Examples with IAtom org.openscience.cdk.interfaces.IAtom used on opensource projects

Example 46 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class ResidueCreator method createResidues.

/**
 * Create all residues from the argument monomers database according to rules entered in paramaters of the constructor.
 * @param monosDBName A monomers database.
 * @return All possible residues found.
 */
public FamilyDB createResidues(MonomersDB monosDB) {
    FamilyDB famDB = new FamilyDB();
    famDB.init(monosDB);
    for (Family family : famDB.getFamilies()) {
        this.residuesFromMonomers(family);
        for (Residue res : family.getResidues()) {
            IMolecule oldMol = res.getMolecule();
            res.setMol(new Molecule(AtomContainerManipulator.removeHydrogens(res.getMolecule())));
            IMolecule newMol = res.getMolecule();
            Map<IAtom, IAtom> conversion = new HashMap<>();
            int idx = 0;
            for (IAtom a : oldMol.atoms()) {
                if (!"H".equals(a.getSymbol())) {
                    conversion.put(a, newMol.getAtom(idx));
                    idx++;
                }
            }
            Map<IAtom, Rule> oldLinks = new HashMap<>(res.getAtomicLinks());
            res.getAtomicLinks().clear();
            for (IAtom oldA : oldLinks.keySet()) {
                Rule rule = oldLinks.get(oldA);
                res.addLink(conversion.get(oldA), rule);
            }
        }
    }
    return famDB;
}