Examples with Residue model.Residue used on opensource projects

Example 1 with Residue

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

the class ResidueJsonLoader method objectFromJson.

@Override
protected Family objectFromJson(JSONObject obj) {
    Residue res = new Residue((String) obj.get("mono"), (String) obj.get("smarts"), true);
    res.setIdx(((Number) obj.get("id")).intValue());
    JSONArray array = (JSONArray) obj.get("links");
    for (Object o : array) {
        JSONObject jso = (JSONObject) o;
        String name = (String) jso.get("name");
        Rule rule = null;
        try {
            rule = this.rules.getObject(name);
        } catch (NullPointerException e) {
            System.err.println("Unknown link " + name);
        }
        int idx = ((Number) jso.get("atom")).intValue();
        IAtom ia = res.getMolecule().getAtom(idx);
        res.addLink(ia, rule);
    }
    // Family construction
    Family fam = new Family();
    try {
        for (String name : ((String) obj.get("family")).split("€")) {
            Monomer m = this.monos.getObject(name);
            fam.addMonomer(m);
        }
    } catch (NullPointerException e) {
        System.err.println("Unloaded residue " + res.getMonoName());
    }
    fam.addResidue(res);
    for (Object jso : (JSONArray) obj.get("depandances")) {
        int idx = ((Number) jso).intValue();
        fam.addDependance(idx, new Integer(res.getId()));
    }
    return fam;
}

Example 2 with Residue

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

the class HTMLColoredCoverageVue method calculateColorsof.

private Map<String, List<Color>> calculateColorsof(Set<String> set) {
    Map<String, List<Color>> colors = new HashMap<>();
    for (String name : set) {
        List<Color> c = colors.containsKey(name) ? colors.get(name) : new ArrayList<Color>();
        for (Residue res : this.colors.keySet()) {
            if (this.families.areInSameFamily(name, res.getMonoName())) {
                c.addAll(this.colors.get(res));
            }
        }
        colors.put(name, c);
    }
    return colors;
}

Example 3 with Residue

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

the class PictureCoverageGenerator method createPNG.

public ColorsMap createPNG(Coverage coverage, File outfile) {
    ColorsMap coverageColors = new ColorsMap();
    AtomColorer ac = this.cag.getColorer();
    IMolecule mol = coverage.getMolecule(false);
    List<Color> colors = ColorsGenerator.HsbColorsGeneration(coverage.nbMatchesForCoverage());
    int i = 0;
    for (Match match : coverage.getUsedMatches()) {
        Residue res = match.getResidue();
        List<Color> matchesColor = coverageColors.containsKey(res) ? coverageColors.get(res) : new ArrayList<Color>();
        for (int idx : match.getAtoms()) {
            if (!"H".equals(coverage.getMolecule(true).getAtom(idx).getSymbol()))
                ac.setColor(mol.getAtom(idx), colors.get(i));
        }
        matchesColor.add(colors.get(i));
        coverageColors.put(res, matchesColor);
        i++;
    }
    this.createPNG(mol, outfile);
    ac.resetColors();
    return coverageColors;
}

Example 4 with Residue

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

the class CoveragesJsonLoader method getJSONGraph.

@SuppressWarnings("unchecked")
private JSONObject getJSONGraph(Coverage cov) {
    ContractedGraph cg = new ContractedGraph(cov);
    MonomerGraph mg = cg.toMonomerGraph(families);
    JSONObject graph = new JSONObject();
    // Monomers
    JSONArray monos = new JSONArray();
    for (Monomer mono : mg.nodes) if (mono != null)
        monos.add(mono.getName());
    else
        monos.add("?");
    graph.put("monos", monos);
    // Residues (equivalent to monomers)
    JSONArray residues = new JSONArray();
    for (Residue res : mg.residues) if (res != null)
        residues.add(res.getId());
    else
        residues.add("?");
    graph.put("residues", residues);
    // Links
    JSONArray links = new JSONArray();
    for (MonomerLinks ml : mg.links) {
        JSONObject link = new JSONObject();
        JSONArray idxs = new JSONArray();
        idxs.add(ml.mono1);
        idxs.add(ml.mono2);
        link.put("idxs", idxs);
        JSONArray type = new JSONArray();
        type.add(ml.label1);
        type.add(ml.label2);
        link.put("types", type);
        links.add(link);
    }
    graph.put("links", links);
    return graph;
}

Example 5 with Residue

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

the class ResiduesInfosGeneration method main.

public static void main(String[] args) {
    MonomersDB monoDB = new MonomersJsonLoader().loadFile("data/monomers.json");
    RulesDB rules = RulesJsonLoader.loader.loadFile("data/rules.json");
    ResidueJsonLoader rjl = new ResidueJsonLoader(rules, monoDB);
    FamilyDB families = rjl.loadFile("data/residues.json");
    StringBuffer sb = new StringBuffer();
    for (Family fam : families.getFamilies()) {
        sb.append(fam.getName() + "\n");
        sb.append("Norine link : http://bioinfo.lifl.fr/norine/res_amino.jsp?code=" + fam.getMonomers().get(0).getCode() + "\n");
        sb.append("Num of residues : " + fam.getResidues().size() + "\n");
        sb.append("Root residues (with max links) :" + "\n");
        for (Residue res : fam.getRoots()) sb.append("\t" + res.getName() + " : " + res.getAtomicLinks().size() + "\n");
        sb.append("\n");
    }
    File out = new File("results/infosMonos.txt");
    try {
        FileWriter fw = new FileWriter(out);
        fw.write(sb.toString());
        fw.close();
    } catch (IOException e) {
        e.printStackTrace();
    }
}