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

Example 16 with IAtom

use of org.openscience.cdk.interfaces.IAtom 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);
}

Example 17 with IAtom

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

the class ChainLearning method recurChildrenAdds.

private void recurChildrenAdds(FamilyChainsDB fc, Residue from, Set<Residue> children) {
    for (Residue child : children) {
        List<ChainAdd> adds = fc.getAdds(child);
        // If extensions already exist, jump to the next son.
        if (adds.size() > 0)
            continue;
        List<MappedChain> mcs = this.calculateMapping(fc, child, from, new MappedChain(child));
        // Collections.sort(mcs, new MappedChainComparator());
        MappedChain mc = mcs.get(0);
        // Hydrogen adds
        for (int atomIdx : mc.getAtomsMapping()) {
            IAtom a = mc.getChemObject().getMolecule().getAtom(atomIdx);
            int chainIdx = mc.getAtomsMapping().indexOf(atomIdx);
            Map<Integer, Integer> mapping = mc.getHydrogensMapping();
            int mappingHydrogens = mapping.containsKey(atomIdx) ? mapping.get(atomIdx) : 0;
            int molHydrogens = a.getImplicitHydrogenCount();
            if (mappingHydrogens < molHydrogens)
                adds.add(new HydrogenAdd(from, chainIdx, molHydrogens - mappingHydrogens));
        }
        // Extensions
        IMolecule resMol = mc.getChemObject().getMolecule();
        for (IBond bond : resMol.bonds()) {
            int bondIdx = resMol.getBondNumber(bond);
            if (mc.getBondsMapping().contains(bondIdx))
                continue;
            Extension ext = new Extension(bond);
            List<MappedChain> tmpMappings = Isomorphism.searchFromPreviousMapping(mc, ext, MatchingType.EXACT);
            for (MappedChain tmp : tmpMappings) if (tmp.getBondsMapping().get(tmp.getBondsMapping().size() - 1) == bondIdx) {
                Chain chain = tmp.getChain();
                BondAdd ba = new BondAdd(from, ext, chain.getPosition1(), chain.getPosition2());
                adds.add(ba);
            }
        }
        /**/
        this.recurChildrenAdds(fc, child, fc.getFamily().getChildrenOf(child));
    }
}

Example 18 with IAtom

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

the class Modulation method indexCoverage.

/**
 * Read a coverage and extract for each position all the possible matchings
 * @param cov
 * @return
 */
private void indexCoverage(Coverage cov) {
    this.index = new HashMap<>();
    this.usedIndex = new HashMap<>();
    IMolecule mol = cov.getChemicalObject().getMolecule();
    for (IAtom a : mol.atoms()) {
        this.index.put(mol.getAtomNumber(a), new HashSet<Match>());
        this.usedIndex.put(mol.getAtomNumber(a), new HashSet<Match>());
    }
    // Global index
    for (Match match : cov.getMatches()) for (int i : match.getAtoms()) this.index.get(i).add(match);
    // Used index
    for (Match match : cov.getUsedMatches()) for (int i : match.getAtoms()) this.usedIndex.get(i).add(match);
}

Example 19 with IAtom

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

the class Coverage method getCorrectness.

public double getCorrectness(FamilyDB families) {
    if (!this.alreadyCalculate)
        this.calculateGreedyCoverage();
    if (this.corrects == null)
        this.calculateCorrectIncorrectNotFound(families);
    int pepAtoms = 0;
    for (@SuppressWarnings("unused") IAtom a : this.co.getMolecule().atoms()) pepAtoms++;
    int corAtoms = 0;
    for (Residue res : this.corrects.keySet()) {
        int resAtoms = res.getMolecule().getAtomCount();
        corAtoms += resAtoms * this.corrects.get(res);
    }
    double ratio = new Double(corAtoms) / new Double(pepAtoms);
    return ratio;
}

Example 20 with IAtom

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

the class Extension method equals.

@Override
public boolean equals(Object obj) {
    if (!(obj instanceof Extension))
        return false;
    Extension ext = (Extension) obj;
    if (!ext.bond.getOrder().equals(this.bond.getOrder()))
        return false;
    IAtom oa0 = ext.bond.getAtom(0);
    int oh0 = oa0.getImplicitHydrogenCount();
    IAtom oa1 = ext.bond.getAtom(1);
    int oh1 = oa1.getImplicitHydrogenCount();
    IAtom ta0 = this.bond.getAtom(0);
    int th0 = ta0.getImplicitHydrogenCount();
    IAtom ta1 = this.bond.getAtom(1);
    int th1 = ta1.getImplicitHydrogenCount();
    if (oa0.getSymbol().equals(ta0.getSymbol()) && oa1.getSymbol().equals(ta1.getSymbol()) && th0 == oh0 && th1 == oh1)
        return true;
    if (oa0.getSymbol().equals(ta1.getSymbol()) && oa1.getSymbol().equals(ta0.getSymbol()) && th0 == oh1 && th1 == oh0)
        return true;
    return false;
}