/** Converts a Molecule Element from a CDK Molecule object */
public MoleculeType convert(IMolecule molecule) throws MSMLConversionException {
try {
MoleculeType molMoleculeElement = ObjectFactorySingelton.getFactory().createMoleculeType();
setMetaData(molMoleculeElement, molecule);
// molMoleculeElement.setMoleculeClass(MoleculeClassType.HETERO);//?
// Add Atom block:
Iterable<IAtom> atomBlock = molecule.atoms();
AtomArrayType atomArrayElement = convertAtoms(atomBlock, molMoleculeElement.getId());
// Save hashes of atoms to map the atom back to the atom ID
ArrayList<String> hashes = generateHashCodes(atomBlock);
molMoleculeElement.setAtomArray(atomArrayElement);
// Add bond block
Iterable<IBond> bondBlock = molecule.bonds();
BondArrayType bondArrayElement = convertBonds(bondBlock, molMoleculeElement.getId(), hashes);
molMoleculeElement.setBondArray(bondArrayElement);
// Add properties block
for (Entry<Object, Object> prop : molecule.getProperties().entrySet()) {
if (_excludedProperties.contains(prop.getKey())) continue;
CustomProperty cmlProp = ObjectFactorySingelton.getFactory().createCustomProperty();
cmlProp.setKey((String) prop.getKey());
cmlProp.setValue((String) prop.getValue());
molMoleculeElement.getCustomProperty().add(cmlProp);
}
return molMoleculeElement;
} catch (Exception e) {
String msg = "Conversion of MDL molecule structure failed! " + e.getMessage();
LOGGER.error(msg, e);
throw new MSMLConversionException(msg, e);
}
}
/**
* Initiate process. It is needed to call the addExplicitHydrogensToSatisfyValency from the class
* tools.HydrogenAdder.
*
* @param reactants reactants of the reaction
* @param agents agents of the reaction (Must be in this case null)
* @exception CDKException Description of the Exception
*/
@TestMethod("testInitiate_IMoleculeSet_IMoleculeSet")
public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws CDKException {
logger.debug("initiate reaction: HeterolyticCleavagePBReaction");
if (reactants.getMoleculeCount() != 1) {
throw new CDKException("HeterolyticCleavagePBReaction only expects one reactant");
}
if (agents != null) {
throw new CDKException("HeterolyticCleavagePBReaction don't expects agents");
}
IReactionSet setOfReactions =
DefaultChemObjectBuilder.getInstance().newInstance(IReactionSet.class);
IMolecule reactant = reactants.getMolecule(0);
/* if the parameter hasActiveCenter is not fixed yet, set the active centers*/
IParameterReact ipr = super.getParameterClass(SetReactionCenter.class);
if (ipr != null && !ipr.isSetParameter()) setActiveCenters(reactant);
Iterator<IBond> bondis = reactant.bonds().iterator();
while (bondis.hasNext()) {
IBond bondi = bondis.next();
IAtom atom1 = bondi.getAtom(0);
IAtom atom2 = bondi.getAtom(1);
if (bondi.getFlag(CDKConstants.REACTIVE_CENTER)
&& bondi.getOrder() != IBond.Order.SINGLE
&& atom1.getFlag(CDKConstants.REACTIVE_CENTER)
&& atom2.getFlag(CDKConstants.REACTIVE_CENTER)
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0
&& reactant.getConnectedSingleElectronsCount(atom2) == 0) {
/**/
for (int j = 0; j < 2; j++) {
ArrayList<IAtom> atomList = new ArrayList<IAtom>();
if (j == 0) {
atomList.add(atom1);
atomList.add(atom2);
} else {
atomList.add(atom2);
atomList.add(atom1);
}
ArrayList<IBond> bondList = new ArrayList<IBond>();
bondList.add(bondi);
IMoleculeSet moleculeSet = reactant.getBuilder().newInstance(IMoleculeSet.class);
moleculeSet.addMolecule(reactant);
IReaction reaction = mechanism.initiate(moleculeSet, atomList, bondList);
if (reaction == null) continue;
else setOfReactions.addReaction(reaction);
}
}
}
return setOfReactions;
}
/**
* set the active center for this molecule. The active center will be those which correspond with
* A-B. If the bond is simple, it will be broken forming two fragments
*
* <pre>
* A: Atom
* #/=/-: bond
* B: Atom
* </pre>
*
* @param reactant The molecule to set the activity
* @throws CDKException
*/
private void setActiveCenters(IMolecule reactant) throws CDKException {
Iterator<IBond> bonds = reactant.bonds().iterator();
while (bonds.hasNext()) {
IBond bond = bonds.next();
IAtom atom1 = bond.getAtom(0);
IAtom atom2 = bond.getAtom(1);
if (bond.getOrder() != IBond.Order.SINGLE
&& (atom1.getFormalCharge() == CDKConstants.UNSET ? 0 : atom1.getFormalCharge()) == 0
&& (atom2.getFormalCharge() == CDKConstants.UNSET ? 0 : atom2.getFormalCharge()) == 0
&& reactant.getConnectedSingleElectronsCount(atom1) == 0
&& reactant.getConnectedSingleElectronsCount(atom2) == 0) {
atom1.setFlag(CDKConstants.REACTIVE_CENTER, true);
atom2.setFlag(CDKConstants.REACTIVE_CENTER, true);
bond.setFlag(CDKConstants.REACTIVE_CENTER, true);
}
}
}