Examples with Family model.Family used on opensource projects

Example 1 with Family

use of model.Family 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 Family

use of model.Family 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();
    }
}

Example 3 with Family

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

the class Coverage method getIncorrectMonomers.

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

Example 4 with Family

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

the class Coverage method calculateCorrectIncorrectNotFound.

public void calculateCorrectIncorrectNotFound(FamilyDB families) {
    this.corrects = new HashMap<>();
    this.incorrects = new HashMap<>();
    this.notFound = new HashMap<>();
    List<Monomer> realMonos = new ArrayList<>();
    for (Monomer m : this.co.getGraph().nodes) realMonos.add(m);
    for (Match match : this.usedMatches) {
        Residue r = match.getResidue();
        // For each is correct ?
        boolean correct = false;
        Family fam = null;
        try {
            fam = families.getObject(r.getMonoName());
        } catch (NullPointerException e) {
            e.printStackTrace();
        }
        for (Monomer m : fam.getMonomers()) {
            if (realMonos.contains(m)) {
                correct = true;
                realMonos.remove(m);
                break;
            }
        }
        if (correct) {
            int nb = this.corrects.containsKey(r) ? this.corrects.get(r) : 0;
            this.corrects.put(r, nb + 1);
        } else {
            int nb = this.incorrects.containsKey(r) ? this.incorrects.get(r) : 0;
            this.incorrects.put(r, nb + 1);
        }
    }
    for (Monomer m : realMonos) {
        String name = null;
        try {
            Family fam = families.getObject(m.getName());
            name = fam.getShortName();
        } catch (NullPointerException e) {
            name = m.getName();
        }
        int nb = this.notFound.containsKey(name) ? this.notFound.get(name) : 0;
        this.notFound.put(name, nb + 1);
    }
}

Example 5 with Family

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

the class ChainLearning method learn.

/**
 * Learn Sequences from families using the learning base.
 * @param families families to index.
 */
public void learn(FamilyDB families) {
    this.chains.clear();
    this.finalChains.clear();
    this.db = new ChainsDB();
    List<Residue> roots = new ArrayList<>();
    for (Family family : families.getObjects()) {
        for (Residue root : family.getRoots()) {
            roots.add(root);
        }
    }
    // --- Roots ---
    // Init for size 1
    ResidueMappings residueIndex_1 = new ResidueMappings();
    this.initLearn(roots, residueIndex_1);
    // Markovian recursive
    ResidueMappings previous = null;
    ResidueMappings current = residueIndex_1;
    for (int size = 2; size <= this.markovianSize; size++) {
        previous = current;
        current = this.learnMarkovianNext(previous);
    }
    // Greedy recursive
    for (Residue root : current.keySet()) {
        MappedChain bestMarkov = this.getBest(current.get(root));
        MappedChain greedyMB = this.learnGreedy(bestMarkov);
        this.chains.put(greedyMB.getChain().getSmiles(), greedyMB.getChain());
        this.finalChains.put(greedyMB.getChemObject().getId(), greedyMB.getChain());
    }
    // Create index structures all over families.
    for (Family fam : families.getObjects()) {
        FamilyChainsDB fc = new FamilyChainsDB(fam);
        this.db.addObject(fam.getName(), fc);
        this.addAddsToSons(fc, fam);
    }
}