
return orderSum;
return sum;
}

/**
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2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
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Expand Up @@ -2567,7 +2567,7 @@ private boolean isAcceptable(IAtom atom, IAtomContainer container, IAtomType typ
}

// confirm correct bond orders
if (type.getProperty(CDKConstants.PI_BOND_COUNT) != null && container.getMaximumBondOrder(atom).ordinal() + 1 > (Integer) type.getProperty(CDKConstants.PI_BOND_COUNT) + 1)
if (type.getProperty(CDKConstants.PI_BOND_COUNT) != null && container.getMaximumBondOrder(atom).numeric() > (Integer) type.getProperty(CDKConstants.PI_BOND_COUNT) + 1)
return false;

// confirm correct valency
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6 changes: 1 addition & 5 deletions src/main/org/openscience/cdk/geometry/cip/CIPTool.java
View file
Expand Up @@ -269,10 +269,6 @@ public static ILigand[] getLigandLigands(ILigand ligand) {
* @return int reflecting the duplication number
*/
private static int getDuplication(Order order) {
if (order == Order.SINGLE) return 1;
if (order == Order.DOUBLE) return 2;
if (order == Order.TRIPLE) return 3;
if (order == Order.QUADRUPLE) return 4;
return 0;
return order == null ? 0 : order.numeric();
}
}
11 changes: 2 additions & 9 deletions src/main/org/openscience/cdk/graph/invariant/HuLuIndexTool.java
View file
Expand Up @@ -196,15 +196,8 @@ public static double[] getAtomWeights(AtomContainer atomContainer) throws NoSuch
if (Math.abs(apspMatrix[i][headAtomPosition] - apspMatrix[i][endAtomPosition]) == 1)
{
int min = Math.min(apspMatrix[i][headAtomPosition],apspMatrix[i][endAtomPosition]);
if (bond.getOrder() == IBond.Order.SINGLE) {
interLayerBondSum[min] += 1;
} else if (bond.getOrder() == IBond.Order.DOUBLE) {
interLayerBondSum[min] += 2;
} else if (bond.getOrder() == IBond.Order.TRIPLE) {
interLayerBondSum[min] += 3;
} else if (bond.getOrder() == IBond.Order.QUADRUPLE) {
interLayerBondSum[min] += 4;
}
IBond.Order order = bond.getOrder();
interLayerBondSum[min] += order == null ? 0 : order.numeric();
}
}

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2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/io/MDLV2000Writer.java
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Expand Up @@ -374,7 +374,7 @@ public void writeMolecule(IAtomContainer container) throws Exception {
else if (Order.QUADRUPLE == bond.getOrder())
throw new CDKException("MDL molfiles do not support quadruple bonds.");
else
bondType=(int)bond.getOrder().ordinal()+1;
bondType = bond.getOrder().numeric();
line += formatMDLInt(bondType,3);

line += " ";
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2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/libio/cml/Convertor.java
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Expand Up @@ -725,7 +725,7 @@ public CMLBond cdkBondToCMLBond(IBond cdkBond) {
// scalar.setDataType("xsd:float");
scalar.setDictRef("cdk:bondOrder");
scalar.setTitle("order");
scalar.setValue(cdkBond.getOrder().ordinal()+1);
scalar.setValue(cdkBond.getOrder().numeric());
cmlBond.appendChild(scalar);
}
if (cdkBond.getFlag(CDKConstants.ISAROMATIC)) {
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2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/modeling/builder3d/ForceFieldConfigurator.java
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Expand Up @@ -280,7 +280,7 @@ public IRingSet assignAtomTyps(IMolecule molecule) throws CDKException {
atom.setFlag(CDKConstants.ISINRING, false);
isInHeteroRing = false;
}
atom.setProperty("MAX_BOND_ORDER", new Double(molecule.getMaximumBondOrder(atom).ordinal()+1));
atom.setProperty("MAX_BOND_ORDER", new Double(molecule.getMaximumBondOrder(atom).numeric()));

try {
hoseCode = hcg.getHOSECode(molecule, atom, 3);
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17 changes: 6 additions & 11 deletions src/main/org/openscience/cdk/silent/AtomContainer.java
View file
Expand Up @@ -906,15 +906,10 @@ public double getBondOrderSum(IAtom atom)
for (int i = 0; i < bondCount; i++)
{
if (bonds[i].contains(atom)) {
if (bonds[i].getOrder() == IBond.Order.SINGLE) {
count += 1;
} else if (bonds[i].getOrder() == IBond.Order.DOUBLE) {
count += 2;
} else if (bonds[i].getOrder() == IBond.Order.TRIPLE) {
count += 3;
} else if (bonds[i].getOrder() == IBond.Order.QUADRUPLE) {
count += 4;
}
IBond.Order order = bonds[i].getOrder();
if(order != null){
count += order.numeric();
}
}
}
return count;
Expand All @@ -931,7 +926,7 @@ public Order getMaximumBondOrder(IAtom atom) {
IBond.Order max = IBond.Order.SINGLE;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom) &&
bonds[i].getOrder().ordinal() > max.ordinal()) {
bonds[i].getOrder().numeric() > max.numeric()) {
max = bonds[i].getOrder();
}
}
Expand All @@ -951,7 +946,7 @@ public Order getMinimumBondOrder(IAtom atom)
IBond.Order min = IBond.Order.QUADRUPLE;
for (int i = 0; i < bondCount; i++) {
if (bonds[i].contains(atom) &&
bonds[i].getOrder().ordinal() < min.ordinal()) {
bonds[i].getOrder().numeric() < min.numeric()) {
min = bonds[i].getOrder();
}
}
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21 changes: 8 additions & 13 deletions src/main/org/openscience/cdk/silent/Ring.java
View file
Expand Up @@ -132,20 +132,15 @@ public IBond getNextBond(IBond bond, IAtom atom)
*/
public int getBondOrderSum()
{
int orderSum = 0;
for (int i = 0; i < getBondCount(); i++) {
if (getBond(i).getOrder() == IBond.Order.SINGLE) {
orderSum += 1;
} else if (getBond(i).getOrder() == IBond.Order.DOUBLE) {
orderSum += 2;
} else if (getBond(i).getOrder() == IBond.Order.TRIPLE) {
orderSum += 3;
} else if (getBond(i).getOrder() == IBond.Order.QUADRUPLE) {
orderSum += 4;
}
int sum = 0;
for (int i = 0; i < getBondCount(); i++) {
IBond.Order order = getBond(i).getOrder();
if(order != null) {
sum += order.numeric();
}
}
return orderSum;
}
return sum;
}

/**
* @inheritDoc
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4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/smsd/algorithm/matchers/DefaultBondMatcher.java
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Expand Up @@ -129,8 +129,8 @@ public boolean matches(IAtomContainer targetContainer, IBond targetBond) {
* @return
*/
private boolean isBondTypeMatch(IBond targetBond) {
int reactantBondType = queryBond.getOrder().ordinal();
int productBondType = targetBond.getOrder().ordinal();
int reactantBondType = queryBond.getOrder().numeric();
int productBondType = targetBond.getOrder().numeric();
if ((queryBond.getFlag(CDKConstants.ISAROMATIC) == targetBond.getFlag(CDKConstants.ISAROMATIC))
&& (reactantBondType == productBondType)) {
return true;
Expand Down
4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/smsd/algorithm/matchers/DefaultVFBondMatcher.java
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Expand Up @@ -132,8 +132,8 @@ public boolean matches(TargetProperties targetConatiner, IBond targetBond) {
* @return
*/
private boolean isBondTypeMatch(IBond targetBond) {
int reactantBondType = queryBond.getOrder().ordinal();
int productBondType = targetBond.getOrder().ordinal();
int reactantBondType = queryBond.getOrder().numeric();
int productBondType = targetBond.getOrder().numeric();
if ((queryBond.getFlag(CDKConstants.ISAROMATIC) == targetBond.getFlag(CDKConstants.ISAROMATIC))
&& (reactantBondType == productBondType)) {
return true;
Expand Down
4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/smsd/algorithm/mcgregor/QueryProcessor.java
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Expand Up @@ -114,7 +114,7 @@ protected void process(

Integer indexI = query.getAtomNumber(query.getBond(atomIndex).getAtom(0));
Integer indexJ = query.getAtomNumber(query.getBond(atomIndex).getAtom(1));
Integer order = query.getBond(atomIndex).getOrder().ordinal() + 1;
Integer order = query.getBond(atomIndex).getOrder().numeric();

// System.out.println(AtomI + "= , =" + AtomJ );
for (Integer unMappedAtomIndex = 0; unMappedAtomIndex < unmapped_numA; unMappedAtomIndex++) {
Expand Down Expand Up @@ -164,7 +164,7 @@ protected void process(
Integer indexJ = query.getAtomNumber(query.getBond(atomIndex).getAtom(1));
Integer order = 0;
if (query.getBond(atomIndex).getOrder() != null) {
order = query.getBond(atomIndex).getOrder().ordinal() + 1;
order = query.getBond(atomIndex).getOrder().numeric();
}

// System.out.println(AtomI + "= , =" + AtomJ );
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/smsd/algorithm/mcgregor/TargetProcessor.java
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Expand Up @@ -108,7 +108,7 @@ protected void process(

Integer indexI = target.getAtomNumber(target.getBond(atomIndex).getAtom(0));
Integer indexJ = target.getAtomNumber(target.getBond(atomIndex).getAtom(1));
Integer order = target.getBond(atomIndex).getOrder().ordinal() + 1;
Integer order = target.getBond(atomIndex).getOrder().numeric();

for (int b = 0; b < unmapped_numB; b++) {
if (unmapped_atoms_molB.get(b).equals(indexI)) {
Expand Down
12 changes: 6 additions & 6 deletions src/main/org/openscience/cdk/smsd/algorithm/single/SingleMapping.java
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Expand Up @@ -135,8 +135,8 @@ private void setSourceSingleAtomMap(IQueryAtomContainer source, boolean removeHy

double totalOrder = 0;
for (IBond bond : Bonds) {
Order bondOrder = bond.getOrder();
totalOrder += bondOrder.ordinal() + be.getEnergies(bond);
Order order = bond.getOrder();
totalOrder += order.numeric() + be.getEnergies(bond);
}
if (targetAtom.getFormalCharge() != sourceAtom.getFormalCharge()) {
totalOrder += 0.5;
Expand Down Expand Up @@ -164,8 +164,8 @@ private void setSourceSingleAtomMap(boolean removeHydrogen) throws CDKException

double totalOrder = 0;
for (IBond bond : Bonds) {
Order bondOrder = bond.getOrder();
totalOrder += bondOrder.ordinal() + be.getEnergies(bond);
Order order = bond.getOrder();
totalOrder += order.numeric() + be.getEnergies(bond);
}
if (targetAtom.getFormalCharge() != sourceAtom.getFormalCharge()) {
totalOrder += 0.5;
Expand Down Expand Up @@ -194,8 +194,8 @@ private void setTargetSingleAtomMap(boolean removeHydrogen) throws CDKException

double totalOrder = 0;
for (IBond bond : Bonds) {
Order bondOrder = bond.getOrder();
totalOrder += bondOrder.ordinal() + be.getEnergies(bond);
Order order = bond.getOrder();
totalOrder += order.numeric() + be.getEnergies(bond);
}
if (sourceAtoms.getFormalCharge() != targetAtom.getFormalCharge()) {
totalOrder += 0.5;
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/smsd/labelling/AtomContainerPrinter.java
View file
Expand Up @@ -60,7 +60,7 @@ public String toString(IAtomContainer atomContainer) {
int a1N = atomContainer.getAtomNumber(a1);
String a0S = a0.getSymbol();
String a1S = a1.getSymbol();
int o = bond.getOrder().ordinal();
int o = bond.getOrder().numeric();
if (a0N < a1N) {
edges.add(new Edge(a0N, a1N, o, a0S, a1S));
} else {
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2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/templates/AminoAcids.java
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Expand Up @@ -82,7 +82,7 @@ public static int[][] aaBondInfo() {
info[counter][0] = counter;
info[counter][1] = acid.getAtomNumber(bond.getAtom(0));
info[counter][2] = acid.getAtomNumber(bond.getAtom(1));
info[counter][3] = (int)bond.getOrder().ordinal();
info[counter][3] = bond.getOrder().numeric();
counter++;
}
}
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6 changes: 3 additions & 3 deletions src/main/org/openscience/cdk/tools/CDKValencyChecker.java
View file
Expand Up @@ -92,9 +92,9 @@ public boolean isSaturated(IAtom atom, IAtomContainer container) throws CDKExcep

int typeMaxBondOrder = piBondCount + 1;
int typeBondOrderSum = formalNeighborCount + piBondCount;
if (bondOrderSum + hcount == typeBondOrderSum &&
maxBondOrder.ordinal() <= typeMaxBondOrder) {

if (bondOrderSum + hcount == typeBondOrderSum &&
maxBondOrder.numeric() <= typeMaxBondOrder) {
return true;
}
return false;
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4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/tools/HOSECodeGenerator.java
View file
Expand Up @@ -381,7 +381,7 @@ private void breadthFirstSearch(IAtom root,boolean addTreeNode) throws CDKExcept
tempNode = new TreeNode(atom.getSymbol(), new TreeNode(root.getSymbol(), null, root, (double) 0, 0, (long) 0), atom, 4, atomContainer.getConnectedBondsCount(atom), 0);
} else
{
tempNode = new TreeNode(atom.getSymbol(), new TreeNode(root.getSymbol(), null, root, (double) 0, 0, (long) 0), atom, bond.getOrder().ordinal()+1, atomContainer.getConnectedBondsCount(atom), 0);
tempNode = new TreeNode(atom.getSymbol(), new TreeNode(root.getSymbol(), null, root, (double) 0, 0, (long) 0), atom, bond.getOrder().numeric(), atomContainer.getConnectedBondsCount(atom), 0);
}

sphereNodes.add(tempNode);
Expand Down Expand Up @@ -446,7 +446,7 @@ private void nextSphere(List<TreeNode> sphereNodes) throws CDKException
nextSphereNodes.add(new TreeNode(toNode.getSymbol(), treeNode, toNode, 4, atomContainer.getConnectedBondsCount(toNode), treeNode.score));
} else
{
nextSphereNodes.add(new TreeNode(toNode.getSymbol(), treeNode, toNode, bond.getOrder().ordinal()+1, atomContainer.getConnectedBondsCount(toNode), treeNode.score));
nextSphereNodes.add(new TreeNode(toNode.getSymbol(), treeNode, toNode, bond.getOrder().numeric(), atomContainer.getConnectedBondsCount(toNode), treeNode.score));
}
}
}
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26 changes: 8 additions & 18 deletions src/main/org/openscience/cdk/tools/manipulator/AtomContainerManipulator.java
View file
Expand Up @@ -807,14 +807,9 @@ public static void clearAtomConfigurations(IAtomContainer container) {
public static int getSingleBondEquivalentSum(IAtomContainer container) {
int sum = 0;
for (IBond bond : container.bonds()) {
if (bond.getOrder() == CDKConstants.BONDORDER_SINGLE) {
sum += 1;
} else if (bond.getOrder() == CDKConstants.BONDORDER_DOUBLE) {
sum += 2;
} else if (bond.getOrder() == CDKConstants.BONDORDER_TRIPLE) {
sum += 3;
} else if (bond.getOrder() == CDKConstants.BONDORDER_QUADRUPLE) {
sum += 4;
IBond.Order order = bond.getOrder();
if(order != null) {
sum += order.numeric();
}
}
return sum;
Expand Down Expand Up @@ -876,16 +871,11 @@ public static IAtomContainer createAllCarbonAllSingleNonAromaticBondAtomContaine
public static double getBondOrderSum(IAtomContainer container, IAtom atom) {
double count = 0;
for (IBond bond : container.getConnectedBondsList(atom)) {
if (bond.getOrder() == IBond.Order.SINGLE) {
count += 1.0;
} else if (bond.getOrder() == IBond.Order.DOUBLE) {
count += 2.0;
} else if (bond.getOrder() == IBond.Order.TRIPLE) {
count += 3.0;
} else if (bond.getOrder() == IBond.Order.QUADRUPLE) {
count += 4.0;
}
}
IBond.Order order = bond.getOrder();
if(order != null) {
count += order.numeric();
}
}
return count;
}

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14 changes: 4 additions & 10 deletions src/main/org/openscience/cdk/tools/manipulator/BondManipulator.java
View file
Expand Up @@ -312,16 +312,10 @@ public static int getSingleBondEquivalentSum(List<IBond> bonds) {
public static int getSingleBondEquivalentSum(Iterator<IBond> bonds) {
int sum = 0;
while (bonds.hasNext()) {
IBond nextBond = bonds.next();
if (nextBond.getOrder() == IBond.Order.SINGLE) {
sum += 1;
} else if (nextBond.getOrder() == IBond.Order.DOUBLE) {
sum += 2;
} else if (nextBond.getOrder() == IBond.Order.TRIPLE) {
sum += 3;
} else if (nextBond.getOrder() == IBond.Order.QUADRUPLE) {
sum += 4;
}
IBond.Order order = bonds.next().getOrder();
if(order != null) {
sum += order.numeric();
}
}
return sum;
}
Expand Down

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