Examples with Family model.Family used on opensource projects

Example 6 with Family

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

the class FamilyDB method init.

public void init(MonomersDB monoDB) {
    Map<String, List<Monomer>> clusters = new HashMap<>();
    for (Monomer mono : monoDB.getObjects()) {
        String smiles = null;
        try {
            smiles = SmilesConverter.conv.toCanonicalSmiles(mono.getSmiles());
        } catch (InvalidSmilesException e) {
            System.err.println("Impossible to parse " + mono.getName() + " id:" + mono.getId());
            System.err.println(mono.getSmiles());
            continue;
        }
        List<Monomer> cluster = clusters.containsKey(smiles) ? clusters.get(smiles) : new ArrayList<Monomer>();
        cluster.add(mono);
        clusters.put(smiles, cluster);
    }
    for (String smiles : clusters.keySet()) {
        Family family = new Family();
        for (Monomer mono : clusters.get(smiles)) {
            family.addMonomer(mono);
            this.addObject(mono.getCode(), family);
        }
    }
}

Example 7 with Family

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

the class ResidueCreatorTests method linksLoadingTest.

@Test
public void linksLoadingTest() {
    ResidueJsonLoader rjl = new ResidueJsonLoader(this.rules, this.monos);
    rjl.saveFile(this.families, "tmp.json");
    Residue.resetResidues();
    FamilyDB loaded = rjl.loadFile("tmp.json");
    new File("tmp.json").delete();
    Family famTyr = null;
    try {
        famTyr = loaded.getObject("Tyr");
    } catch (NullPointerException e) {
        e.printStackTrace();
    }
    Residue tyrN = null;
    for (Residue res : famTyr.getResidues()) if ("Tyr_pepN".equals(res.getName())) {
        tyrN = res;
        break;
    }
    Entry<IAtom, Rule> entry = tyrN.getAtomicLinks().entrySet().iterator().next();
    IAtom a = entry.getKey();
    Assert.assertEquals(a.getSymbol(), "N");
}

Example 8 with Family

use of model.Family 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 9 with Family

use of model.Family 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 10 with Family

use of model.Family 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;
}