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Renamed the ligancy classes to use the term tetrahedral since they im…
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…plicitly encode for tetrahedral chirality

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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@rajarshi @egonw
rajarshi authored and egonw committed May 24, 2010
1 parent b8110ae commit 3043c17
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Showing 5 changed files with 37 additions and 185 deletions.
65 changes: 0 additions & 65 deletions src/main/org/openscience/cdk/interfaces/ILigancyFourChirality.java
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8 changes: 4 additions & 4 deletions src/main/org/openscience/cdk/smiles/SmilesParser.java
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Expand Up @@ -44,15 +44,15 @@
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IChemObjectBuilder;
import org.openscience.cdk.interfaces.ILigancyFourChirality;
import org.openscience.cdk.interfaces.ITetrahedralChirality;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IAtomType.Hybridization;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.ILigancyFourChirality.Stereo;
import org.openscience.cdk.stereo.LigancyFourChirality;
import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
import org.openscience.cdk.stereo.TetrahedralChirality;
import org.openscience.cdk.tools.CDKHydrogenAdder;
import org.openscience.cdk.tools.ILoggingTool;
import org.openscience.cdk.tools.LoggingToolFactory;
Expand Down Expand Up @@ -233,7 +233,7 @@ public IMolecule parseSmiles(String smiles) throws InvalidSmilesException {
TemporaryChiralityStorage chirality = chiralityInfo.get(atom);
logger.debug("Chiral atom found: ", atom);
IAtom[] atoms = chirality.atoms;
ILigancyFourChirality l4Chiral = new LigancyFourChirality(
ITetrahedralChirality l4Chiral = new TetrahedralChirality(
atom,
new IAtom[]{
atoms[0], atoms[1], atoms[2], atoms[3]
Expand Down
83 changes: 0 additions & 83 deletions src/main/org/openscience/cdk/stereo/LigancyFourChirality.java
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52 changes: 26 additions & 26 deletions src/test/org/openscience/cdk/smiles/SmilesParserTest.java
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Expand Up @@ -39,13 +39,13 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.ILigancyFourChirality;
import org.openscience.cdk.interfaces.ITetrahedralChirality;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IMoleculeSet;
import org.openscience.cdk.interfaces.IPseudoAtom;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.interfaces.IStereoElement;
import org.openscience.cdk.interfaces.ILigancyFourChirality.Stereo;
import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;
import org.openscience.cdk.isomorphism.IsomorphismTester;
import org.openscience.cdk.isomorphism.UniversalIsomorphismTester;
import org.openscience.cdk.layout.StructureDiagramGenerator;
Expand Down Expand Up @@ -1872,8 +1872,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -1896,8 +1896,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -1915,8 +1915,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -1934,8 +1934,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand Down Expand Up @@ -1965,8 +1965,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -1985,8 +1985,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -1999,8 +1999,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -2019,8 +2019,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -2038,8 +2038,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -2057,8 +2057,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -2076,8 +2076,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
IAtom[] ligands = l4Chiral.getLigands();
for (IAtom atom : ligands) Assert.assertNotNull(atom);
Expand All @@ -2096,8 +2096,8 @@ public void testAromaticity() throws InvalidSmilesException{
Assert.assertTrue(stereoElements.hasNext());
IStereoElement stereoElement = stereoElements.next();
Assert.assertNotNull(stereoElement);
Assert.assertTrue(stereoElement instanceof ILigancyFourChirality);
ILigancyFourChirality l4Chiral = (ILigancyFourChirality)stereoElement;
Assert.assertTrue(stereoElement instanceof ITetrahedralChirality);
ITetrahedralChirality l4Chiral = (ITetrahedralChirality)stereoElement;
Assert.assertEquals("C", l4Chiral.getChiralAtom().getSymbol());
if (l4Chiral.getStereo() == Stereo.CLOCKWISE) {
IAtom[] ligands = l4Chiral.getLigands();
Expand Down
14 changes: 7 additions & 7 deletions src/test/org/openscience/cdk/stereo/LigancyFourChiralityTest.java
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Expand Up @@ -32,7 +32,7 @@
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IBond.Order;
import org.openscience.cdk.interfaces.ILigancyFourChirality.Stereo;
import org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo;

/**
* @cdk.module test-data
Expand Down Expand Up @@ -64,15 +64,15 @@ public static void setup() throws Exception {

@Test
public void testLigancyFourChirality_IAtom_arrayIAtom_ILigancyFourChirality_STEREO() {
LigancyFourChirality chirality = new LigancyFourChirality(
TetrahedralChirality chirality = new TetrahedralChirality(
molecule.getAtom(1), ligands, Stereo.CLOCKWISE
);
Assert.assertNotNull(chirality);
}

@Test
public void testGetBuilder() {
LigancyFourChirality chirality = new LigancyFourChirality(
TetrahedralChirality chirality = new TetrahedralChirality(
molecule.getAtom(1), ligands, Stereo.CLOCKWISE
);
Assert.assertEquals(
Expand All @@ -83,7 +83,7 @@ public void testGetBuilder() {

@Test
public void testGetChiralAtom() {
LigancyFourChirality chirality = new LigancyFourChirality(
TetrahedralChirality chirality = new TetrahedralChirality(
molecule.getAtom(1), ligands, Stereo.CLOCKWISE
);
Assert.assertNotNull(chirality);
Expand All @@ -92,20 +92,20 @@ public void testGetChiralAtom() {

@Test
public void testGetStereo() {
LigancyFourChirality chirality = new LigancyFourChirality(
TetrahedralChirality chirality = new TetrahedralChirality(
molecule.getAtom(1), ligands, Stereo.CLOCKWISE
);
Assert.assertNotNull(chirality);
Assert.assertEquals(molecule.getAtom(1), chirality.getChiralAtom());
for (int i=0; i<ligands.length; i++) {
Assert.assertEquals(ligands[i], chirality.getLigands()[i]);
}
Assert.assertEquals(LigancyFourChirality.Stereo.CLOCKWISE, chirality.getStereo());
Assert.assertEquals(TetrahedralChirality.Stereo.CLOCKWISE, chirality.getStereo());
}

@Test
public void testGetLigandAtoms() {
LigancyFourChirality chirality = new LigancyFourChirality(
TetrahedralChirality chirality = new TetrahedralChirality(
molecule.getAtom(1), ligands, Stereo.CLOCKWISE
);
Assert.assertNotNull(chirality);
Expand Down

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