Examples with Residue model.Residue used on opensource projects

Example 21 with Residue

use of model.Residue 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;
}

Example 22 with Residue

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

the class ResidueJsonLoader method getArrayOfElements.

@SuppressWarnings("unchecked")
@Override
protected JSONArray getArrayOfElements(Family obj) {
    JSONArray array = new JSONArray();
    for (Residue res : obj.getResidues()) {
        JSONObject jso = new JSONObject();
        jso.put("name", res.getName());
        jso.put("id", new Integer(res.getId()));
        jso.put("mono", res.getMonoName());
        List<String> names = obj.getMonoNames();
        Collections.sort(names);
        String familyName = "";
        for (int idx = 0; idx < names.size(); idx++) {
            if (idx > 0)
                familyName += '€';
            familyName += names.get(idx);
        }
        jso.put("family", familyName);
        JSONArray links = new JSONArray();
        String smiles = this.fillLinksJSO(links, res);
        jso.put("smarts", smiles);
        jso.put("links", links);
        JSONArray depandances = new JSONArray();
        for (Link link : obj.getDepandances()) if (link.getTo().intValue() == new Integer(res.getId()).intValue())
            depandances.add(new Integer(link.getFrom()));
        jso.put("depandances", depandances);
        array.add(jso);
    }
    return array;
}

Example 23 with Residue

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

the class OutputZiper method createSupplementaries.

@SuppressWarnings("unchecked")
private void createSupplementaries(String path, Map<Coverage, ColorsMap> allColors) {
    File sup = new File(path);
    if (sup.exists())
        sup.delete();
    JSONArray array = new JSONArray();
    for (Coverage cov : allColors.keySet()) {
        JSONObject jso = new JSONObject();
        jso.put("id", cov.getId());
        jso.put("ratio", cov.getCoverageRatio());
        ColorsMap cm = allColors.get(cov);
        JSONArray colorsArray = new JSONArray();
        jso.put("colors", colorsArray);
        for (Residue res : cm.keySet()) {
            JSONObject resObj = new JSONObject();
            JSONArray resColors = new JSONArray();
            for (Color col : cm.get(res)) {
                resColors.add(Integer.toHexString(col.getRGB()));
            }
            resObj.put(res.getId(), resColors);
            colorsArray.add(resObj);
        }
        array.add(jso);
    }
    try {
        FileWriter fw = new FileWriter(sup);
        fw.write(array.toJSONString());
        fw.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 24 with Residue

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

the class Coverage method getCorrectMonomers.

public Map<String, Integer> getCorrectMonomers(FamilyDB families) {
    this.calculateCorrectIncorrectNotFound(families);
    Map<String, Integer> corrects = new HashMap<>();
    for (Residue res : this.corrects.keySet()) {
        Family fam = families.getObject(res.getMonoName());
        String name = fam.getShortName();
        int val = corrects.containsKey(name) ? corrects.get(name) : 0;
        corrects.put(name, val + this.corrects.get(res));
    }
    return corrects;
}

Example 25 with Residue

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

the class ContractedGraph method toMonomerGraph.

/**
 * Transform this contracted graph into a classical monomer graph.
 * @param fams The family database needed to always refer the same monomer of a family.
 * @return The monomer graph
 */
public MonomerGraph toMonomerGraph(FamilyDB fams) {
    // Transformation to a monomer graph
    List<Vertex> verticiesOrder = new ArrayList<>();
    List<Monomer> monos = new ArrayList<>();
    List<Residue> residues = new ArrayList<>();
    for (Object o : this.vertexSet()) {
        Vertex v = (Vertex) o;
        verticiesOrder.add(v);
        Residue res = v.res;
        if (res != null) {
            Family fam = null;
            try {
                fam = fams.getObject(res.getMonoName());
            } catch (NullPointerException e) {
                e.printStackTrace();
            }
            monos.add(fam.getPrincipalMonomer());
            residues.add(res);
        } else {
            monos.add(null);
            residues.add(null);
        }
    }
    Monomer[] array = new Monomer[monos.size()];
    for (int i = 0; i < monos.size(); i++) array[i] = monos.get(i);
    Residue[] resArray = new Residue[monos.size()];
    for (int i = 0; i < monos.size(); i++) resArray[i] = residues.get(i);
    MonomerGraph monoGraph = new MonomerGraph(array, resArray);
    for (Object o : this.edgeSet()) {
        LabeledEdge e = (LabeledEdge) o;
        int mono1 = verticiesOrder.indexOf((Vertex) e.getSource());
        int mono2 = verticiesOrder.indexOf((Vertex) e.getTarget());
        monoGraph.createLink(mono1, mono2, e.sourceLabel, e.targetLabel);
    }
    return monoGraph;
}