Examples with ChainAdd algorithms.isomorphism.chains.ChainAdd used on opensource projects

Example 1 with ChainAdd

use of algorithms.isomorphism.chains.ChainAdd in project Smiles2Monomers by yoann-dufresne.

the class ChainsFamilyMatching method matchFamilly.

@Override
public Coverage matchFamilly(Family family) {
    if (this.co == null)
        return null;
    this.coverage = new Coverage(co);
    FamilyChainsDB fc = this.chains.getObject(family.getJsonName());
    this.toMatch.addAll(family.getRoots());
    while (!toMatch.isEmpty()) {
        Residue res = toMatch.remove();
        List<MappedChain> mcs = null;
        List<ChainAdd> adds = fc.getAdds(res);
        // If the residue is a root
        if (adds.size() == 0) {
            Chain rootChain = fc.getRootChains().get(res);
            mcs = Isomorphism.searchAChain(rootChain, this.co, this.matchingType);
        } else // From previous mapping
        {
            mcs = new ArrayList<>();
            Residue from = adds.get(0).getFrom();
            for (MappedChain mc : mappings.get(from)) {
                try {
                    MappedChain clone = mc;
                    for (ChainAdd add : adds) clone = add.applyAndClone(mc, this.matchingType);
                    mcs.add(clone);
                } catch (Exception e) {
                }
            }
        }
        // Save results and recursive add
        if (mcs.size() > 0) {
            this.mappings.put(res, mcs);
            this.addToCoverage(family, mcs, res);
            for (Residue child : fc.getFamily().getChildrenOf(res)) {
                if (fc.getAdds(child).get(0).getFrom().equals(res)) {
                    this.toMatch.add(child);
                }
            }
        }
    }
    this.mappings.clear();
    return this.coverage;
}

Example 2 with ChainAdd

use of algorithms.isomorphism.chains.ChainAdd in project Smiles2Monomers by yoann-dufresne.

the class FamilyChainIO method objectFromJson.

@Override
protected FamilyChainsDB objectFromJson(JSONObject jso) {
    // FC creation
    String famName = (String) jso.get("family");
    if (famName.contains("€"))
        famName = famName.split("€")[0];
    Family fam = this.families.getObject(famName);
    FamilyChainsDB fc = new FamilyChainsDB(fam);
    // Roots
    JSONObject jsonRoots = (JSONObject) jso.get("roots");
    for (Object objIdx : jsonRoots.keySet()) {
        String idx = (String) objIdx;
        fc.addRootChain(this.residues.getObject(idx), new Chain((String) jsonRoots.get(objIdx)));
    }
    // Adds
    JSONObject jsonAdds = (JSONObject) jso.get("extensions");
    for (Object objIdx : jsonAdds.keySet()) {
        String idx = (String) objIdx;
        Residue current = this.residues.getObject(idx);
        JSONArray jsonAddsList = (JSONArray) jsonAdds.get(objIdx);
        for (Object obj : jsonAddsList) {
            JSONObject add = (JSONObject) obj;
            Residue from = this.residues.getObject((String) add.get("from"));
            ChainAdd ca = null;
            // TODO : Change it for better usage of genericity.
            switch((String) add.get("type")) {
                case "hydrogen":
                    ca = new HydrogenAdd(from, ((Number) add.get("idx")).intValue(), ((Number) add.get("num")).intValue());
                    break;
                case "extension":
                    ca = new BondAdd(from, new Extension((String) add.get("ext")), ((Number) add.get("idx1")).intValue(), ((Number) add.get("idx2")).intValue());
                    break;
                default:
                    break;
            }
            fc.addAnAdd(current, ca);
        }
    }
    return fc;
}