/**
* Creates a bucky ball molecule.
*
* @return bucky ball molecule
*/
private IAtomContainer createBuckyBall() throws CDKException {
IAtomContainer molecule = null;
String filename = "data/mdl/buckyball.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
molecule = (IAtomContainer) reader.read(new AtomContainer());
Assert.assertTrue("Atom count is 60 ", molecule.getAtomCount() == 60);
Assert.assertTrue("Bond count is 90 ", molecule.getBondCount() == 90);
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);
}
/** @cdk.bug 891021 */
@Test
public void testBug891021() throws Exception {
IAtomContainer molecule = null;
String filename = "data/mdl/too.many.rings.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
molecule = (IAtomContainer) reader.read((IChemObject) new AtomContainer());
logger.debug("Testing " + filename);
IRingSet ringSet = new SSSRFinder(molecule).findSSSR();
logger.debug("Found ring set of size: " + ringSet.getAtomContainerCount());
Assert.assertEquals(57, ringSet.getAtomContainerCount());
}
@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);
}
@Test
public void testLoopProblem() throws Exception {
String filename = "data/mdl/ring_03419.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
IAtomContainer molecule = (IAtomContainer) reader.read((IChemObject) new AtomContainer());
logger.debug("Testing " + filename);
IRingSet ringSet = new SSSRFinder(molecule).findSSSR();
logger.debug("Found ring set of size: " + ringSet.getAtomContainerCount());
Assert.assertEquals(12, ringSet.getAtomContainerCount());
for (int f = 0; f < ringSet.getAtomContainerCount(); f++) {
IRing ring = (IRing) ringSet.getAtomContainer(f);
logger.debug("ring: " + toString(ring, molecule));
}
}
/** A unit test for JUnit */
@Test
public void testCycloOctadien() {
try {
String filename = "data/mdl/cyclooctadien.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
IAtomContainer mol1 = reader.read(new AtomContainer());
SmilesGenerator sg = new SmilesGenerator();
String moleculeSmile = sg.createSMILES(mol1);
Assert.assertEquals(moleculeSmile, "C=1CCC=CCCC=1");
} catch (Exception exc) {
exc.printStackTrace();
System.out.println(exc);
Assert.fail(exc.getMessage());
}
}
/**
* A unit test for JUnit
*
* @cdk.bug 1089770
*/
@Test
public void testSFBug1089770_1() {
try {
String filename = "data/mdl/bug1089770-1.mol";
InputStream ins = this.getClass().getClassLoader().getResourceAsStream(filename);
MDLV2000Reader reader = new MDLV2000Reader(ins, Mode.STRICT);
IAtomContainer mol1 = reader.read(new AtomContainer());
SmilesGenerator sg = new SmilesGenerator();
String moleculeSmile = sg.createSMILES(mol1);
// logger.debug(filename + " -> " + moleculeSmile);
Assert.assertEquals(moleculeSmile, "C1CCC=2CCCC=2(C1)");
} catch (Exception exc) {
exc.printStackTrace();
System.out.println(exc);
Assert.fail(exc.getMessage());
}
}
/** Returns true if another IMolecule can be read. */
public boolean hasNext() {
if (!nextAvailableIsKnown) {
hasNext = false;
// now try to parse the next Molecule
try {
if ((currentLine = input.readLine()) != null) {
currentFormat = (IChemFormat) MDLFormat.getInstance();
StringBuffer buffer = new StringBuffer();
while (currentLine != null && !currentLine.equals("M END")) {
// still in a molecule
buffer.append(currentLine);
buffer.append(System.getProperty("line.separator"));
currentLine = input.readLine();
// do MDL molfile version checking
if (currentLine.contains("V2000") || currentLine.contains("v2000")) {
currentFormat = (IChemFormat) MDLV2000Format.getInstance();
} else if (currentLine.contains("V3000") || currentLine.contains("v3000")) {
currentFormat = (IChemFormat) MDLV3000Format.getInstance();
}
}
buffer.append(currentLine);
buffer.append(System.getProperty("line.separator"));
logger.debug("MDL file part read: ", buffer);
ISimpleChemObjectReader reader = factory.createReader(currentFormat);
reader.setReader(new StringReader(buffer.toString()));
if (currentFormat instanceof MDLV2000Format) {
reader.addChemObjectIOListener(this);
((MDLV2000Reader) reader).customizeJob();
}
nextMolecule = (IMolecule) reader.read(builder.newInstance(IMolecule.class));
// note that a molecule may have 0 atoms, but still
// be useful (by having SD tags for example), so just
// check for null'ness rather than atom count
hasNext = nextMolecule != null;
// now read the data part
currentLine = input.readLine();
readDataBlockInto(nextMolecule);
} else {
hasNext = false;
}
} catch (Exception exception) {
logger.error("Error while reading next molecule: " + exception.getMessage());
logger.debug(exception);
hasNext = false;
}
if (!hasNext) nextMolecule = null;
nextAvailableIsKnown = true;
}
return hasNext;
}
/**
* Read a Reaction from a file in MDL RXN format
*
* @return The Reaction that was read from the MDL file.
*/
private IReaction readReaction(IChemObjectBuilder builder) throws CDKException {
IReaction reaction = builder.newReaction();
try {
input.readLine(); // first line should be $RXN
input.readLine(); // second line
input.readLine(); // third line
input.readLine(); // fourth line
} catch (IOException exception) {
logger.debug(exception);
throw new CDKException("Error while reading header of RXN file", exception);
}
int reactantCount = 0;
int productCount = 0;
try {
String countsLine = input.readLine();
/* this line contains the number of reactants
and products */
StringTokenizer tokenizer = new StringTokenizer(countsLine);
reactantCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + reactantCount + " reactants in file");
productCount = Integer.valueOf(tokenizer.nextToken()).intValue();
logger.info("Expecting " + productCount + " products in file");
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while counts line of RXN file", exception);
}
// now read the reactants
try {
for (int i = 1; i <= reactantCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // announceMDLFileLine
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
// Changed this to mdlv2000 reader
MDLV2000Reader reader =
new MDLV2000Reader(new StringReader(molFile.toString()), super.mode);
IMolecule reactant = (IMolecule) reader.read(builder.newMolecule());
// add reactant
reaction.addReactant(reactant);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading reactant", exception);
}
// now read the products
try {
for (int i = 1; i <= productCount; i++) {
StringBuffer molFile = new StringBuffer();
input.readLine(); // String announceMDLFileLine =
String molFileLine = "";
do {
molFileLine = input.readLine();
molFile.append(molFileLine);
molFile.append(System.getProperty("line.separator"));
} while (!molFileLine.equals("M END"));
// read MDL molfile content
MDLV2000Reader reader = new MDLV2000Reader(new StringReader(molFile.toString()));
IMolecule product = (IMolecule) reader.read(builder.newMolecule());
// add reactant
reaction.addProduct(product);
}
} catch (CDKException exception) {
// rethrow exception from MDLReader
throw exception;
} catch (Exception exception) {
logger.debug(exception);
throw new CDKException("Error while reading products", exception);
}
// now try to map things, if wanted
logger.info("Reading atom-atom mapping from file");
// distribute all atoms over two AtomContainer's
IAtomContainer reactingSide = builder.newAtomContainer();
java.util.Iterator molecules = reaction.getReactants().molecules().iterator();
while (molecules.hasNext()) {
reactingSide.add((IMolecule) molecules.next());
}
IAtomContainer producedSide = builder.newAtomContainer();
molecules = reaction.getProducts().molecules().iterator();
while (molecules.hasNext()) {
producedSide.add((IMolecule) molecules.next());
}
// map the atoms
int mappingCount = 0;
// IAtom[] reactantAtoms = reactingSide.getAtoms();
// IAtom[] producedAtoms = producedSide.getAtoms();
for (int i = 0; i < reactingSide.getAtomCount(); i++) {
for (int j = 0; j < producedSide.getAtomCount(); j++) {
IAtom eductAtom = reactingSide.getAtom(i);
IAtom productAtom = producedSide.getAtom(j);
if (eductAtom.getID() != null && eductAtom.getID().equals(productAtom.getID())) {
reaction.addMapping(builder.newMapping(eductAtom, productAtom));
mappingCount++;
break;
}
}
}
logger.info("Mapped atom pairs: " + mappingCount);
return reaction;
}
