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Example 1 with ResidueJsonLoader

use of io.loaders.json.ResidueJsonLoader in project Smiles2Monomers by yoann-dufresne.

the class ChainLearningTests method setUp.

@Before
public void setUp() throws Exception {
    // Loading test monomers
    MonomersDB premonos = new MonomersJsonLoader().loadFile("data_tests/monos.json");
    // Creation of a subset of monos
    this.monos = new MonomersDB();
    this.monos.addObject("Dpr", premonos.getObject("Dpr"));
    this.monos.addObject("D-Ser", premonos.getObject("D-Ser"));
    // Loading test rules
    RulesDB rules = RulesJsonLoader.loader.loadFile("data_tests/rules.json");
    // Loading test residues
    ResidueJsonLoader rjl = new ResidueJsonLoader(rules, this.monos);
    this.families = rjl.loadFile("data_tests/res.json");
    // Loading test polymers
    PolymersJsonLoader pjl = new PolymersJsonLoader(premonos);
    PolymersDB base = pjl.loadFile("data_tests/peps.json");
    // Creation of learning base with only 1 polymer.
    this.learningBase = new PolymersDB();
    this.learningBase.addObject("AM-toxin II", base.getObject("306"));
    // Construct reference
    this.constructReference();
}
Also used : RulesDB(db.RulesDB) MonomersJsonLoader(io.loaders.json.MonomersJsonLoader) PolymersDB(db.PolymersDB) MonomersDB(db.MonomersDB) PolymersJsonLoader(io.loaders.json.PolymersJsonLoader) ResidueJsonLoader(io.loaders.json.ResidueJsonLoader) Before(org.junit.Before)

Example 2 with ResidueJsonLoader

use of io.loaders.json.ResidueJsonLoader 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();
    }
}
Also used : RulesDB(db.RulesDB) MonomersJsonLoader(io.loaders.json.MonomersJsonLoader) Residue(model.Residue) MonomersDB(db.MonomersDB) FileWriter(java.io.FileWriter) Family(model.Family) FamilyDB(db.FamilyDB) IOException(java.io.IOException) ResidueJsonLoader(io.loaders.json.ResidueJsonLoader) File(java.io.File)

Example 3 with ResidueJsonLoader

use of io.loaders.json.ResidueJsonLoader in project Smiles2Monomers by yoann-dufresne.

the class Json2HTML method main.

public static void main(String[] args) {
    if (args.length < 6) {
        System.err.println("Command line :\n\tjava main.AtomicToMonomeric <monomersFile> <peptidesFile> <rulesFile> <residuesFile> <coveragesFile> <outType> [outFile]  [-v]");
        System.err.println("  outType can be \"-zip\" or \"-html\"");
        System.exit(42);
    }
    String monoDBname = args[0];
    String pepDBname = args[1];
    String rulesDBname = args[2];
    String residuesDBname = args[3];
    String covsFile = args[4];
    boolean zip = args[5].equals("-zip") ? true : false;
    String outFile = null;
    if (zip && args.length < 7) {
        System.err.println("Command line :\n\tjava main.AtomicToMonomeric <monomersFile> <peptidesFile> <rulesFile> <residuesFile> <coveragesFile> <outType> [outFile]  [-v]");
        System.err.println("  outType can be \"-zip\" or \"-html\"");
        System.exit(42);
    } else if (zip && args.length >= 7)
        outFile = args[6];
    // Loading databases
    System.out.println("--- Loading ---");
    // Maybe loading can be faster for the learning base, using serialized molecules instead of CDK SMILES parsing method.
    long loadingTime = System.currentTimeMillis();
    MonomersDB monoDB = new MonomersJsonLoader(false).loadFile(monoDBname);
    MonomersSerialization ms = new MonomersSerialization();
    ms.deserialize(monoDB, "data/serials/monos.serial");
    PolymersJsonLoader pcl = new PolymersJsonLoader(monoDB, true);
    PolymersDB pepDB = pcl.loadFile(pepDBname);
    RulesDB rules = RulesJsonLoader.loader.loadFile(rulesDBname);
    ResidueJsonLoader rjl = new ResidueJsonLoader(rules, monoDB);
    FamilyDB families = rjl.loadFile(residuesDBname);
    loadingTime = (System.currentTimeMillis() - loadingTime) / 1000;
    System.out.println("--- Json to HTML ---");
    long creationTime = System.currentTimeMillis();
    CoveragesJsonLoader cl = new CoveragesJsonLoader(pepDB, families);
    CoveragesDB covs = cl.loadFile(covsFile);
    List<Coverage> covsList = covs.getObjects();
    Collections.sort(covsList);
    // Common generations
    File imgs = new File("tmp_imgs_" + covsFile.substring(covsFile.lastIndexOf("/") + 1, covsFile.lastIndexOf(".")));
    if (!imgs.exists())
        imgs.mkdir();
    ImagesGeneration ig = new ImagesGeneration();
    Map<Coverage, ColorsMap> allColors = ig.generate(imgs, monoDB, covsList);
    if (!zip) {
        // HTML
        File resultDir = null;
        if (covsFile.contains("/"))
            resultDir = new File(covsFile.substring(0, covsFile.lastIndexOf("/")));
        else
            resultDir = new File(".");
        if (!resultDir.exists())
            resultDir.mkdir();
        Coverages2HTML c2h = new Coverages2HTML(covsList, monoDB, families);
        File htmlFile = new File(resultDir.getPath() + "/test.html");
        c2h.createResults(htmlFile, imgs, allColors);
    } else {
        // Zip File
        OutputZiper oz = new OutputZiper(outFile);
        oz.createZip(imgs.getPath(), covsFile, pepDBname, monoDBname, residuesDBname, allColors);
    }
    ig.cleanTmp(imgs);
    creationTime = (System.currentTimeMillis() - creationTime) / 1000;
    System.out.println();
    System.out.println("Total time to load datas : " + loadingTime + "s");
    System.out.println("Total time to create HTML : " + creationTime + "s");
    System.out.println();
    System.out.println("--- Program ended ---");
}
Also used : MonomersJsonLoader(io.loaders.json.MonomersJsonLoader) MonomersDB(db.MonomersDB) Coverage(algorithms.utils.Coverage) FamilyDB(db.FamilyDB) MonomersSerialization(io.loaders.serialization.MonomersSerialization) RulesDB(db.RulesDB) ImagesGeneration(io.imgs.ImagesGeneration) CoveragesDB(db.CoveragesDB) PolymersDB(db.PolymersDB) PolymersJsonLoader(io.loaders.json.PolymersJsonLoader) OutputZiper(io.zip.OutputZiper) CoveragesJsonLoader(io.loaders.json.CoveragesJsonLoader) Coverages2HTML(io.html.Coverages2HTML) ResidueJsonLoader(io.loaders.json.ResidueJsonLoader) File(java.io.File) ColorsMap(io.imgs.PictureCoverageGenerator.ColorsMap)

Example 4 with ResidueJsonLoader

use of io.loaders.json.ResidueJsonLoader 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 ---");
}
Also used : MonomersJsonLoader(io.loaders.json.MonomersJsonLoader) MonomersDB(db.MonomersDB) ResidueCreator(algorithms.ResidueCreator) FamilyDB(db.FamilyDB) ChainLearning(algorithms.isomorphism.chains.ChainLearning) MonomersSerialization(io.loaders.serialization.MonomersSerialization) RulesDB(db.RulesDB) FamilyChainIO(io.loaders.json.FamilyChainIO) Residue(model.Residue) PolymersDB(db.PolymersDB) PolymersJsonLoader(io.loaders.json.PolymersJsonLoader) ResidueJsonLoader(io.loaders.json.ResidueJsonLoader) File(java.io.File)

Example 5 with ResidueJsonLoader

use of io.loaders.json.ResidueJsonLoader in project Smiles2Monomers by yoann-dufresne.

the class ProcessPolymers method main.

public static void main(String[] args) {
    // ----------------- Parameters ---------------------------
    String monoDBname = "data/monomers.json";
    String pepDBname = "data/polymers.json";
    String rulesDBname = "data/rules.json";
    String residuesDBname = "data/residues.json";
    String chainsDBFile = "data/chains.json";
    String outfile = "results/coverages.json";
    String outfolderName = "results/";
    String imgsFoldername = "images/";
    boolean html = false;
    boolean zip = false;
    String serialFolder = "data/serials/";
    boolean lightMatch = true;
    boolean verbose = false;
    int removeDistance = 2;
    int retryCount = 2;
    int modulationDepth = 2;
    // Parsing
    loop: for (int idx = 0; idx < args.length; idx++) {
        if (args[idx].startsWith("-")) {
            switch(args[idx]) {
                case "-rul":
                    rulesDBname = args[idx + 1];
                    break;
                case "-mono":
                    monoDBname = args[idx + 1];
                    break;
                case "-poly":
                    pepDBname = args[idx + 1];
                    break;
                case "-res":
                    residuesDBname = args[idx + 1];
                    break;
                case "-cha":
                    chainsDBFile = args[idx + 1];
                    break;
                case "-serial":
                    serialFolder = args[idx + 1];
                    break;
                case "-outfile":
                    outfile = args[idx + 1];
                    break;
                case "-outfolder":
                    outfolderName = args[idx + 1];
                    break;
                case "-imgs":
                    imgsFoldername = args[idx + 1];
                    break;
                case "-strict":
                    lightMatch = false;
                    continue loop;
                case "-v":
                    verbose = true;
                    continue loop;
                case "-html":
                    html = true;
                    continue loop;
                case "-zip":
                    zip = true;
                    continue loop;
                default:
                    System.err.println("Wrong option " + args[idx]);
                    System.exit(1);
                    break;
            }
            idx++;
        } else {
            System.err.println("Wrong parameter " + args[idx]);
            System.exit(1);
        }
    }
    // ------------------- Loadings ------------------------
    System.out.println("--- Loading ---");
    // Maybe loading can be faster for the learning base, using serialized molecules instead of CDK SMILES parsing method.
    long loadingTime = System.currentTimeMillis();
    MonomersDB monoDB = new MonomersJsonLoader(false).loadFile(monoDBname);
    MonomersSerialization ms = new MonomersSerialization();
    ms.deserialize(monoDB, serialFolder + "monos.serial");
    boolean d2 = html || zip;
    PolymersJsonLoader pjl = new PolymersJsonLoader(monoDB, d2);
    PolymersDB polDB = pjl.loadFile(pepDBname);
    RulesDB rulesDB = RulesJsonLoader.loader.loadFile(rulesDBname);
    ResidueJsonLoader rjl = new ResidueJsonLoader(rulesDB, monoDB);
    // Need optimizations
    FamilyDB families = rjl.loadFile(residuesDBname);
    FamilyChainIO fcio = new FamilyChainIO(families);
    ChainsDB chains = fcio.loadFile(chainsDBFile);
    loadingTime = System.currentTimeMillis() - loadingTime;
    System.out.println("Loading time : " + (loadingTime / 1000) + "s");
    // ------------------- Spliting ------------------------
    System.out.println("--- Monomers search ---");
    long searchTime = System.currentTimeMillis();
    MonomericSpliting.setVerbose(verbose);
    MonomericSpliting split = new MonomericSpliting(families, chains, removeDistance, retryCount, modulationDepth);
    split.setAllowLightMatchs(lightMatch);
    Coverage[] covs = split.computeCoverages(polDB);
    searchTime = System.currentTimeMillis() - searchTime;
    System.out.println("Search time : " + (searchTime / 1000) + "s");
    // ------------------- Output ------------------------
    System.out.println("--- Output creations ---");
    long outputTime = System.currentTimeMillis();
    // Creation of the out directory
    File outfolder = new File(outfolderName);
    if (!outfolder.exists())
        outfolder.mkdir();
    CoveragesJsonLoader cjl = new CoveragesJsonLoader(polDB, families);
    cjl.saveFile(covs, outfile);
    // Images generation
    if (html || zip) {
        File imgsFolder = new File(imgsFoldername);
        if (!imgsFolder.exists())
            imgsFolder.mkdir();
        ImagesGeneration ig = new ImagesGeneration();
        ig.generateMonomerImages(imgsFolder, monoDB);
        Map<Coverage, ColorsMap> colors = ig.generatePeptidesImages(imgsFolder, covs);
        if (html) {
            // HTML
            Coverages2HTML c2h = new Coverages2HTML(covs, monoDB, families);
            File htmlFile = new File(outfolderName + "/s2m.html");
            c2h.createResults(htmlFile, imgsFolder, colors);
        }
        if (zip) {
            // Zip File
            OutputZiper oz = new OutputZiper(outfolderName + "/s2m.zip");
            oz.createZip(imgsFolder.getPath(), outfile, pepDBname, monoDBname, residuesDBname, colors);
        }
    }
    outputTime = System.currentTimeMillis() - outputTime;
    System.out.println("Ouputing time : " + (outputTime / 1000) + "s");
    System.out.println("--- Ended ---");
}
Also used : MonomericSpliting(algorithms.MonomericSpliting) MonomersJsonLoader(io.loaders.json.MonomersJsonLoader) MonomersDB(db.MonomersDB) ChainsDB(algorithms.isomorphism.chains.ChainsDB) Coverage(algorithms.utils.Coverage) FamilyDB(db.FamilyDB) MonomersSerialization(io.loaders.serialization.MonomersSerialization) RulesDB(db.RulesDB) FamilyChainIO(io.loaders.json.FamilyChainIO) ImagesGeneration(io.imgs.ImagesGeneration) PolymersDB(db.PolymersDB) PolymersJsonLoader(io.loaders.json.PolymersJsonLoader) OutputZiper(io.zip.OutputZiper) CoveragesJsonLoader(io.loaders.json.CoveragesJsonLoader) Coverages2HTML(io.html.Coverages2HTML) ResidueJsonLoader(io.loaders.json.ResidueJsonLoader) File(java.io.File) ColorsMap(io.imgs.PictureCoverageGenerator.ColorsMap)

Aggregations

ResidueJsonLoader (io.loaders.json.ResidueJsonLoader)7 MonomersJsonLoader (io.loaders.json.MonomersJsonLoader)6 FamilyDB (db.FamilyDB)5 MonomersDB (db.MonomersDB)5 RulesDB (db.RulesDB)5 File (java.io.File)5 PolymersDB (db.PolymersDB)4 PolymersJsonLoader (io.loaders.json.PolymersJsonLoader)4 MonomersSerialization (io.loaders.serialization.MonomersSerialization)3 Residue (model.Residue)3 Coverage (algorithms.utils.Coverage)2 Coverages2HTML (io.html.Coverages2HTML)2 ImagesGeneration (io.imgs.ImagesGeneration)2 ColorsMap (io.imgs.PictureCoverageGenerator.ColorsMap)2 CoveragesJsonLoader (io.loaders.json.CoveragesJsonLoader)2 FamilyChainIO (io.loaders.json.FamilyChainIO)2 OutputZiper (io.zip.OutputZiper)2 Family (model.Family)2 Before (org.junit.Before)2 MonomericSpliting (algorithms.MonomericSpliting)1