/** @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);
}
}
/**
* Gets the mol file from a specified KEGG ID.
*
* @param accessionID the accession id (e.g. C00509)
* @return the string
* @throws CDKException
*/
public static IAtomContainer getMol(String accessionID, String keggPath, boolean getAll)
throws CDKException {
String ret = "";
try {
KEGGLocator locator = new KEGGLocator();
KEGGPortType serv = locator.getKEGGPort();
// get molecule by accession ID
String str = "-f m cpd:" + accessionID;
boolean webservice = false;
String mol = "";
try {
// Open the file that is the first
// command line parameter
FileInputStream fstream = new FileInputStream(keggPath + accessionID + ".mol");
// Get the object of DataInputStream
DataInputStream in = new DataInputStream(fstream);
BufferedReader br = new BufferedReader(new InputStreamReader(in));
// Read File Line By Line
String line;
while ((line = br.readLine()) != null) {
// Print the content on the console
mol += line + "\n";
}
// Close the input stream
in.close();
} catch (FileNotFoundException e) {
webservice = true;
}
// if this file is not found use webservice...otherwise use local molfile
if (webservice) ret = serv.bget(str);
else ret = mol;
} catch (Exception e) {
System.err.println(e.toString());
}
MDLReader reader;
List<IAtomContainer> containersList;
reader = new MDLReader(new StringReader(ret));
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IAtomContainer molecule = containersList.get(0);
if (getAll) return molecule;
if (!MolecularFormulaTools.isBiologicalCompound(molecule)) molecule = null;
return molecule;
}
/*
* @cdk.bug 1241421
*/
@Test
public void testModelBuilder3D_bug_1241421() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/bug1241421.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
ac = mb3d.generate3DCoordinates(ac, false);
checkAverageBondLength(ac);
}
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");
}
@Test
public void testModelBuilder3D_reserpine() throws Exception {
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/reserpine.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
ac = mb3d.generate3DCoordinates(ac, false);
for (int i = 0; i < ac.getAtomCount(); i++) {
Assert.assertNotNull(ac.getAtom(i).getPoint3d());
}
checkAverageBondLength(ac);
}
/** @cdk.bug 1315823 */
@Test
public void testModelBuilder3D_232() throws Exception {
Assume.assumeTrue(runSlowTests());
ModelBuilder3D mb3d = ModelBuilder3D.getInstance();
String filename = "data/mdl/allmol232.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins);
ChemFile chemFile = (ChemFile) reader.read((ChemObject) new ChemFile());
List containersList = ChemFileManipulator.getAllAtomContainers(chemFile);
IMolecule ac = new NNMolecule((IAtomContainer) containersList.get(0));
addExplicitHydrogens(ac);
ac = mb3d.generate3DCoordinates(ac, false);
Assert.assertNotNull(ac.getAtom(0).getPoint3d());
checkAverageBondLength(ac);
}
/**
* 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 checkUniqueMolecularDescriptorNames() throws Exception {
DescriptorEngine engine = new DescriptorEngine(DescriptorEngine.MOLECULAR);
List<DescriptorSpecification> specs = engine.getDescriptorSpecifications();
// we work with a simple molecule with 3D coordinates
String filename = "data/mdl/lobtest2.sdf";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
ISimpleChemObjectReader reader = new MDLV2000Reader(ins);
ChemFile content = (ChemFile) reader.read(new ChemFile());
List cList = ChemFileManipulator.getAllAtomContainers(content);
IAtomContainer ac = (IAtomContainer) cList.get(0);
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(ac);
engine.process(ac);
int ncalc = 0;
List<String> descNames = new ArrayList<String>();
for (DescriptorSpecification spec : specs) {
DescriptorValue value = (DescriptorValue) ac.getProperty(spec);
if (value == null) continue;
ncalc++;
String[] names = value.getNames();
descNames.addAll(Arrays.asList(names));
}
List<String> dups = new ArrayList<String>();
Set<String> uniqueNames = new HashSet<String>();
for (String name : descNames) {
if (!uniqueNames.add(name)) dups.add(name);
}
Assert.assertEquals(specs.size(), ncalc);
Assert.assertEquals(descNames.size(), uniqueNames.size());
if (dups.size() != 0) {
System.out.println("Following names were duplicated");
for (String dup : dups) {
System.out.println("dup = " + dup);
}
}
}
@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);
}
/**
* Loads one or more files into IAtomContainer objects.
*
* <p>This method does not need knowledge of the format since it is autodetected. Note that if
* aromaticity detection or atom typing is specified and fails for a specific molecule, that
* molecule will be set to <i>null</i>
*
* @param filenames An array of String's containing the filenames of the structures we want to
* load
* @param doAromaticity If true, then aromaticity perception is performed
* @param doTyping If true, atom typing and configuration is performed. This will use the internal
* CDK atom typing scheme
* @return An array of AtoContainer's
* @throws CDKException if there is an error when reading a file
*/
public static IAtomContainer[] loadMolecules(
String[] filenames, boolean doAromaticity, boolean doTyping, boolean doIsotopes)
throws CDKException, IOException {
Vector<IAtomContainer> v = new Vector<IAtomContainer>();
IChemObjectBuilder builder = DefaultChemObjectBuilder.getInstance();
try {
int i;
int j;
for (i = 0; i < filenames.length; i++) {
File input = new File(filenames[i]);
ReaderFactory readerFactory = new ReaderFactory();
ISimpleChemObjectReader reader = readerFactory.createReader(new FileReader(input));
if (reader == null) { // see if it's a SMI file
if (filenames[i].endsWith(".smi")) {
reader = new SMILESReader(new FileReader(input));
}
}
IChemFile content = (IChemFile) reader.read(builder.newInstance(IChemFile.class));
if (content == null) continue;
List<IAtomContainer> c = ChemFileManipulator.getAllAtomContainers(content);
// we should do this loop in case we have files
// that contain multiple molecules
v.addAll(c);
}
} catch (Exception e) {
e.printStackTrace();
throw new CDKException(e.toString());
}
// convert the vector to a simple array
IAtomContainer[] retValues = new IAtomContainer[v.size()];
for (int i = 0; i < v.size(); i++) {
retValues[i] = v.get(i);
}
// before returning, lets make see if we
// need to perceive aromaticity and atom typing
if (doAromaticity) {
for (int i = 0; i < retValues.length; i++) {
try {
CDKHueckelAromaticityDetector.detectAromaticity(retValues[i]);
} catch (CDKException e) {
retValues[i] = null;
}
}
}
if (doTyping) {
for (int i = 0; i < retValues.length; i++) {
try {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(retValues[i]);
} catch (CDKException e) {
retValues[i] = null;
}
}
}
if (doIsotopes) {
IsotopeFactory ifac = IsotopeFactory.getInstance(DefaultChemObjectBuilder.getInstance());
for (IAtomContainer retValue : retValues) {
ifac.configureAtoms(retValue);
}
}
return retValues;
}