/** @cdk.bug 1535055 */
@Test
public void testBug1535055() throws Exception {
SmilesParser sp = new SmilesParser(DefaultChemObjectBuilder.getInstance());
IAtomContainer mol = sp.parseSmiles("COC(=O)c1ccc2c(c1)c1ccccc1[nH]2");
CDKHueckelAromaticityDetector.detectAromaticity(mol);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol);
SmilesGenerator sg = new SmilesGenerator();
sg.setUseAromaticityFlag(true);
String s1 = sg.createSMILES(mol);
String filename = "data/cml/bug1535055.cml";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
CMLReader reader = new CMLReader(ins);
IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
// test the resulting ChemFile content
Assert.assertNotNull(chemFile);
IAtomContainer mol2 = ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
CDKHueckelAromaticityDetector.detectAromaticity(mol2);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol2);
String s2 = sg.createSMILES(mol2);
Assert.assertTrue(s1.contains("[nH]"));
Assert.assertTrue(s2.contains("[nH]"));
}
/**
* Sets the given cml. Does not update other fields like for example smiles
*
* @param cml
*/
public void setCML(String cml) {
InputStream inputStream = new ByteArrayInputStream(cml.getBytes());
CMLReader cmlReader = new CMLReader(inputStream);
try {
IChemFile readFile = (IChemFile) cmlReader.read(new ChemFile());
setAtomContainer((AtomContainer) ChemFileManipulator.getAllAtomContainers(readFile).get(0));
} catch (CDKException e) {
throw new RuntimeException("failed to read atomContainer", e);
}
}
public IAtomContainer getAtomContainer() {
if (atomContainer == null) {
InputStream in = FileStoreKeeper.FILE_STORE.retrieve(fileStoreKey);
CMLReader cmlReader = new CMLReader(in);
try {
IChemFile readFile = (IChemFile) cmlReader.read(new ChemFile());
setAtomContainer((AtomContainer) ChemFileManipulator.getAllAtomContainers(readFile).get(0));
} catch (CDKException e) {
throw new RuntimeException("failed to read atomContainer", e);
}
}
return atomContainer;
}
/**
* A unit test for JUnit
*
* @exception Exception Description of the Exception
*/
@Test
public void testResolveOverlap2() throws Exception {
logger.debug("Test case with neither bond nor atom overlap");
String filename = "data/cml/overlaptest2.cml";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
CMLReader reader = new CMLReader(ins);
IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
IAtomContainer atomContainer =
(IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
// MoleculeViewer2D.display(new AtomContainer(atomContainer), false);
double score = new OverlapResolver().getOverlapScore(atomContainer, new Vector(), new Vector());
Assert.assertEquals(0.0, score, 0.0001);
logger.debug("End of test case with neither bond nor atom overlap");
}
/**
* A unit test for JUnit
*
* @exception Exception Description of the Exception
*/
@Test
public void testResolveOverlap4() throws Exception {
double overlapScore = 0;
logger.debug("Test case with atom clash");
String filename = "data/cml/overlaptest.cml";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
CMLReader reader = new CMLReader(ins);
IChemFile chemFile = (IChemFile) reader.read(new ChemFile());
IAtomContainer atomContainer =
(IAtomContainer) ChemFileManipulator.getAllAtomContainers(chemFile).get(0);
// MoleculeViewer2D.display(new AtomContainer(atomContainer), false);
OverlapResolver or = new OverlapResolver();
overlapScore = or.resolveOverlap(atomContainer, null);
// MoleculeViewer2D.display(new AtomContainer(atomContainer), false);
Assert.assertEquals(0.0, overlapScore, 0.0001);
logger.debug("End of test case with atom clash");
}
@Test
public void testMDMoleculeCustomizationRoundtripping() throws Exception {
StringWriter writer = new StringWriter();
CMLWriter cmlWriter = new CMLWriter(writer);
cmlWriter.registerCustomizer(new MDMoleculeCustomizer());
MDMolecule molecule = makeMDBenzene();
cmlWriter.write(molecule);
String serializedMol = writer.toString();
logger.debug("****************************** testMDMoleculeCustomizationRoundtripping()");
logger.debug(serializedMol);
logger.debug("******************************");
logger.debug("****************************** testMDMoleculeCustomization Write first");
logger.debug(serializedMol);
logger.debug("******************************");
CMLReader reader = new CMLReader(new ByteArrayInputStream(serializedMol.getBytes()));
reader.registerConvention("md:mdMolecule", new MDMoleculeConvention(new ChemFile()));
IChemFile file = (IChemFile) reader.read(new ChemFile());
List containers = ChemFileManipulator.getAllAtomContainers(file);
Assert.assertEquals(1, containers.size());
Object molecule2 = containers.get(0);
Assert.assertTrue(molecule2 instanceof MDMolecule);
MDMolecule mdMol = (MDMolecule) molecule2;
Assert.assertEquals(6, mdMol.getAtomCount());
Assert.assertEquals(6, mdMol.getBondCount());
List residues = mdMol.getResidues();
Assert.assertEquals(2, residues.size());
Assert.assertEquals(3, ((Residue) residues.get(0)).getAtomCount());
Assert.assertEquals(3, ((Residue) residues.get(1)).getAtomCount());
Assert.assertEquals("myResidue1", ((Residue) residues.get(0)).getName());
Assert.assertEquals("myResidue2", ((Residue) residues.get(1)).getName());
Assert.assertEquals(0, ((Residue) residues.get(0)).getNumber());
Assert.assertEquals(1, ((Residue) residues.get(1)).getNumber());
List chargeGroup = mdMol.getChargeGroups();
Assert.assertEquals(2, chargeGroup.size());
Assert.assertEquals(2, ((ChargeGroup) chargeGroup.get(0)).getAtomCount());
Assert.assertEquals(4, ((ChargeGroup) chargeGroup.get(1)).getAtomCount());
Assert.assertNotNull(((ChargeGroup) chargeGroup.get(0)).getSwitchingAtom());
Assert.assertEquals("a2", ((ChargeGroup) chargeGroup.get(0)).getSwitchingAtom().getID());
Assert.assertNotNull(((ChargeGroup) chargeGroup.get(1)).getSwitchingAtom());
Assert.assertEquals("a5", ((ChargeGroup) chargeGroup.get(1)).getSwitchingAtom().getID());
Assert.assertEquals(2, ((ChargeGroup) chargeGroup.get(0)).getNumber());
Assert.assertEquals(3, ((ChargeGroup) chargeGroup.get(1)).getNumber());
writer = new StringWriter();
cmlWriter = new CMLWriter(writer);
cmlWriter.registerCustomizer(new MDMoleculeCustomizer());
cmlWriter.write(mdMol);
String serializedMDMol = writer.toString();
logger.debug("****************************** testMDMoleculeCustomizationRoundtripping()");
logger.debug(serializedMol);
logger.debug("******************************");
logger.debug("****************************** testMDMoleculeCustomization Write second");
logger.debug(serializedMDMol);
logger.debug("******************************");
Assert.assertEquals(serializedMol, serializedMDMol);
}
private IChemFile parseCMLString(String cmlString) throws Exception {
IChemFile chemFile = null;
CMLReader reader = new CMLReader(new ByteArrayInputStream(cmlString.getBytes()));
chemFile = (IChemFile) reader.read(new org.openscience.cdk.ChemFile());
return chemFile;
}