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

Example 1 with IBond

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

the class IsomorphismTests method setUp.

@Before
public void setUp() throws Exception {
    // Database
    Monomer[] monos = new Monomer[1];
    Polymer pepTest = new Polymer(0, "malformin A1", "O=C1NC2C(=O)NC(C(=O)NC(C(=O)NC(C(=O)NC1CSSC2)C(C)CC)CC(C)C)C(C)C", monos);
    // Extensions
    IAtom a = new Atom("C");
    IBond b1 = new Bond(new Atom("S"), a, Order.SINGLE);
    this.ext1 = new Extension(b1);
    a = new Atom("C");
    IAtom a2 = new Atom("C");
    IBond b2 = new Bond(a, a2, Order.SINGLE);
    this.ext2 = new Extension(b2);
    // Mapped blocs
    this.mb0 = new MappedChain(pepTest, null, new ArrayList<Integer>(), new ArrayList<Integer>(), new ArrayList<MatchingType>(), new HashMap<Integer, Integer>());
    // For blocs Tests
    this.bloc = new Chain("S,0,c,0,0,-1,-1;c,0,c,0,0,-1,1");
}

Example 2 with IBond

use of org.openscience.cdk.interfaces.IBond 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 3 with IBond

use of org.openscience.cdk.interfaces.IBond 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 4 with IBond

use of org.openscience.cdk.interfaces.IBond 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 5 with IBond

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

the class BondAdd method searchAtoms.

public void searchAtoms(MappedChain mc, MatchingType type) throws AtomNotFound {
    this.mol = mc.getChemObject().getMolecule();
    // Init real atom idxs.
    int atomIdx = -1;
    int neiIdx = -1;
    this.expected = null;
    if (this.idx1 == -1) {
        atomIdx = mc.getAtomsMapping().get(this.idx2);
        neiIdx = this.idx1;
        expected = this.ext.getBond().getAtom(0);
    } else {
        atomIdx = mc.getAtomsMapping().get(this.idx1);
        neiIdx = this.idx2;
        this.expected = this.ext.getBond().getAtom(1);
    }
    // Search in neighborhood.
    IAtom atom = this.mol.getAtom(atomIdx);
    List<IAtom> neighbors = this.mol.getConnectedAtomsList(atom);
    this.neiAtom = null;
    // Adding with two atoms already in the previous mapped chain
    if (neiIdx != -1) {
        this.neiAtom = this.mol.getAtom(mc.getAtomsMapping().get(neiIdx));
        if (!neighbors.contains(this.neiAtom)) {
            throw new AtomNotFound();
        }
    } else // Adding with only one atom in the previous matching
    {
        for (IAtom a : neighbors) {
            if (mc.getAtomsMapping().contains(this.mol.getAtomNumber(a)))
                continue;
            IBond bond = this.mol.getBond(atom, a);
            if (this.expected.getSymbol().equals(a.getSymbol())) {
                if (bond.getOrder() == this.ext.getBond().getOrder() && this.expected.getFlag(CDKConstants.ISAROMATIC) == a.getFlag(CDKConstants.ISAROMATIC) && this.expected.getImplicitHydrogenCount().intValue() <= a.getImplicitHydrogenCount().intValue()) {
                    this.neiAtom = a;
                    this.neiHydro = this.expected.getImplicitHydrogenCount().intValue();
                    if (this.expected.getImplicitHydrogenCount().intValue() == a.getImplicitHydrogenCount().intValue()) {
                        this.matchingType = MatchingType.EXACT;
                        break;
                    } else if (type != MatchingType.EXACT) {
                        this.matchingType = MatchingType.STRONG;
                        break;
                    }
                } else if (type == MatchingType.LIGHT) {
                    this.neiAtom = a;
                    this.neiHydro = 0;
                    this.matchingType = MatchingType.LIGHT;
                    break;
                }
            }
        }
        if (this.neiAtom == null) {
            throw new AtomNotFound();
        }
    }
    this.bond = this.mol.getBond(atom, neiAtom);
}