private List<List<Integer>> getAtomMappings(List bondMapping, IAtomContainer atomContainer) {
List<List<Integer>> atomMapping = new ArrayList<List<Integer>>();
// loop over each mapping
for (Object aBondMapping : bondMapping) {
List list = (List) aBondMapping;
List<Integer> tmp = new ArrayList<Integer>();
IAtom atom1 = null;
IAtom atom2 = null;
// loop over this mapping
for (Object aList : list) {
RMap map = (RMap) aList;
int bondID = map.getId1();
// get the atoms in this bond
IBond bond = atomContainer.getBond(bondID);
atom1 = bond.getAtom(0);
atom2 = bond.getAtom(1);
Integer idx1 = atomContainer.getAtomNumber(atom1);
Integer idx2 = atomContainer.getAtomNumber(atom2);
if (!tmp.contains(idx1)) tmp.add(idx1);
if (!tmp.contains(idx2)) tmp.add(idx2);
}
if (tmp.size() > 0) atomMapping.add(tmp);
// If there is only one bond, check if it matches both ways.
if (list.size() == 1 && atom1.getAtomicNumber() == atom2.getAtomicNumber()) {
List<Integer> tmp2 = new ArrayList<Integer>();
tmp2.add(tmp.get(0));
tmp2.add(tmp.get(1));
atomMapping.add(tmp2);
}
}
return atomMapping;
}
@Test
public void testAtomicNumber() throws Exception {
String cmlString =
"<molecule><atomArray><atom id='a1' elementType=\"C\"><scalar dataType=\"xsd:integer\" dictRef=\"cdk:atomicNumber\">6</scalar></atom></atomArray></molecule>";
IChemFile chemFile = parseCMLString(cmlString);
IMolecule mol = checkForSingleMoleculeFile(chemFile);
Assert.assertEquals(1, mol.getAtomCount());
IAtom atom = mol.getAtom(0);
Assert.assertEquals("C", atom.getSymbol());
Assert.assertEquals(6, atom.getAtomicNumber().intValue());
}
/**
* 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);
}
}
