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[Cdk-commits] SF.net SVN: cdk: [7788] trunk/cdk/src
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From: <sh...@us...> - 2007-01-31 13:42:31
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Revision: 7788
http://svn.sourceforge.net/cdk/?rev=7788&view=rev
Author: shk3
Date: 2007-01-31 05:42:28 -0800 (Wed, 31 Jan 2007)
Log Message:
-----------
more tests for BondTools
Modified Paths:
--------------
trunk/cdk/src/org/openscience/cdk/test/geometry/BondToolsTest.java
trunk/cdk/src/org/openscience/cdk/test/smiles/SmilesGeneratorTest.java
Added Paths:
-----------
trunk/cdk/src/data/mdl/squareplanar.mol
trunk/cdk/src/data/mdl/tetrahedral_1_lazy.mol
trunk/cdk/src/data/mdl/tetrahedral_with_four_wedges.mol
trunk/cdk/src/data/mdl/trigonal_bipyramidal.mol
Added: trunk/cdk/src/data/mdl/squareplanar.mol
===================================================================
--- trunk/cdk/src/data/mdl/squareplanar.mol (rev 0)
+++ trunk/cdk/src/data/mdl/squareplanar.mol 2007-01-31 13:42:28 UTC (rev 7788)
@@ -0,0 +1,15 @@
+
+ CDK 1/31/07,13:54
+
+ 5 4 0 0 0 0 0 0 0 0999 V2000
+ 259.0000 1023.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 295.0000 1023.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 241.0000 991.8231 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 223.0000 1023.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 277.0000 1054.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 1 0 0 0
+ 1 3 1 1 0 0 0
+ 1 4 1 6 0 0 0
+ 1 5 1 6 0 0 0
+M END
+
Added: trunk/cdk/src/data/mdl/tetrahedral_1_lazy.mol
===================================================================
--- trunk/cdk/src/data/mdl/tetrahedral_1_lazy.mol (rev 0)
+++ trunk/cdk/src/data/mdl/tetrahedral_1_lazy.mol 2007-01-31 13:42:28 UTC (rev 7788)
@@ -0,0 +1,14 @@
+
+ CDK 1/31/07,13:9
+
+ 5 4 0 0 0 0 0 0 0 0999 V2000
+ 259.0000 1023.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 295.0000 1023.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 241.0000 1054.1769 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 241.0000 991.8231 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 223.0000 1023.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 3 1 0 0 0 0
+ 1 4 1 1 0 0 0
+ 1 5 1 0 0 0 0
+M END
Added: trunk/cdk/src/data/mdl/tetrahedral_with_four_wedges.mol
===================================================================
--- trunk/cdk/src/data/mdl/tetrahedral_with_four_wedges.mol (rev 0)
+++ trunk/cdk/src/data/mdl/tetrahedral_with_four_wedges.mol 2007-01-31 13:42:28 UTC (rev 7788)
@@ -0,0 +1,14 @@
+
+ CDK 1/31/07,14:22
+
+ 5 4 0 0 0 0 0 0 0 0999 V2000
+ 440.0000 621.6769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 476.0000 621.6769 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 422.0000 652.8538 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 422.0000 590.5000 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 404.0000 621.6769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 6 0 0 0
+ 1 3 1 1 0 0 0
+ 1 4 1 1 0 0 0
+ 1 5 1 6 0 0 0
+M END
Added: trunk/cdk/src/data/mdl/trigonal_bipyramidal.mol
===================================================================
--- trunk/cdk/src/data/mdl/trigonal_bipyramidal.mol (rev 0)
+++ trunk/cdk/src/data/mdl/trigonal_bipyramidal.mol 2007-01-31 13:42:28 UTC (rev 7788)
@@ -0,0 +1,16 @@
+
+ CDK 1/31/07,13:48
+
+ 6 5 0 0 0 0 0 0 0 0999 V2000
+ 259.0000 1023.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 295.0000 1023.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
+ 241.0000 1054.1769 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
+ 241.0000 991.8231 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
+ 223.0000 1023.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
+ 277.0000 1054.0000 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
+ 1 2 1 0 0 0 0
+ 1 3 1 0 0 0 0
+ 1 4 1 1 0 0 0
+ 1 5 1 6 0 0 0
+ 1 6 1 0 0 0 0
+M END
Modified: trunk/cdk/src/org/openscience/cdk/test/geometry/BondToolsTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/geometry/BondToolsTest.java 2007-01-31 12:55:34 UTC (rev 7787)
+++ trunk/cdk/src/org/openscience/cdk/test/geometry/BondToolsTest.java 2007-01-31 13:42:28 UTC (rev 7788)
@@ -22,6 +22,8 @@
import java.io.InputStream;
+import javax.vecmath.Point3d;
+
import junit.framework.Test;
import junit.framework.TestSuite;
@@ -109,6 +111,127 @@
fail(exc.getMessage());
}
}
+
+
+ public void testCloseEnoughToBond_IAtom_IAtom_double(){
+ try{
+ String filename = "data/mdl/testdoublebondconfig.mol";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ IMolecule mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ mol.getAtom(0).setPoint3d(new Point3d(mol.getAtom(0).getPoint2d().x,mol.getAtom(0).getPoint2d().y,0));
+ mol.getAtom(1).setPoint3d(new Point3d(mol.getAtom(1).getPoint2d().x,mol.getAtom(1).getPoint2d().y,0));
+ mol.getAtom(8).setPoint3d(new Point3d(mol.getAtom(8).getPoint2d().x,mol.getAtom(8).getPoint2d().y,0));
+ assertTrue(BondTools.closeEnoughToBond(mol.getAtom(0),mol.getAtom(1),1));
+ assertFalse(BondTools.closeEnoughToBond(mol.getAtom(0),mol.getAtom(8),1));
+ } catch (Exception exc) {
+ exc.printStackTrace();
+ fail(exc.getMessage());
+ }
+ }
+
+ public void testGiveAngleBothMethods_Point2d_Point2d_Point2d_boolean(){
+ try{
+ String filename = "data/mdl/testdoublebondconfig.mol";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ IMolecule mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertEquals(2.0943946986086157,BondTools.giveAngleBothMethods(mol.getAtom(0).getPoint2d(),mol.getAtom(2).getPoint2d(),mol.getAtom(3).getPoint2d(),true),0.2);
+ assertEquals(2.0943946986086157,BondTools.giveAngleBothMethods(mol.getAtom(0).getPoint2d(),mol.getAtom(2).getPoint2d(),mol.getAtom(3).getPoint2d(),false),0.2);
+ } catch (Exception exc) {
+ exc.printStackTrace();
+ fail(exc.getMessage());
+ }
+ }
+
+ public void testIsTetrahedral_IAtomContainer_IAtom_boolean(){
+ try{
+ String filename = "data/mdl/tetrahedral_1.mol";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ IMolecule mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertEquals(BondTools.isTetrahedral(mol,mol.getAtom(0),true),1);
+ assertEquals(BondTools.isTetrahedral(mol,mol.getAtom(1),true),0);
+ filename = "data/mdl/tetrahedral_1_lazy.mol";
+ ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ reader = new MDLV2000Reader(ins);
+ chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertEquals(BondTools.isTetrahedral(mol,mol.getAtom(0),true),0);
+ assertEquals(BondTools.isTetrahedral(mol,mol.getAtom(0),false),3);
+ } catch (Exception exc) {
+ exc.printStackTrace();
+ fail(exc.getMessage());
+ }
+ }
+
+ public void testIsTrigonalBipyramidalOrOctahedral_IAtomContainer_IAtom(){
+ try{
+ String filename = "data/mdl/trigonal_bipyramidal.mol";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ IMolecule mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertEquals(BondTools.isTrigonalBipyramidalOrOctahedral(mol,mol.getAtom(0)),1);
+ assertEquals(BondTools.isTrigonalBipyramidalOrOctahedral(mol,mol.getAtom(1)),0);
+ } catch (Exception exc) {
+ exc.printStackTrace();
+ fail(exc.getMessage());
+ }
+ }
+
+ public void testIsStereo_IAtomContainer_IAtom(){
+ try{
+ String filename = "data/mdl/trigonal_bipyramidal.mol";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ IMolecule mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertTrue(BondTools.isStereo(mol,mol.getAtom(0)));
+ assertFalse(BondTools.isStereo(mol,mol.getAtom(1)));
+ } catch (Exception exc) {
+ exc.printStackTrace();
+ fail(exc.getMessage());
+ }
+ }
+
+ public void testIsSquarePlanar_IAtomContainer_IAtom(){
+ try{
+ String filename = "data/mdl/squareplanar.mol";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ IMolecule mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertTrue(BondTools.isSquarePlanar(mol,mol.getAtom(0)));
+ assertFalse(BondTools.isSquarePlanar(mol,mol.getAtom(1)));
+ } catch (Exception exc) {
+ exc.printStackTrace();
+ fail(exc.getMessage());
+ }
+ }
+
+ public void testStereosAreOpposite_IAtomContainer_IAtom(){
+ try{
+ String filename = "data/mdl/squareplanar.mol";
+ InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ MDLV2000Reader reader = new MDLV2000Reader(ins);
+ ChemFile chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ IMolecule mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertFalse(BondTools.stereosAreOpposite(mol,mol.getAtom(0)));
+ filename = "data/mdl/tetrahedral_with_four_wedges.mol";
+ ins = this.getClass().getClassLoader().getResourceAsStream(filename);
+ reader = new MDLV2000Reader(ins);
+ chemFile = (ChemFile)reader.read((ChemObject)new ChemFile());
+ mol=chemFile.getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ assertTrue(BondTools.stereosAreOpposite(mol,mol.getAtom(0)));
+ } catch (Exception exc) {
+ exc.printStackTrace();
+ fail(exc.getMessage());
+ }
+ }
}
Modified: trunk/cdk/src/org/openscience/cdk/test/smiles/SmilesGeneratorTest.java
===================================================================
--- trunk/cdk/src/org/openscience/cdk/test/smiles/SmilesGeneratorTest.java 2007-01-31 12:55:34 UTC (rev 7787)
+++ trunk/cdk/src/org/openscience/cdk/test/smiles/SmilesGeneratorTest.java 2007-01-31 13:42:28 UTC (rev 7788)
@@ -180,10 +180,10 @@
String smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
assertNotNull(smiles1);
assertEquals("[H]OC(=O)[C@](F)(N([H])[H])C([H])([H])[H]", smiles1);
+
+ //by setting additional stereo descriptors, we should get another smiles
mol1.getBond(1).setStereo(CDKConstants.STEREO_BOND_DOWN);
mol1.getBond(2).setStereo(CDKConstants.STEREO_BOND_UP);
-
- // what is tested below?
smiles1 = sg.createSMILES(mol1, true, new boolean[mol1.getBondCount()]);
assertNotNull(smiles1);
assertEquals("[H]OC(=O)[C@](F)(C([H])([H])[H])N([H])[H]", smiles1);
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