Search in sources :

Example 1 with FamilyChainIO

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

the class ChainLearningTests method saveTest.

/**/
@Test
public void saveTest() {
    String line = null;
    String expected = "[{\"roots\":{\"86\":\"C,0,C,1,2,-1,-1;C,0,N,1,1,0,-1;C,0,C,0,1,-1,0;C,1,O,0,0,3,-1\",\"87\":\"C,0,O,2,0,-1,-1;C,0,C,1,2,-1,0;C,0,C,0,1,-1,2;C,0,N,1,1,2,-1;C,1,O,0,0,3,-1\"},\"family\":\"D-Ser\",\"extensions\":{\"79\":[{\"idx2\":-1,\"idx1\":3,\"from\":\"85\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"78\":[{\"idx2\":-1,\"idx1\":3,\"from\":\"84\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"77\":[{\"num\":1,\"idx\":1,\"from\":\"84\",\"type\":\"hydrogen\"}],\"82\":[{\"idx2\":-1,\"idx1\":3,\"from\":\"87\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"83\":[{\"idx2\":-1,\"idx1\":3,\"from\":\"86\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"80\":[{\"idx2\":-1,\"idx1\":3,\"from\":\"81\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"81\":[{\"num\":1,\"idx\":1,\"from\":\"87\",\"type\":\"hydrogen\"}],\"86\":[],\"87\":[],\"84\":[{\"num\":1,\"idx\":4,\"from\":\"87\",\"type\":\"hydrogen\"}],\"85\":[{\"num\":1,\"idx\":2,\"from\":\"86\",\"type\":\"hydrogen\"}]}},{\"roots\":{\"95\":\"C,0,N,2,1,-1,-1;C,0,C,1,2,-1,0;C,0,N,1,1,2,-1;C,0,C,0,1,-1,2;C,1,O,0,0,4,-1\"},\"family\":\"Dpr\",\"extensions\":{\"95\":[],\"94\":[{\"idx2\":-1,\"idx1\":4,\"from\":\"95\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"93\":[{\"num\":1,\"idx\":3,\"from\":\"95\",\"type\":\"hydrogen\"}],\"92\":[{\"num\":1,\"idx\":1,\"from\":\"95\",\"type\":\"hydrogen\"}],\"91\":[{\"idx2\":-1,\"idx1\":4,\"from\":\"93\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"90\":[{\"idx2\":-1,\"idx1\":4,\"from\":\"92\",\"type\":\"extension\",\"ext\":\"C,0,O,0,1\"}],\"89\":[{\"num\":1,\"idx\":1,\"from\":\"93\",\"type\":\"hydrogen\"}]}}]";
    // 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");
    try {
        BufferedReader br = new BufferedReader(new FileReader(new File("data_tests/chains.json")));
        line = br.readLine();
        br.close();
    } catch (IOException e) {
        fail(e.getMessage());
    }
    Assert.assertTrue(line.equals(expected));
}
Also used : FamilyChainIO(io.loaders.json.FamilyChainIO) ChainsDB(algorithms.isomorphism.chains.ChainsDB) FamilyChainsDB(algorithms.isomorphism.chains.FamilyChainsDB) BufferedReader(java.io.BufferedReader) FileReader(java.io.FileReader) IOException(java.io.IOException) ChainLearning(algorithms.isomorphism.chains.ChainLearning) File(java.io.File) Test(org.junit.Test)

Example 2 with FamilyChainIO

use of io.loaders.json.FamilyChainIO 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 3 with FamilyChainIO

use of io.loaders.json.FamilyChainIO 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)

Example 4 with FamilyChainIO

use of io.loaders.json.FamilyChainIO 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);
}
Also used : FamilyChainIO(io.loaders.json.FamilyChainIO) FamilyChainsDB(algorithms.isomorphism.chains.FamilyChainsDB) Residue(model.Residue) ChainsDB(algorithms.isomorphism.chains.ChainsDB) FamilyChainsDB(algorithms.isomorphism.chains.FamilyChainsDB) ChainLearning(algorithms.isomorphism.chains.ChainLearning) Test(org.junit.Test)

Aggregations

FamilyChainIO (io.loaders.json.FamilyChainIO)4 ChainLearning (algorithms.isomorphism.chains.ChainLearning)3 ChainsDB (algorithms.isomorphism.chains.ChainsDB)3 File (java.io.File)3 FamilyChainsDB (algorithms.isomorphism.chains.FamilyChainsDB)2 FamilyDB (db.FamilyDB)2 MonomersDB (db.MonomersDB)2 PolymersDB (db.PolymersDB)2 RulesDB (db.RulesDB)2 MonomersJsonLoader (io.loaders.json.MonomersJsonLoader)2 PolymersJsonLoader (io.loaders.json.PolymersJsonLoader)2 ResidueJsonLoader (io.loaders.json.ResidueJsonLoader)2 MonomersSerialization (io.loaders.serialization.MonomersSerialization)2 Residue (model.Residue)2 Test (org.junit.Test)2 MonomericSpliting (algorithms.MonomericSpliting)1 ResidueCreator (algorithms.ResidueCreator)1 Coverage (algorithms.utils.Coverage)1 Coverages2HTML (io.html.Coverages2HTML)1 ImagesGeneration (io.imgs.ImagesGeneration)1