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

Example 26 with IMolecule

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

the class Chain method getPrevArity.

public int getPrevArity() {
    IAtom a = null;
    if (this.atoms == null)
        this.getMolecule();
    if (this.position1 == -1 && this.position2 == -1)
        return 1;
    else if (this.position1 != -1) {
        a = this.atoms.get(this.position1);
    } else {
        a = this.atoms.get(this.position2);
    }
    IMolecule mol = this.getMolecule();
    int valency = 1;
    try {
        valency = sc.calculateNumberOfImplicitHydrogens(a);
    } catch (CDKException e) {
        e.printStackTrace();
    }
    int hydrogens = a.getImplicitHydrogenCount();
    int connected = mol.getConnectedAtomsCount(a);
    int arity = valency - connected - hydrogens + 1;
    return arity < 1 ? 1 : arity;
}

Example 27 with IMolecule

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

the class ResidueCreator method removeExclusions.

/*
	 * Remove results corresponding to an exclusion in rule
	 */
private void removeExclusions(List<List<RMap>> matches, String ex, IMolecule mol) {
    // Verifying exclusions
    boolean areExclusion = false;
    IMolecule exclusionMol = null;
    try {
        exclusionMol = SmilesConverter.conv.transform(ex, false, false, true);
    } catch (InvalidSmilesException e) {
        System.err.println("Impossible to parse " + ex);
        return;
    }
    try {
        areExclusion = UniversalIsomorphismTester.isSubgraph(mol, exclusionMol);
    } catch (CDKException e) {
        e.printStackTrace();
    }
    if (areExclusion) {
        List<RMap> toExclude = null;
        boolean flag = false;
        List<List<RMap>> exclusions = null;
        try {
            exclusions = UniversalIsomorphismTester.getSubgraphAtomsMaps(mol, exclusionMol);
        } catch (CDKException e) {
            e.printStackTrace();
        }
        for (List<RMap> exclusion : exclusions) {
            for (List<RMap> match : matches) {
                for (RMap rmMatch : match) {
                    for (RMap exId : exclusion) {
                        if (rmMatch.getId1() == exId.getId1()) {
                            flag = true;
                            break;
                        }
                    }
                    if (flag)
                        break;
                }
                if (flag) {
                    toExclude = match;
                    break;
                }
            }
            if (flag) {
                matches.remove(toExclude);
                toExclude = null;
                flag = false;
            }
        }
    }
/**/
}

Example 28 with IMolecule

use of org.openscience.cdk.interfaces.IMolecule 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;
}