From: <eg...@us...> - 2006-05-12 06:56:20
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Revision: 6239 Author: egonw Date: 2006-05-11 23:56:11 -0700 (Thu, 11 May 2006) ViewCVS: http://svn.sourceforge.net/cdk/?rev=6239&view=rev Log Message: ----------- Moved RebondTool to standard module Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/graph/rebond/RebondTool.java trunk/cdk/src/org/openscience/cdk/test/MstandardTests.java trunk/cdk/src/org/openscience/cdk/test/graph/rebond/RebondToolTest.java trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java Modified: trunk/cdk/src/org/openscience/cdk/graph/rebond/RebondTool.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/graph/rebond/RebondTool.java 2006-05-11 21:10:57 UTC (rev 6238) +++ trunk/cdk/src/org/openscience/cdk/graph/rebond/RebondTool.java 2006-05-12 06:56:11 UTC (rev 6239) @@ -40,12 +40,13 @@ * atom types are configured such that the covalent bond radii * for all atoms are set. The AtomTypeFactory can be used for this. * - * @cdk.keyword rebonding - * @cdk.keyword bond, recalculation - * @cdk.dictref blue-obelisk:rebondFrom3DCoordinates + * @cdk.keyword rebonding + * @cdk.keyword bond, recalculation + * @cdk.dictref blue-obelisk:rebondFrom3DCoordinates * - * @author Miguel Howard + * @author Miguel Howard * @cdk.created 2003-05-23 + * @cdk.module standard * * @see org.openscience.cdk.graph.rebond.Bspt */ Modified: trunk/cdk/src/org/openscience/cdk/test/MstandardTests.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/MstandardTests.java 2006-05-11 21:10:57 UTC (rev 6238) +++ trunk/cdk/src/org/openscience/cdk/test/MstandardTests.java 2006-05-12 06:56:11 UTC (rev 6239) @@ -34,6 +34,7 @@ import org.openscience.cdk.test.geometry.GeometryToolsTest; import org.openscience.cdk.test.graph.ConnectivityCheckerTest; import org.openscience.cdk.test.graph.PathToolsTest; +import org.openscience.cdk.test.graph.rebond.RebondToolTest; import org.openscience.cdk.test.isomorphism.IsomorphismTesterTest; import org.openscience.cdk.test.isomorphism.UniversalIsomorphismTesterTest; import org.openscience.cdk.test.math.MathToolsTest; @@ -89,6 +90,7 @@ suite.addTest(RingSetManipulatorTest.suite()); suite.addTest(SetOfAtomContainersManipulatorTest.suite()); suite.addTest(SetOfMoleculesManipulatorTest.suite()); + suite.addTest(RebondToolTest.suite()); return suite; } Modified: trunk/cdk/src/org/openscience/cdk/test/graph/rebond/RebondToolTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/graph/rebond/RebondToolTest.java 2006-05-11 21:10:57 UTC (rev 6238) +++ trunk/cdk/src/org/openscience/cdk/test/graph/rebond/RebondToolTest.java 2006-05-12 06:56:11 UTC (rev 6239) @@ -38,7 +38,7 @@ /** * Checks the funcitonality of the RebondTool. * - * @cdk.module test-extra + * @cdk.module test-standard */ public class RebondToolTest extends CDKTestCase { Modified: trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2006-05-11 21:10:57 UTC (rev 6238) +++ trunk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java 2006-05-12 06:56:11 UTC (rev 6239) @@ -35,9 +35,17 @@ import org.openscience.cdk.BioPolymer; import org.openscience.cdk.ChemFile; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBioPolymer; +import org.openscience.cdk.interfaces.IChemFile; +import org.openscience.cdk.interfaces.IChemModel; +import org.openscience.cdk.interfaces.IChemSequence; import org.openscience.cdk.io.IChemObjectReader; import org.openscience.cdk.io.PDBReader; +import org.openscience.cdk.nonotify.NNChemFile; import org.openscience.cdk.protein.data.PDBAtom; +import org.openscience.cdk.tools.manipulator.ChemFileManipulator; /** * TestCase for the PDBReader class. @@ -74,36 +82,26 @@ IChemObjectReader oReader = new PDBReader(ins); assertNotNull(oReader); - ChemFile oChemFile = (ChemFile)oReader.read(new ChemFile()); + IChemFile oChemFile = (IChemFile)oReader.read(new NNChemFile()); assertNotNull(oChemFile); assertEquals(oChemFile.getChemSequenceCount(), 1); - oChemFile.setProperty(new String("test.chemfile"), new String("test.chemfile")); - assertEquals(new String("test.chemfile"), oChemFile.getProperty("test.chemfile")); - - org.openscience.cdk.interfaces.IChemSequence oSeq = oChemFile.getChemSequence(0); + IChemSequence oSeq = oChemFile.getChemSequence(0); assertNotNull(oSeq); assertEquals(oSeq.getChemModelCount(), 1); - oSeq.setProperty(new String("test.chemsequence"), new String("test.chemsequence")); - assertEquals(new String("test.chemsequence"), oSeq.getProperty("test.chemsequence")); - - org.openscience.cdk.interfaces.IChemModel oModel = oSeq.getChemModel(0); + IChemModel oModel = oSeq.getChemModel(0); assertNotNull(oModel); assertEquals(1, oModel.getSetOfMolecules().getMoleculeCount()); - oModel.setProperty(new String("test.chemmodel"), new String("test.chemmodel")); - assertEquals(new String("test.chemmodel"), oModel.getProperty("test.chemmodel")); - - BioPolymer oMol = (BioPolymer)oModel.getSetOfMolecules().getMolecule(0); + IAtomContainer container = oModel.getSetOfMolecules().getMolecule(0); + assertTrue(container instanceof IBioPolymer); + IBioPolymer oMol = (IBioPolymer)container; assertNotNull(oMol); assertEquals(oMol.getAtomCount(), 14); assertNotNull(oMol.getMonomer("MOLA1", "A")); - oMol.setProperty(new String("test.molecule"), new String("test.molecule")); - assertEquals(new String("test.molecule"), oMol.getProperty("test.molecule")); - - org.openscience.cdk.interfaces.IAtom nAtom = oMol.getFirstAtom(); + IAtom nAtom = oMol.getFirstAtom(); assertNotNull(nAtom); assertTrue(nAtom instanceof PDBAtom); PDBAtom oAtom = (PDBAtom)nAtom; @@ -154,7 +152,7 @@ IChemObjectReader reader = new PDBReader(ins); assertNotNull(reader); - ChemFile chemFile = (ChemFile) reader.read(new ChemFile()); + ChemFile chemFile = (ChemFile) reader.read(new NNChemFile()); assertNotNull(chemFile); assertEquals(1, chemFile.getChemSequenceCount()); @@ -162,11 +160,13 @@ assertNotNull(seq); assertEquals(1, seq.getChemModelCount()); - org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0); + IChemModel model = seq.getChemModel(0); assertNotNull(model); assertEquals(1, model.getSetOfMolecules().getMoleculeCount()); - BioPolymer mol = (BioPolymer) model.getSetOfMolecules().getMolecule(0); + IAtomContainer container = model.getSetOfMolecules().getMolecule(0); + assertTrue(container instanceof IBioPolymer); + IBioPolymer mol = (IBioPolymer)container; assertNotNull(mol); assertEquals(327, mol.getAtomCount()); assertEquals(46, mol.getMonomerCount()); @@ -175,7 +175,7 @@ assertNotNull(mol.getMonomer("ILEA7", "A")); assertEquals(8, mol.getMonomer("ILEA7", "A").getAtomCount()); - org.openscience.cdk.interfaces.IAtom nAtom = mol.getAtomAt(94); + IAtom nAtom = mol.getAtomAt(94); assertNotNull(nAtom); assertTrue(nAtom instanceof PDBAtom); PDBAtom atom = (PDBAtom)nAtom; @@ -199,4 +199,39 @@ fail(ex.toString()); } } + + public void test114D() { + String filename = "data/pdb/114D.pdb"; + InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename); + + try { + IChemObjectReader reader = new PDBReader(ins); + assertNotNull(reader); + + IChemFile chemFile = (IChemFile) reader.read(new NNChemFile()); + assertNotNull(chemFile); + assertEquals(1, chemFile.getChemSequenceCount()); + + org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0); + assertNotNull(seq); + assertEquals(1, seq.getChemModelCount()); + + IChemModel model = seq.getChemModel(0); + assertNotNull(model); + assertEquals(1, model.getSetOfMolecules().getMoleculeCount()); + + IAtomContainer container = model.getSetOfMolecules().getMolecule(0); + assertTrue(container instanceof IBioPolymer); + IBioPolymer polymer = (IBioPolymer)container; + + // chemical validation + assertEquals(552, ChemFileManipulator.getAtomCount(chemFile)); + assertEquals(2, polymer.getStrandCount()); + assertEquals(24, polymer.getMonomerCount()); + + } catch (Exception ex) { + fail(ex.toString()); + } + } + } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |