@Test public void testGetAtomCount_IChemFile() { int count = ChemFileManipulator.getAtomCount(chemFile); Assert.assertEquals(6, count); }
@Test public void testMixedNamespaces() throws Exception { InputStream in = getClass().getResourceAsStream("US06358966-20020319-C00001-enr.cml"); CMLReader reader = new CMLReader(in); try { IChemFile cfile = reader.read(DefaultChemObjectBuilder.getInstance().newInstance(IChemFile.class)); Assert.assertEquals(34, ChemFileManipulator.getAtomCount(cfile)); Assert.assertEquals(39, ChemFileManipulator.getBondCount(cfile)); } finally { reader.close(); } } }
void assertAtomCount(int expectedAtomCount, IChemObject chemObject) { if (expectedAtomCount != -1) { if (chemObject instanceof IChemFile) { Assert.assertEquals(expectedAtomCount, ChemFileManipulator.getAtomCount((IChemFile) chemObject)); } else if (chemObject instanceof IChemModel) { Assert.assertEquals(expectedAtomCount, ChemModelManipulator.getAtomCount((IChemModel) chemObject)); } else if (chemObject instanceof IAtomContainer) { Assert.assertEquals(expectedAtomCount, ((IAtomContainer) chemObject).getAtomCount()); } else if (chemObject instanceof IReaction) { Assert.assertEquals(expectedAtomCount, ReactionManipulator.getAtomCount((IReaction) chemObject)); } } }
public void testObjectCountsChemFile(IChemFile chemFile, int chemSequenceCount, int chemModelCount, int moleculeCount, int atomCount, int strandCount, int monomerCount, int structureCount) throws Exception { IAtomContainer container = getFirstAtomContainer(chemFile, chemSequenceCount, chemModelCount, moleculeCount); Assert.assertTrue(container instanceof IBioPolymer); IBioPolymer polymer = (IBioPolymer) container; // chemical validation Assert.assertEquals(atomCount, ChemFileManipulator.getAtomCount(chemFile)); Assert.assertEquals(strandCount, polymer.getStrandCount()); Assert.assertEquals(monomerCount, polymer.getMonomerCount()); Assert.assertTrue(polymer instanceof PDBPolymer); PDBPolymer pdb = (PDBPolymer) polymer; // PDB validation Assert.assertEquals(structureCount, pdb.getStructures().size()); }
Assert.assertEquals(552, ChemFileManipulator.getAtomCount(chemFile)); Assert.assertEquals(2, polymer.getStrandCount()); Assert.assertEquals(24, polymer.getMonomerCount());