From: Egon W. <eg...@us...> - 2005-02-03 21:10:23
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/test/io In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv30967/src/org/openscience/cdk/test/io Modified Files: PDBReaderTest.java Log Message: Applied patch by Martin Eklund that adds a Strand layer between Polymer and Monomer. A CDK Polymer practically maps to a protein, hence the extension. Index: PDBReaderTest.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/test/io/PDBReaderTest.java,v retrieving revision 1.11 retrieving revision 1.12 diff -u -r1.11 -r1.12 --- PDBReaderTest.java 12 Jan 2005 15:22:08 -0000 1.11 +++ PDBReaderTest.java 3 Feb 2005 21:10:13 -0000 1.12 @@ -37,6 +37,7 @@ import org.openscience.cdk.Atom; import org.openscience.cdk.BioPolymer; +import org.openscience.cdk.Bond; import org.openscience.cdk.ChemFile; import org.openscience.cdk.ChemModel; import org.openscience.cdk.ChemSequence; @@ -117,7 +118,7 @@ BioPolymer oMol = (BioPolymer)oModel.getSetOfMolecules().getMolecule(0); assertNotNull(oMol); assertEquals(oMol.getAtomCount(), 14); - assertNotNull(oMol.getMonomer("MOL1")); + assertNotNull(oMol.getMonomer("MOL1", "A")); oMol.setProperty(new String("test.molecule"), new String("test.molecule")); assertEquals(new String("test.molecule"), oMol.getProperty("test.molecule")); @@ -201,10 +202,10 @@ assertNotNull(mol); assertEquals(327, mol.getAtomCount()); assertEquals(46, mol.getMonomerCount()); - assertNotNull(mol.getMonomer("THR1")); - assertEquals(7, mol.getMonomer("THR1").getAtomCount()); - assertNotNull(mol.getMonomer("ILE7")); - assertEquals(8, mol.getMonomer("ILE7").getAtomCount()); + assertNotNull(mol.getMonomer("THR1", "A")); + assertEquals(7, mol.getMonomer("THR1", "A").getAtomCount()); + assertNotNull(mol.getMonomer("ILE7", "A")); + assertEquals(8, mol.getMonomer("ILE7", "A").getAtomCount()); Atom atom = mol.getAtomAt(94); assertNotNull(atom); @@ -221,6 +222,14 @@ assertEquals(null, atom.getProperty("pdb.segID")); assertEquals(null, atom.getProperty("pdb.element")); assertEquals(null, atom.getProperty("pdb.charge")); + + Bond bond = mol.getBondAt(95); + assertNotNull(bond); + assertEquals("Test failed. Bond order not the same.", 2.0, bond.getOrder(), 0.001); + Atom[] atoms = bond.getAtoms(); + assertEquals("C", atoms[0].getSymbol()); + assertEquals("C", atoms[1].getSymbol()); + assertEquals(null, bond.getProperties()); } catch (Exception ex) { fail(ex.toString()); |