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Removed IBond.Order.UNSET
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Change-Id: I8617b9f0d2d4f7e9e052ab4f0440d45d2dfd285b
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@egonw
egonw committed Nov 13, 2012
1 parent f2bfd74 commit f24e1ea
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Showing 9 changed files with 24 additions and 25 deletions.
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
View file
Expand Up @@ -2600,7 +2600,7 @@ private boolean isAcceptable(IAtom atom, IAtomContainer container, IAtomType typ
if (typeOrder != null) {
for (IBond bond : container.getConnectedBondsList(atom)) {
IBond.Order order = bond.getOrder();
if (order != CDKConstants.UNSET && order != IBond.Order.UNSET) {
if (order != CDKConstants.UNSET && order != (IBond.Order)CDKConstants.UNSET) {
if (BondManipulator.isHigherOrder(order, typeOrder)) return false;
} else if (bond.getFlag(CDKConstants.SINGLE_OR_DOUBLE)) {
if (typeOrder != IBond.Order.SINGLE &&
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4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/config/atomtypes/OWLAtomTypeHandler.java
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Expand Up @@ -100,7 +100,7 @@ private void endAtomTypeElement(String local) {
atomTypes.add(currentAtomType);
currentAtomType.setProperty(CDKConstants.PI_BOND_COUNT, piBondCount);
currentAtomType.setFormalNeighbourCount(neighborCount);
if (maxBondOrder != Order.UNSET) currentAtomType.setMaxBondOrder(maxBondOrder);
if (maxBondOrder != (Order)CDKConstants.UNSET) currentAtomType.setMaxBondOrder(maxBondOrder);
if (bondOrderSum > 0.1) currentAtomType.setBondOrderSum(bondOrderSum);
} else if ("formalCharge".equals(local)) {
if (currentChars.charAt(0) == '+') {
Expand Down Expand Up @@ -133,7 +133,7 @@ private void startAtomTypeElement(String local, Attributes atts) {
currentAtomType.setAtomTypeName(atts.getValue("rdf:ID"));
piBondCount = 0;
neighborCount = 0;
maxBondOrder = Order.UNSET;
maxBondOrder = (Order)CDKConstants.UNSET;
bondOrderSum = 0.0;
} else if ("hasElement".equals(local)) {
String attrValue = atts.getValue("rdf:resource");
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4 changes: 1 addition & 3 deletions src/main/org/openscience/cdk/interfaces/IBond.java
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Expand Up @@ -49,8 +49,7 @@ public enum Order {
SINGLE(1),
DOUBLE(2),
TRIPLE(3),
QUADRUPLE(4),
UNSET(0);
QUADRUPLE(4);

private final Integer bondedElectronPairs;

Expand All @@ -66,7 +65,6 @@ private Order(Integer bondedElectronPairs){
* Order.DOUBLE.numeric() // 2
* Order.TRIPLE.numeric() // 3
* Order.QUADRUPLE.numeric() // 4
* Order.UNSET.numeric() // 0
* }</pre>
*
* @return number of bonded electron pairs
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4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/io/MDLV2000Reader.java
View file
Expand Up @@ -709,9 +709,9 @@ private IAtomContainer readAtomContainer(IAtomContainer molecule) throws CDKExce
} else if (order == 4) {
// aromatic bond
if (stereo != null) {
newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.UNSET, stereo);
newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, (IBond.Order)CDKConstants.UNSET, stereo);
} else {
newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, IBond.Order.UNSET);
newBond = molecule.getBuilder().newInstance(IBond.class,a1, a2, (IBond.Order)CDKConstants.UNSET);
}
// mark both atoms and the bond as aromatic and raise the SINGLE_OR_DOUBLE-flag
newBond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
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15 changes: 8 additions & 7 deletions src/main/org/openscience/cdk/tools/manipulator/BondManipulator.java
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Expand Up @@ -24,15 +24,16 @@
* */
package org.openscience.cdk.tools.manipulator;

import java.util.Iterator;
import java.util.List;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IBond.Order;

import java.util.Iterator;
import java.util.List;

/**
* Class with convenience methods that provide methods to manipulate
* AtomContainer's. For example:
Expand Down Expand Up @@ -281,13 +282,13 @@ public static IBond.Order getMaximumBondOrder(IBond firstBond, IBond secondBond)
*/
@TestMethod("testGetMaximumBondOrder_Order_Order,testGetMaximumBondOrder_Unset_Unset")
public static IBond.Order getMaximumBondOrder(IBond.Order firstOrder, IBond.Order secondOrder) {
if (firstOrder == Order.UNSET) {
if(secondOrder == Order.UNSET)
if (firstOrder == (Order)CDKConstants.UNSET) {
if(secondOrder == (Order)CDKConstants.UNSET)
throw new IllegalArgumentException("Both bond orders are unset");
return secondOrder;
}
if (secondOrder == Order.UNSET) {
if(firstOrder == Order.UNSET)
if (secondOrder == (Order)CDKConstants.UNSET) {
if(firstOrder == (Order)CDKConstants.UNSET)
throw new IllegalArgumentException("Both bond orders are unset");
return firstOrder;
}
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2 changes: 1 addition & 1 deletion src/test/org/openscience/cdk/atomtype/AbstractAtomTypeTest.java
View file
Expand Up @@ -150,7 +150,7 @@ private void assertConsistentProperties(IAtomContainer mol, IAtom atom, IAtomTyp
Order expectedMax = matched.getMaxBondOrder();
for (IBond bond : connections) {
IBond.Order order = bond.getOrder();
if (order != CDKConstants.UNSET && order != IBond.Order.UNSET) {
if (order != CDKConstants.UNSET) {
if (BondManipulator.isHigherOrder(order, expectedMax)) {
Assert.fail(
"At least one bond order exceeds the maximum for the atom type"
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6 changes: 3 additions & 3 deletions src/test/org/openscience/cdk/atomtype/CDKAtomTypeMatcherTest.java
View file
Expand Up @@ -2104,7 +2104,7 @@ public void fix_Ca_1() throws Exception {
IAtomContainer molecule = new AtomContainer();
molecule.add(new Ring(6, "C"));
for (IBond bond : molecule.bonds()) {
bond.setOrder(IBond.Order.UNSET);
bond.setOrder((IBond.Order)CDKConstants.UNSET);
bond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
}
for (IAtom atom : molecule.atoms()) {
Expand Down Expand Up @@ -2135,7 +2135,7 @@ public void fix_Ca_1() throws Exception {
};
IAtomContainer molecule = MoleculeFactory.makePyrrole();
for (IBond bond : molecule.bonds()) {
bond.setOrder(IBond.Order.UNSET);
bond.setOrder((IBond.Order)CDKConstants.UNSET);
bond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
}
for (IAtom atom : molecule.atoms()) {
Expand Down Expand Up @@ -2302,7 +2302,7 @@ public void fix_Ca_1() throws Exception {
};
IAtomContainer molecule = MoleculeFactory.makePyridine();
for (IBond bond : molecule.bonds()) {
bond.setOrder(IBond.Order.UNSET);
bond.setOrder((IBond.Order)CDKConstants.UNSET);
bond.setFlag(CDKConstants.SINGLE_OR_DOUBLE, true);
}
assertAtomTypes(testedAtomTypes, expectedTypes, molecule);
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2 changes: 1 addition & 1 deletion src/test/org/openscience/cdk/io/MDLV2000ReaderTest.java
View file
Expand Up @@ -976,7 +976,7 @@ public void testBondOrderFour() throws Exception {
IAtomContainer molecule = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class);
molecule = reader.read(molecule);
Assert.assertEquals(9, molecule.getAtomCount());
Assert.assertEquals(IBond.Order.UNSET, molecule.getBond(0).getOrder());
Assert.assertEquals((IBond.Order)CDKConstants.UNSET, molecule.getBond(0).getOrder());
Assert.assertTrue(molecule.getBond(0).getFlag(CDKConstants.SINGLE_OR_DOUBLE));
Assert.assertEquals(IBond.Order.SINGLE, molecule.getBond(1).getOrder());
Assert.assertFalse(molecule.getBond(1).getFlag(CDKConstants.SINGLE_OR_DOUBLE));
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10 changes: 5 additions & 5 deletions src/test/org/openscience/cdk/tools/manipulator/BondManipulatorTest.java
View file
Expand Up @@ -172,21 +172,21 @@ public void testGetMaximumBondOrder_IBond_IBond() {

@Test
public void testGetMaximumBondOrder_IBond_IBond_Unset() {
IBond bond1 = new Bond(); bond1.setOrder(IBond.Order.UNSET);
IBond bond1 = new Bond(); bond1.setOrder((IBond.Order)CDKConstants.UNSET);
IBond bond2 = new Bond(); bond2.setOrder(IBond.Order.DOUBLE);
Assert.assertEquals(IBond.Order.DOUBLE, BondManipulator.getMaximumBondOrder(bond1, bond2));
}

@Test(expected = IllegalArgumentException.class)
public void testGetMaximumBondOrder_IBond_IBond_null() {
IBond bond1 = new Bond(); bond1.setOrder(IBond.Order.UNSET);
IBond bond1 = new Bond(); bond1.setOrder((IBond.Order)CDKConstants.UNSET);
IBond bond2 = new Bond(); bond2.setOrder(IBond.Order.DOUBLE);
BondManipulator.getMaximumBondOrder(null, bond2);
}

@Test(expected=IllegalArgumentException.class)
public void testGetMaximumBondOrder_Unset_Unset() {
BondManipulator.getMaximumBondOrder(IBond.Order.UNSET, IBond.Order.UNSET);
BondManipulator.getMaximumBondOrder((IBond.Order)CDKConstants.UNSET, (IBond.Order)CDKConstants.UNSET);
}

@Test
Expand All @@ -209,11 +209,11 @@ public void testGetMaximumBondOrder_Order_Order_Single() {
public void testGetMaximumBondOrder_Order_Order_Unset() {
Assert.assertEquals(
IBond.Order.SINGLE,
BondManipulator.getMaximumBondOrder(IBond.Order.SINGLE, IBond.Order.UNSET)
BondManipulator.getMaximumBondOrder(IBond.Order.SINGLE, (IBond.Order)CDKConstants.UNSET)
);
Assert.assertEquals(
IBond.Order.SINGLE,
BondManipulator.getMaximumBondOrder(IBond.Order.UNSET, IBond.Order.SINGLE)
BondManipulator.getMaximumBondOrder((IBond.Order)CDKConstants.UNSET, IBond.Order.SINGLE)
);
}

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