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Normalised all getFlag and setFlag usages to use the CDKConstants
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Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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@johnmay @egonw
johnmay authored and egonw committed Sep 18, 2012
1 parent 55d15bc commit 2db7a94
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Showing 9 changed files with 39 additions and 36 deletions.
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
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Expand Up @@ -80,7 +80,7 @@ public class GasteigerPEPEPartialCharges implements IChargeCalculator {
private int STEP_SIZE = 5;
private AtomTypeFactory factory;
/** Flag is set if the formal charge of a chemobject is changed due to resonance.*/
private static int ISCHANGEDFC = 0;
private static int ISCHANGEDFC = 0x1;

/** Corresponds an empirical influence between the electrostatic potential and
* the neighbours.*/
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5 changes: 3 additions & 2 deletions ...in/org/openscience/cdk/qsar/descriptors/atomic/EffectiveAtomPolarizabilityDescriptor.java
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Expand Up @@ -24,6 +24,7 @@
*/
package org.openscience.cdk.qsar.descriptors.atomic;

import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.annotations.TestClass;
import org.openscience.cdk.annotations.TestMethod;
import org.openscience.cdk.charges.Polarizability;
Expand Down Expand Up @@ -135,14 +136,14 @@ public DescriptorValue calculate(IAtom atom, IAtomContainer ac) {
Integer originalHCount = atom.getImplicitHydrogenCount();
Integer originalValency = atom.getValency();
IAtomType.Hybridization originalHybridization = atom.getHybridization();
boolean originalFlag = atom.getFlag(4);
boolean originalFlag = atom.getFlag(CDKConstants.VISITED);
polarizability = pol.calculateGHEffectiveAtomPolarizability(ac, atom, 100, true);
// restore original props
atom.setAtomTypeName(originalAtomtypeName);
atom.setFormalNeighbourCount(originalNeighborCount);
atom.setValency(originalValency);
atom.setImplicitHydrogenCount(originalHCount);
atom.setFlag(4, originalFlag);
atom.setFlag(CDKConstants.VISITED, originalFlag);
atom.setHybridization(originalHybridization);
return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
new DoubleResult(polarizability),
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2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestChainDescriptor.java
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Expand Up @@ -185,7 +185,7 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
//logger.debug("LargestChainDescriptor");
boolean[] originalFlag4 = new boolean[container.getAtomCount()];
for (int i=0; i<originalFlag4.length; i++) {
originalFlag4[i] = container.getAtom(i).getFlag(4);
originalFlag4[i] = container.getAtom(i).getFlag(CDKConstants.VISITED);
}
if (checkRingSystem) {
IRingSet rs;
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4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/qsar/descriptors/molecular/LargestPiSystemDescriptor.java
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Expand Up @@ -165,7 +165,7 @@ private DescriptorValue getDummyDescriptorValue(Exception e) {
public DescriptorValue calculate(IAtomContainer container) {
boolean[] originalFlag4 = new boolean[container.getAtomCount()];
for (int i=0; i<originalFlag4.length; i++) {
originalFlag4[i] = container.getAtom(i).getFlag(4);
originalFlag4[i] = container.getAtom(i).getFlag(CDKConstants.VISITED);
}
if (checkAromaticity) {
try {
Expand Down Expand Up @@ -210,7 +210,7 @@ public DescriptorValue calculate(IAtomContainer container) {
}
// restore original flag values
for (int i=0; i<originalFlag4.length; i++) {
container.getAtom(i).setFlag(4, originalFlag4[i]);
container.getAtom(i).setFlag(CDKConstants.VISITED, originalFlag4[i]);
}

return new DescriptorValue(getSpecification(), getParameterNames(), getParameters(),
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12 changes: 6 additions & 6 deletions src/main/org/openscience/cdk/smsd/filters/ChemicalFilters.java
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Expand Up @@ -472,11 +472,11 @@ private synchronized Double getMappedMoleculeEnergies(Map<Integer, Integer> MCSA
IAtomContainer product = DefaultChemObjectBuilder.getInstance().newInstance(IAtomContainer.class, pMol);

for (IAtom eAtom : Educt.atoms()) {
eAtom.setFlag(0, false);
eAtom.setFlag(CDKConstants.ISPLACED, false);
}

for (IAtom pAtom : product.atoms()) {
pAtom.setFlag(0, false);
pAtom.setFlag(CDKConstants.ISPLACED, false);
}

if (MCSAtomSolution != null) {
Expand All @@ -487,8 +487,8 @@ private synchronized Double getMappedMoleculeEnergies(Map<Integer, Integer> MCSA
IAtom eAtom = Educt.getAtom(ENum);
IAtom pAtom = product.getAtom(PNum);

eAtom.setFlag(0, true);
pAtom.setFlag(0, true);
eAtom.setFlag(CDKConstants.ISPLACED, true);
pAtom.setFlag(CDKConstants.ISPLACED, true);
}
}

Expand Down Expand Up @@ -784,8 +784,8 @@ private double getEnergy(IAtomContainer Educt, IAtomContainer product) throws CD

private double getBondEnergy(IBond bond, BondEnergies bondEnergy) {
double energy = 0.0;
if ((bond.getAtom(0).getFlag(0) == true && bond.getAtom(1).getFlag(0) == false)
|| (bond.getAtom(0).getFlag(0) == false && bond.getAtom(1).getFlag(0) == true)) {
if ((bond.getAtom(0).getFlag(CDKConstants.ISPLACED) == true && bond.getAtom(1).getFlag(CDKConstants.ISPLACED) == false)
|| (bond.getAtom(0).getFlag(CDKConstants.ISPLACED) == false && bond.getAtom(1).getFlag(CDKConstants.ISPLACED) == true)) {
Integer val = bondEnergy.getEnergies(bond.getAtom(0), bond.getAtom(1), bond.getOrder());
if (val != null) {
energy = val;
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5 changes: 3 additions & 2 deletions src/test/org/openscience/cdk/geometry/cip/ImmutableHydrogenTest.java
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Expand Up @@ -29,6 +29,7 @@

import org.junit.Assert;
import org.junit.Test;
import org.openscience.cdk.CDKConstants;
import org.openscience.cdk.CDKTestCase;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IChemObjectChangeEvent;
Expand Down Expand Up @@ -104,7 +105,7 @@ public void testReturnsNull() {
Assert.assertNull(hydrogen.getExactMass());
Assert.assertNull(hydrogen.getNaturalAbundance());
Assert.assertNull(hydrogen.getFlags());
Assert.assertFalse(hydrogen.getFlag(0));
Assert.assertFalse(hydrogen.getFlag(CDKConstants.ISPLACED));
Assert.assertNull(hydrogen.getID());
Assert.assertNull(hydrogen.getProperties());
Assert.assertNull(hydrogen.getProperty(new String()));
Expand Down Expand Up @@ -133,7 +134,7 @@ public void testSetIsSilent() throws Exception {
hydrogen.setExactMass(12.0);
hydrogen.setNaturalAbundance(100.0);
hydrogen.setFlags(null);
hydrogen.setFlag(1, true);
hydrogen.setFlag(CDKConstants.ISINRING, true);
hydrogen.setID("Me");
hydrogen.setProperties(new Properties());
hydrogen.setProperty(new String(), new String());
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31 changes: 16 additions & 15 deletions src/test/org/openscience/cdk/interfaces/AbstractChemObjectTest.java
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Expand Up @@ -97,42 +97,43 @@ public abstract class AbstractChemObjectTest extends AbstractCDKObjectTest {

@Test public void testSetFlags_arrayboolean(){
IChemObject chemObject=newChemObject();
chemObject.setFlag(1,true);
chemObject.setFlag(CDKConstants.ISINRING,true);
IChemObject chemObject2=newChemObject();
chemObject2.setFlags(chemObject.getFlags());
Assert.assertTrue(chemObject2.getFlag(1));
Assert.assertTrue(chemObject2.getFlag(CDKConstants.ISINRING));
}

@Test public void testGetFlags(){
System.out.println("Test flags:");
IChemObject chemObject=newChemObject();
chemObject.setFlag(1,true);
chemObject.setFlag(CDKConstants.ISINRING,true);
IChemObject chemObject2=newChemObject();
chemObject2.setFlags(chemObject.getFlags());
Assert.assertTrue(chemObject2.getFlag(1));
Assert.assertTrue(chemObject2.getFlag(CDKConstants.ISINRING));
}

@Test public void testGetFlags_Array(){
IChemObject chemObject=newChemObject();
chemObject.setFlag(1,true);
chemObject.setFlag(CDKConstants.ISINRING, true);
boolean[] flags = chemObject.getFlags();
Assert.assertTrue(flags[1]);
}

@Test public void testSetFlag_int_boolean() {
IChemObject chemObject = newChemObject();
Assert.assertFalse(chemObject.getFlag(0));
chemObject.setFlag(0, true);
Assert.assertTrue(chemObject.getFlag(0));
chemObject.setFlag(0, false);
Assert.assertFalse(chemObject.getFlag(0));
Assert.assertFalse(chemObject.getFlag(CDKConstants.ISPLACED));
chemObject.setFlag(CDKConstants.ISPLACED, true);
Assert.assertTrue(chemObject.getFlag(CDKConstants.ISPLACED));
chemObject.setFlag(CDKConstants.ISPLACED, false);
Assert.assertFalse(chemObject.getFlag(CDKConstants.ISPLACED));
}
@Test public void testGetFlag_int() {
testSetFlag_int_boolean();
}

@Test public void testClone() throws Exception {
IChemObject chemObject = newChemObject();
chemObject.setFlag(3, true);
chemObject.setFlag(CDKConstants.ISALIPHATIC, true);

// test cloning of itself
Object clone = chemObject.clone();
Expand All @@ -146,12 +147,12 @@ public abstract class AbstractChemObjectTest extends AbstractCDKObjectTest {

@Test public void testClone_Flags() throws Exception {
IChemObject chemObject1 = newChemObject();
chemObject1.setFlag(3, true);
chemObject1.setFlag(CDKConstants.ISALIPHATIC, true);
IChemObject chemObject2 = (IChemObject)chemObject1.clone();

// test cloning of flags field
chemObject2.setFlag(3, false);
Assert.assertTrue(chemObject1.getFlag(3));
chemObject2.setFlag(CDKConstants.ISALIPHATIC, false);
Assert.assertTrue(chemObject1.getFlag(CDKConstants.ISALIPHATIC));
}

@Test public void testClone_Identifier() throws Exception {
Expand Down Expand Up @@ -279,7 +280,7 @@ class DummyChemObjectListener implements IChemObjectListener {

listener.reset();
Assert.assertFalse(listener.changed);
chemObject.setFlag(3, true);
chemObject.setFlag(CDKConstants.ISALIPHATIC, true);
Assert.assertTrue(listener.changed);
}

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2 changes: 1 addition & 1 deletion src/test/org/openscience/cdk/silent/ChemObjectTestHelper.java
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Expand Up @@ -64,7 +64,7 @@ public static void testStateChanged_IChemObjectChangeEvent(IChemObject chemObjec

listener.reset();
Assert.assertFalse(listener.getChanged());
chemObject.setFlag(3, true);
chemObject.setFlag(CDKConstants.ISALIPHATIC, true);
Assert.assertFalse(listener.getChanged());
}

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12 changes: 6 additions & 6 deletions src/test/org/openscience/cdk/tools/manipulator/AtomContainerManipulatorTest.java
View file
Expand Up @@ -196,12 +196,12 @@ public void testConvertImplicitToExplicitHydrogens_IAtomContainer2() throws Exce
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(1, 4, IBond.Order.DOUBLE);
mol.addBond(1, 5, IBond.Order.DOUBLE);
mol.setFlag(5,true);
mol.setFlag(CDKConstants.ISAROMATIC,true);

Assert.assertEquals(6, mol.getAtomCount());
IAtomContainer ac = AtomContainerManipulator.removeHydrogens(mol);
Assert.assertEquals(2, ac.getAtomCount());
Assert.assertTrue(ac.getFlag(5));
Assert.assertTrue(ac.getFlag(CDKConstants.ISAROMATIC));
}

@Test public void testRemoveHydrogensZeroHydrogenCounts() throws IOException, ClassNotFoundException, CDKException{
Expand Down Expand Up @@ -282,7 +282,7 @@ public void testConvertImplicitToExplicitHydrogens_IAtomContainer2() throws Exce
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(1, 4, IBond.Order.DOUBLE);
mol.addBond(1, 5, IBond.Order.DOUBLE);
mol.setFlag(5,true);
mol.setFlag(CDKConstants.ISAROMATIC,true);

IAtom[] atoms = AtomContainerManipulator.getAtomArray(
mol.getConnectedAtomsList(mol.getAtom(0))
Expand All @@ -306,7 +306,7 @@ public void testConvertImplicitToExplicitHydrogens_IAtomContainer2() throws Exce
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(1, 4, IBond.Order.DOUBLE);
mol.addBond(1, 5, IBond.Order.DOUBLE);
mol.setFlag(5,true);
mol.setFlag(CDKConstants.ISAROMATIC,true);

IBond[] bonds = AtomContainerManipulator.getBondArray(
mol.getConnectedBondsList(mol.getAtom(0))
Expand All @@ -330,7 +330,7 @@ public void testConvertImplicitToExplicitHydrogens_IAtomContainer2() throws Exce
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(1, 4, IBond.Order.DOUBLE);
mol.addBond(1, 5, IBond.Order.DOUBLE);
mol.setFlag(5,true);
mol.setFlag(CDKConstants.ISAROMATIC,true);

IBond[] bonds = AtomContainerManipulator.getBondArray(mol);
Assert.assertEquals(5, bonds.length);
Expand All @@ -354,7 +354,7 @@ public void testConvertImplicitToExplicitHydrogens_IAtomContainer2() throws Exce
mol.addBond(0, 3, IBond.Order.SINGLE);
mol.addBond(1, 4, IBond.Order.DOUBLE);
mol.addBond(1, 5, IBond.Order.DOUBLE);
mol.setFlag(5,true);
mol.setFlag(CDKConstants.ISAROMATIC,true);

Assert.assertEquals(mol.getAtom(0), AtomContainerManipulator.getAtomById(mol, "a1"));
Assert.assertEquals(mol.getAtom(1), AtomContainerManipulator.getAtomById(mol, "a2"));
Expand Down

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