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

Example 1 with HydrogenAdd

use of algorithms.isomorphism.chains.HydrogenAdd 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;
}