Examples with Rule model.Rule used on opensource projects

Example 6 with Rule

use of model.Rule in project Smiles2Monomers by yoann-dufresne.

the class ResidueJsonLoader method fillLinksJSO.

@SuppressWarnings("unchecked")
private String fillLinksJSO(JSONArray links, Residue res) {
    IMolecule mol = res.getMolecule();
    AtomContainerManipulator.convertImplicitToExplicitHydrogens(mol);
    String smiles = SmilesConverter.conv.mol2Smiles(mol, false);
    List<IAtom> order = SmilesConverter.conv.getOrder();
    for (IAtom a : res.getAtomicLinks().keySet()) {
        JSONObject jso = new JSONObject();
        Rule rule = res.getAtomicLinks().get(a);
        jso.put("name", rule.getName());
        jso.put("atom", order.indexOf(a));
        links.add(jso);
    }
    AtomContainerManipulator.removeHydrogens(mol);
    return smiles;
}

Example 7 with Rule

use of model.Rule in project Smiles2Monomers by yoann-dufresne.

the class ChainsFamilyMatching method addToCoverage.

private void addToCoverage(Family family, MappedChain mc, Residue res) {
    Match match = new Match(res);
    match.addAtoms(mc.getAtomsMapping());
    match.addBonds(mc.getBondsMapping());
    match.addHydrogens(mc.getHydrogensMapping());
    for (int idx = 0; idx < mc.getMatchings().size(); idx++) {
        match.addQuality(mc.getBondsMapping().get(idx), mc.getMatchings().get(idx));
    }
    // Compute external bonds by aligning chain on residue
    // 1- Retrieve the chain on root residue
    int current = 200;
    List<MappedChain> onResidue = null;
    Residue rootMol = null;
    for (Residue root : family.getRoots()) {
        List<MappedChain> mcs = Isomorphism.searchAChain(mc.getChain(), root, MatchingType.EXACT);
        if (mcs.size() > 0 && current > mcs.size()) {
            current = mcs.size();
            onResidue = mcs;
            rootMol = root;
        }
    }
    // 2- Look for atoms of interest
    MappedChain resMapping = onResidue.get(0);
    for (IAtom ia : rootMol.getAtomicLinks().keySet()) {
        Rule r = rootMol.getAtomicLinks().get(ia);
        int resMolIdx = rootMol.getMolecule().getAtomNumber(ia);
        int chainIdx = resMapping.getAtomsMapping().indexOf(resMolIdx);
        match.addExtLink(mc.getAtomsMapping().get(chainIdx), r);
    }
    // Add the match
    if (!this.coverage.getMatches().contains(match))
        this.coverage.addMatch(match);
}

Example 8 with Rule

use of model.Rule 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;
}