Examples with Residue model.Residue used on opensource projects

Example 16 with Residue

use of model.Residue 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);
    }
}

Example 17 with Residue

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

the class PreComputation method main.

public static void main(String[] args) {
    // ----------------- Parameters ---------------------------
    String rulesDBName = "data/rules.json";
    String monosDBName = "data/monomers.json";
    String jsonPolymers = "data/learning.json";
    String serialFolder = "data/serials/";
    String jsonResidues = "data/residues.json";
    String jsonChains = "data/chains.json";
    int markovianSize = 3;
    // Parsing
    for (int idx = 0; idx < args.length; idx++) {
        if (args[idx].startsWith("-")) {
            switch(args[idx]) {
                case "-rul":
                    rulesDBName = args[idx + 1];
                    break;
                case "-mono":
                    monosDBName = args[idx + 1];
                    break;
                case "-poly":
                    jsonPolymers = args[idx + 1];
                    break;
                case "-res":
                    jsonResidues = args[idx + 1];
                    break;
                case "-cha":
                    jsonChains = args[idx + 1];
                    break;
                case "-serial":
                    serialFolder = args[idx + 1];
                    break;
                case "-markovian":
                    markovianSize = new Integer(args[idx + 1]);
                    break;
                default:
                    System.err.println("Wrong option " + args[idx]);
                    System.exit(1);
                    break;
            }
            idx++;
        } else {
            System.err.println("Wrong parameter " + args[idx]);
            System.exit(1);
        }
    }
    // File existence
    File file = new File(rulesDBName);
    if (!file.exists()) {
        System.err.println("No file at " + rulesDBName);
        System.exit(1);
    }
    file = new File(monosDBName);
    if (!file.exists()) {
        System.err.println("No file at " + monosDBName);
        System.exit(1);
    }
    file = new File(jsonPolymers);
    if (!file.exists()) {
        System.err.println("No file at " + jsonPolymers);
        System.exit(1);
    }
    // ------------------- Loadings ------------------------
    System.out.println("--- Loading ---");
    RulesDB rules = RulesJsonLoader.loader.loadFile(rulesDBName);
    MonomersDB monos = new MonomersJsonLoader(true).loadFile(monosDBName);
    PolymersJsonLoader pjl = new PolymersJsonLoader(monos, false);
    PolymersDB learningBase = pjl.loadFile(jsonPolymers);
    // ----------------- Serializations --------------------
    System.out.println("--- Data serialisation ---");
    File folder = new File(serialFolder);
    if (!folder.exists())
        folder.mkdir();
    MonomersSerialization ms = new MonomersSerialization();
    ms.serialize(monos, serialFolder + "monos.serial");
    // ----------------- residues --------------------------
    ResidueCreator rc = new ResidueCreator(rules);
    rc.setVerbose(false);
    System.out.println("--- Residues creation ---");
    FamilyDB families = rc.createResidues(monos);
    System.out.println("--- Saving residues ---");
    ResidueJsonLoader rjl = new ResidueJsonLoader(rules, monos);
    rjl.saveFile(families, jsonResidues);
    // ----------------- chains ----------------------------
    System.out.println("--- Learning chains ---");
    // Adapt residue structures
    for (Residue res : families.getResidues().getObjects()) res.explicitToImplicitHydrogens();
    ChainLearning learning = new ChainLearning(learningBase);
    learning.setMarkovianSize(markovianSize);
    learning.learn(families);
    // --- Save ---
    System.out.println("--- Saving chains ---");
    FamilyChainIO fcio = new FamilyChainIO(families);
    fcio.saveFile(learning.getDb(), jsonChains);
    System.out.println("--- Ended ---");
}

Example 18 with Residue

use of model.Residue 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 19 with Residue

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

the class ResidueCreatorTests method linksCreationTest.

@Test
public void linksCreationTest() {
    Residue tyrN = null;
    for (Residue res : this.residues) 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 20 with Residue

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

the class ChainLearningTests method loadTest.

/**/
@Test
public void loadTest() {
    // Computing
    ChainLearning learning = new ChainLearning(this.learningBase);
    learning.setMarkovianSize(3);
    learning.learn(this.families);
    ChainsDB db = learning.getDb();
    FamilyChainIO io = new FamilyChainIO(this.families);
    io.saveFile(db, "data_tests/chains.json");
    ChainsDB loaded = io.loadFile("data_tests/chains.json");
    if (loaded.getObjects().size() != db.getObjects().size())
        fail("Not the same number of objects");
    FamilyChainsDB fc = db.getObjects().get(0);
    FamilyChainsDB fcLoaded = loaded.getObjects().get(0);
    if (fc.getRootChains().size() != fcLoaded.getRootChains().size())
        fail("Root chain number different");
    for (Residue res : fc.getFamily().getResidues()) {
        if (fc.getAdds(res).size() != fcLoaded.getAdds(res).size())
            fail("Adds of " + res.getName() + "are not correctly loaded");
    }
    Assert.assertTrue(true);
}