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

Example 6 with IMolecule

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

the class CoveragesJsonLoader method getJSONMatches.

@SuppressWarnings("unchecked")
private JSONObject getJSONMatches(Coverage cov) {
    JSONObject graph = new JSONObject();
    JSONArray atoms = new JSONArray();
    graph.put("atoms", atoms);
    JSONArray bonds = new JSONArray();
    graph.put("bonds", bonds);
    Set<IBond> usedBonds = new HashSet<IBond>();
    int matchId = 0;
    for (Match match : cov.getUsedMatches()) {
        // Atoms
        for (int a : match.getAtoms()) {
            JSONObject atom = new JSONObject();
            // CDK informations
            atom.put("cdk_idx", a);
            // Atom informations
            IAtom ia = cov.getChemicalObject().getMolecule().getAtom(a);
            atom.put("name", ia.getSymbol());
            atom.put("hydrogens", match.getHydrogensFrom(a));
            // Residue informations
            atom.put("res", match.getResidue().getId());
            atom.put("matchIdx", matchId);
            atoms.add(atom);
        }
        // Bonds
        for (int b : match.getBonds()) {
            IBond ib = cov.getChemicalObject().getMolecule().getBond(b);
            usedBonds.add(ib);
            JSONObject bond = new JSONObject();
            // CDK informations
            bond.put("cdk_idx", b);
            // atoms linked
            JSONArray linkedAtoms = new JSONArray();
            for (IAtom a : ib.atoms()) {
                linkedAtoms.add(cov.getChemicalObject().getMolecule().getAtomNumber(a));
            }
            bond.put("arity", ib.getOrder().numeric());
            bond.put("atoms", linkedAtoms);
            bond.put("res", match.getResidue().getId());
            bonds.add(bond);
        }
        matchId++;
    }
    IMolecule mol = cov.getChemicalObject().getMolecule();
    for (IBond ib : mol.bonds()) {
        if (!usedBonds.contains(ib)) {
            JSONObject bond = new JSONObject();
            // CDK informations
            bond.put("cdk_idx", mol.getBondNumber(ib));
            // atoms linked
            JSONArray linkedAtoms = new JSONArray();
            for (IAtom a : ib.atoms()) {
                linkedAtoms.add(mol.getAtomNumber(a));
            }
            bond.put("arity", ib.getOrder().numeric());
            bond.put("atoms", linkedAtoms);
            bonds.add(bond);
        }
    }
    return graph;
}

Example 7 with IMolecule

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

the class Residue method explicitToImplicitHydrogens.

public void explicitToImplicitHydrogens() {
    IMolecule mol = this.getMolecule();
    for (IAtom a : mol.atoms()) a.setImplicitHydrogenCount(0);
    List<IAtom> toRemove = new ArrayList<>();
    for (IAtom a : mol.atoms()) if (a.getAtomTypeName().equals("H")) {
        IAtom connected = mol.getConnectedAtomsList(a).get(0);
        connected.setImplicitHydrogenCount(connected.getImplicitHydrogenCount() + 1);
        toRemove.add(a);
    }
    for (IAtom a : toRemove) {
        mol.removeBond(mol.getConnectedBondsList(a).get(0));
        mol.removeAtom(a);
    }
}

Example 8 with IMolecule

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

the class Isomorphism method searchFromPreviousMapping.

/**/
public static List<MappedChain> searchFromPreviousMapping(MappedChain mc, Extension ext, int idx1, int idx2, MatchingType type) {
    IMolecule mol = mc.getChemObject().getMolecule();
    int extIdx = idx1 == -1 ? idx2 : idx1;
    List<MappedChain> mappings = new ArrayList<>();
    // Connected bonds search
    List<IBond> connectedBonds = null;
    if (extIdx == -1) {
        connectedBonds = new ArrayList<>();
        for (IBond bond : mol.bonds()) connectedBonds.add(bond);
    } else {
        IAtom extAtom = mol.getAtom(mc.getAtomsMapping().get(extIdx));
        connectedBonds = mol.getConnectedBondsList(extAtom);
    }
    for (IBond neighbor : connectedBonds) {
        // No need to search bonds already present in mapping.
        if (mc.getBondsMapping().contains(mol.getBondNumber(neighbor)))
            continue;
        List<BondMapping> bms = ext.match(neighbor, type);
        for (BondMapping bm : bms) {
            // Verification of the compatibility with previous matching
            if (idx1 != -1 && mol.getAtomNumber(bm.a0) != mc.getAtomsMapping().get(idx1))
                continue;
            if (idx2 != -1 && mol.getAtomNumber(bm.a1) != mc.getAtomsMapping().get(idx2))
                continue;
            // Creation of the new mapping
            Chain chain = new Chain(mc.getChain(), ext, idx1, idx2);
            List<Integer> atoms = new ArrayList<>(mc.getAtomsMapping());
            Map<Integer, Integer> hydrogens = new HashMap<>(mc.getHydrogensMapping());
            if (idx1 == -1) {
                int an = mol.getAtomNumber(bm.a0);
                // To avoid cycles where there is no cycle.
                if (mc.getAtomsMapping().contains(an))
                    continue;
                atoms.add(an);
                hydrogens.put(an, bm.h0);
            }
            if (idx2 == -1) {
                int an = mol.getAtomNumber(bm.a1);
                // To avoid cycles where there is no cycle.
                if (mc.getAtomsMapping().contains(an))
                    continue;
                atoms.add(an);
                hydrogens.put(an, bm.h1);
            }
            List<Integer> bonds = new ArrayList<>(mc.getBondsMapping());
            bonds.add(mol.getBondNumber(neighbor));
            List<MatchingType> matchings = new ArrayList<>(mc.getMatchings());
            matchings.add(bm.matchingType);
            MappedChain newMc = new MappedChain(mc.getChemObject(), chain, atoms, bonds, matchings, hydrogens);
            mappings.add(newMc);
        }
    }
    return mappings;
}

Example 9 with IMolecule

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

the class Isomorphism method searchFromPreviousMapping.

/**
 * Search a list of mapped blocs from a smaller mapped bloc
 * @param mb Initial mapped bloc
 * @param ext Extension to the previous mapped bloc
 * @return New mapped blocs.
 */
public static List<MappedChain> searchFromPreviousMapping(MappedChain mb, Extension ext, MatchingType type) {
    List<MappedChain> mbs = new ArrayList<>();
    ChemicalObject co = mb.getChemObject();
    IMolecule mol = co.getMolecule();
    List<Integer> neighbors = mb.getNeighborsBonds(mol);
    // Create a new bloc for each neighbor
    for (int idx : neighbors) {
        // Create bloc
        IBond nb = mol.getBond(idx);
        List<BondMapping> matchings = ext.match(nb, type);
        for (BondMapping bm : matchings) {
            int atomIdx0 = mol.getAtomNumber(bm.a0);
            int atomIdx1 = mol.getAtomNumber(bm.a1);
            int blocPosition0 = mb.getMappingIdx(atomIdx0);
            int blocPosition1 = mb.getMappingIdx(atomIdx1);
            int hydrogen0 = bm.h0;
            int hydrogen1 = bm.h1;
            Chain bloc = new Chain(mb.getChain(), ext, blocPosition0, blocPosition1);
            List<Integer> atoms = new ArrayList<>(mb.getAtomsMapping());
            if (blocPosition0 == -1)
                atoms.add(atomIdx0);
            if (blocPosition1 == -1)
                atoms.add(atomIdx1);
            List<Integer> bonds = new ArrayList<>(mb.getBondsMapping());
            bonds.add(mol.getBondNumber(nb));
            List<MatchingType> matchingTypes = new ArrayList<>(mb.getMatchings());
            matchingTypes.add(bm.matchingType);
            Map<Integer, Integer> hydrogens = new HashMap<>(mb.getHydrogensMapping());
            if (!hydrogens.containsKey(atomIdx0) || hydrogens.get(atomIdx0) <= hydrogen0)
                hydrogens.put(atomIdx0, hydrogen0);
            if (!hydrogens.containsKey(atomIdx1) || hydrogens.get(atomIdx1) <= hydrogen1)
                hydrogens.put(atomIdx1, hydrogen1);
            MappedChain newMb = new MappedChain(co, bloc, atoms, bonds, matchingTypes, hydrogens);
            if (!mbs.contains(newMb))
                mbs.add(newMb);
        }
    }
    return mbs;
}

Example 10 with IMolecule

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

the class ChainLearning method learnGreedy.

// --------------------------------- Greedy ------------------------------------
public MappedChain learnGreedy(MappedChain mb) {
    IMolecule mol = mb.getChemObject().getMolecule();
    List<Integer> neighbors = mb.getNeighborsBonds(mol);
    if (neighbors.size() == 0)
        return mb;
    Extension ext = this.getBestGreedyExt(mol, neighbors);
    MappedChain greedyMB = Isomorphism.searchFromPreviousMapping(mb, ext, MatchingType.EXACT).get(0);
    return this.learnGreedy(greedyMB);
}