Examples with Residue model.Residue used on opensource projects

Example 26 with Residue

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

the class CoveragesJsonLoader method objectFromJson.

@Override
protected Coverage objectFromJson(JSONObject obj) {
    // TODO : Create new parser with the files created by the new output functions
    System.err.println("From classe '" + CoveragesJsonLoader.class.getName() + "' method 'objectFromJson':");
    System.err.println("This is deprecated ! You will have some problems with recent json files !");
    ChemicalObject co = null;
    try {
        co = this.db.getObject("" + ((Number) obj.get("peptide")).intValue());
    } catch (NullPointerException e) {
        System.err.println(e.getMessage());
        System.err.println("Maybe coverage json and molecule json don't match");
        System.exit(2);
    }
    Coverage cov = new Coverage(co);
    JSONArray array = (JSONArray) obj.get("matches");
    for (Object o : array) {
        JSONObject jso = (JSONObject) o;
        Residue res = null;
        try {
            res = this.residues.getObject("" + ((Number) jso.get("residue")).intValue());
        } catch (NullPointerException e) {
            e.printStackTrace();
        }
        JSONObject jMatch = (JSONObject) jso.get("match");
        Match match = new Match(res);
        JSONArray atoms = (JSONArray) jMatch.get("atoms");
        for (Object atObj : atoms) {
            JSONObject atom = (JSONObject) atObj;
            int idx = ((Number) atom.get("a")).intValue();
            match.addAtom(idx);
            match.addHydrogens(idx, ((Number) atom.get("h")).intValue());
        }
        JSONArray bonds = (JSONArray) jMatch.get("bonds");
        for (Object boObj : bonds) {
            int bond = ((Number) boObj).intValue();
            match.addBond(bond);
        }
        cov.addMatch(match);
    }
    cov.calculateGreedyCoverage();
    return cov;
}

Example 27 with Residue

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

the class FamilyDB method addObject.

@Override
public void addObject(String id, Family f) {
    Family prev = null;
    for (Monomer m : f.getMonomers()) if (this.database.containsKey(m.getId())) {
        prev = this.database.get(m.getId());
        break;
    }
    if (prev == null) {
        for (Monomer m : f.getMonomers()) {
            super.addObject(m.getId(), f);
            this.uniqFamilies.add(f);
        }
    } else {
        for (Monomer m : f.getMonomers()) {
            prev.addMonomer(m);
            this.database.put(m.getId(), prev);
        }
        for (Residue res : f.getResidues()) prev.addResidue(res);
        for (Link l : f.getDepandances()) prev.addDependance(l);
    }
}

Example 28 with Residue

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

the class ResiduesDB method getAlphabeticResidues.

public List<Residue> getAlphabeticResidues() {
    List<Residue> residues = new ArrayList<>(this.database.values());
    Collections.sort(residues);
    this.databaseByIdx.clear();
    for (Residue res : residues) {
        // res.setIdx(residues.indexOf(res)+1);
        this.databaseByIdx.put(residues.indexOf(res) + 1, res);
    }
    return residues;
}

Example 29 with Residue

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

the class FamilyChainsDB method toJSON.

@SuppressWarnings("unchecked")
public JSONObject toJSON() {
    JSONObject jso = new JSONObject();
    // Id
    jso.put("family", this.family.getJsonName());
    // Roots
    JSONObject roots = new JSONObject();
    for (Residue res : this.rootChains.keySet()) {
        roots.put(res.getId(), this.rootChains.get(res).getSerial());
    }
    jso.put("roots", roots);
    // Extensions
    JSONObject exts = new JSONObject();
    for (Residue res : this.adds.keySet()) {
        JSONArray adds = new JSONArray();
        for (ChainAdd add : this.adds.get(res)) {
            adds.add(add.toJSON());
        }
        exts.put(res.getId(), adds);
    }
    jso.put("extensions", exts);
    return jso;
}

Example 30 with Residue

use of model.Residue 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);
}