@Before
public void setUp() throws Exception {
// cNH
IAtom a2 = new Atom("C");
a2.setImplicitHydrogenCount(0);
a2.setFlag(CDKConstants.ISAROMATIC, true);
IAtom a1 = new Atom("N");
a1.setImplicitHydrogenCount(1);
this.bond1 = new Bond(a1, a2, Order.DOUBLE);
}
@Test
public void methane_Atom() throws Exception {
IAtom a = new Atom("C");
a.setImplicitHydrogenCount(4);
assertThat(new CDKToBeam().toBeamAtom(a).element(), is(Element.Carbon));
assertThat(new CDKToBeam().toBeamAtom(a).hydrogens(), is(4));
}
@Test
public void defaultIsotope() throws Exception {
IAtom a = new Atom("C");
a.setImplicitHydrogenCount(0);
a.setMassNumber(12);
assertThat(new CDKToBeam().toBeamAtom(a).isotope(), is(-1));
}
@Test
public void aromaticAtom() throws Exception {
IAtom a = new Atom("C");
a.setImplicitHydrogenCount(0);
a.setFlag(CDKConstants.ISAROMATIC, true);
assertTrue(new CDKToBeam().toBeamAtom(a).aromatic());
}
@Test
public void water_Atom() throws Exception {
IAtom a = new Atom("O");
a.setImplicitHydrogenCount(2);
assertThat(new CDKToBeam().toBeamAtom(a).element(), is(Element.Oxygen));
assertThat(new CDKToBeam().toBeamAtom(a).hydrogens(), is(2));
}
@Test
public void chargedAtom() throws Exception {
IAtom a = new Atom("C");
a.setImplicitHydrogenCount(0);
for (int chg = -10; chg < 10; chg++) {
a.setFormalCharge(chg);
assertThat(new CDKToBeam().toBeamAtom(a).charge(), is(chg));
}
}
/**
* Applies the MDL valence model to atoms using the explicit valence (bond order sum) and charge
* to determine the correct number of implicit hydrogens. The model is not applied if the explicit
* valence is less than 0 - this is the case when a query bond was read for an atom.
*
* @param atom the atom to apply the model to
* @param explicitValence the explicit valence (bond order sum)
*/
private void applyMDLValenceModel(IAtom atom, int explicitValence) {
if (explicitValence < 0) return;
if (atom.getValency() != null) {
atom.setImplicitHydrogenCount(atom.getValency() - explicitValence);
} else {
Integer element = atom.getAtomicNumber();
if (element == null) return;
Integer charge = atom.getFormalCharge();
if (charge == null) charge = 0;
int implicitValence = MDLValence.implicitValence(element, charge, explicitValence);
atom.setValency(implicitValence);
atom.setImplicitHydrogenCount(implicitValence - explicitValence);
}
}
/** @cdk.inchi InChI=1/C4H5N/c1-2-4-5-3-1/h1-5H */
@Test
public void xtestPyrrole() throws Exception {
IAtomContainer enol = new AtomContainer();
// atom block
IAtom atom1 = new Atom(Elements.CARBON);
atom1.setHybridization(Hybridization.SP2);
IAtom atom2 = new Atom(Elements.CARBON);
atom2.setHybridization(Hybridization.SP2);
IAtom atom3 = new Atom(Elements.CARBON);
atom3.setHybridization(Hybridization.SP2);
IAtom atom4 = new Atom(Elements.CARBON);
atom4.setHybridization(Hybridization.SP2);
IAtom atom5 = new Atom(Elements.NITROGEN);
atom5.setHybridization(Hybridization.SP2);
atom5.setImplicitHydrogenCount(1);
// bond block
IBond bond1 = new Bond(atom1, atom2);
IBond bond2 = new Bond(atom2, atom3);
IBond bond3 = new Bond(atom3, atom4);
IBond bond4 = new Bond(atom4, atom5);
IBond bond5 = new Bond(atom5, atom1);
enol.addAtom(atom1);
enol.addAtom(atom2);
enol.addAtom(atom3);
enol.addAtom(atom4);
enol.addAtom(atom5);
enol.addBond(bond1);
enol.addBond(bond2);
enol.addBond(bond3);
enol.addBond(bond4);
enol.addBond(bond5);
// perceive atom types
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(enol);
// now have the algorithm have a go at it
enol = fbot.kekuliseAromaticRings(enol);
Assert.assertNotNull(enol);
// Assert.assertTrue(fbot.isOK(enol));
// now check whether it did the right thing
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(0).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(1).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_DOUBLE, enol.getBond(2).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(3).getOrder());
;
Assert.assertEquals(CDKConstants.BONDORDER_SINGLE, enol.getBond(4).getOrder());
;
}
/**
* Clean up chemical model ,removing duplicates empty molecules etc
*
* @param chemModel
* @param avoidOverlap
* @throws CDKException
*/
public static void cleanUpChemModel(final IChemModel chemModel,
final boolean avoidOverlap, final AbstractJChemPaintPanel panel)
throws CDKException {
JChemPaint.setReactionIDs(chemModel);
JChemPaint.replaceReferencesWithClones(chemModel);
// check the model is not completely empty
if (ChemModelManipulator.getBondCount(chemModel) == 0
&& ChemModelManipulator.getAtomCount(chemModel) == 0) {
throw new CDKException(
"Structure does not have bonds or atoms. Cannot depict structure.");
}
JChemPaint.removeDuplicateAtomContainers(chemModel);
JChemPaint.checkCoordinates(chemModel);
JChemPaint.removeEmptyAtomContainers(chemModel);
if (avoidOverlap) {
try {
ControllerHub.avoidOverlap(chemModel);
} catch (final Exception e) {
JOptionPane.showMessageDialog(panel,
GT._("Structure could not be generated"));
throw new CDKException("Cannot depict structure");
}
}
// We update implicit Hs in any case
final CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher
.getInstance(chemModel.getBuilder());
for (final IAtomContainer container : ChemModelManipulator
.getAllAtomContainers(chemModel)) {
for (final IAtom atom : container.atoms()) {
if (!(atom instanceof IPseudoAtom)) {
try {
final IAtomType type = matcher.findMatchingAtomType(
container, atom);
if (type != null
&& type.getFormalNeighbourCount() != null) {
final int connectedAtomCount = container
.getConnectedAtomsCount(atom);
atom.setImplicitHydrogenCount(type
.getFormalNeighbourCount()
- connectedAtomCount);
}
} catch (final CDKException e) {
e.printStackTrace();
}
}
}
}
}
private void fixCarbonHCount(IAtomContainer mol) {
/*
* the following line are just a quick fix for this
* particluar carbon-only molecule until we have a proper
* hydrogen count configurator
*/
double bondCount = 0;
org.openscience.cdk.interfaces.IAtom atom;
for (int f = 0; f < mol.getAtomCount(); f++) {
atom = mol.getAtom(f);
bondCount = mol.getBondOrderSum(atom);
int correction =
(int) bondCount - (atom.getCharge() != null ? atom.getCharge().intValue() : 0);
if (atom.getSymbol().equals("C")) {
atom.setImplicitHydrogenCount(4 - correction);
} else if (atom.getSymbol().equals("N")) {
atom.setImplicitHydrogenCount(3 - correction);
}
if (standAlone) {
System.out.println("Hydrogen count for atom " + f + ": " + atom.getImplicitHydrogenCount());
}
}
}
/**
* @return
* @throws Exception
*/
public int process() throws Exception {
if (file == null) throw new Exception("File not assigned! Use -f command line option.");
if (!file.exists()) throw new FileNotFoundException(file.getAbsolutePath());
int records_read = 0;
int records_processed = 0;
int records_error = 0;
InputStream in = new FileInputStream(file);
/**
* cdk-io module http://ambit.uni-plovdiv.bg:8083/nexus/index.html#nexus-
* search;classname~IteratingMDLReader
*/
IteratingSDFReader reader = null;
SDFWriter writer = new SDFWriter(new OutputStreamWriter(System.out));
try {
reader = new IteratingSDFReader(in, DefaultChemObjectBuilder.getInstance());
LOGGER.log(Level.INFO, String.format("Reading %s", file.getAbsoluteFile()));
while (reader.hasNext()) {
/** Note recent versions allow IAtomContainer molecule = reader.next(); */
Object object = reader.next();
IAtomContainer molecule = null;
if (object instanceof IAtomContainer) molecule = (IAtomContainer) object;
else break;
records_read++;
try {
/** cdk-standard module */
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
// CDKHueckelAromaticityDetector.detectAromaticity(molecule);
for (IAtom atom : molecule.atoms())
if (atom.getImplicitHydrogenCount() == null) {
LOGGER.fine(
atom.getSymbol()
+ "\t"
+ atom.getAtomTypeName()
+ "\t"
+ atom.getImplicitHydrogenCount());
atom.setImplicitHydrogenCount(0);
}
molecule = AtomContainerManipulator.copyAndSuppressedHydrogens(molecule);
/** Generate SMILES and assign as properties */
assignSMILES(molecule);
molecule.setProperty("REACTION", "REACTANT");
molecule.setProperty("SMIRKS", "");
/** Apply reactions */
writer.write(molecule);
for (int r = 0; r < smirks.length; r++) {
if (reactions[r] == null) {
reactions[r] = smrkMan.parse(smirks[r][1]);
}
IAtomContainer reactant = molecule.clone();
if (smrkMan.applyTransformation(reactant, reactions[r])) {
AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(reactant);
reactant.setProperty("REACTION", "PRODUCT OF " + smirks[r][0]);
reactant.setProperty("SMIRKS", smirks[r][1]);
try {
assignSMILES(reactant);
} catch (Exception x) {
LOGGER.log(Level.WARNING, x.getMessage());
}
writer.write(reactant);
}
}
records_processed++;
;
} catch (Exception x) {
System.err.println("*");
records_error++;
LOGGER.log(
Level.SEVERE,
String.format("[Record %d] Error %s\n", records_read, file.getAbsoluteFile()),
x);
}
}
} catch (Exception x) {
LOGGER.log(
Level.SEVERE,
String.format("[Record %d] Error %s\n", records_read, file.getAbsoluteFile()),
x);
} finally {
try {
reader.close();
} catch (Exception x) {
}
try {
writer.close();
} catch (Exception x) {
}
}
LOGGER.log(
Level.INFO,
String.format(
"[Records read/processed/error %d/%d/%d] %s",
records_read, records_processed, records_error, file.getAbsoluteFile()));
return records_read;
}
@Test
public void unknownSymbol_Pseudo() throws Exception {
IAtom a = new PseudoAtom("R1");
a.setImplicitHydrogenCount(0);
assertThat(new CDKToBeam().toBeamAtom(a).element(), is(Element.Unknown));
}
@Test
public void unspecifiedIsotope() throws Exception {
IAtom a = new Atom("C");
a.setImplicitHydrogenCount(0);
assertThat(new CDKToBeam().toBeamAtom(a).isotope(), is(-1));
}
@Test
public void aliphaticAtom() throws Exception {
IAtom a = new Atom("C");
a.setImplicitHydrogenCount(0);
assertFalse(new CDKToBeam().toBeamAtom(a).aromatic());
}