Examples with MonomersDB db.MonomersDB used on opensource projects

Example 11 with MonomersDB

use of db.MonomersDB in project Smiles2Monomers by yoann-dufresne.

the class ContractedGraphTests method setUp.

@Before
public void setUp() throws Exception {
    MonomersDB monos = new MonomersJsonLoader().loadFile("data_tests/monos.json");
    PolymersDB peps = new PolymersJsonLoader(monos).loadFile("data_tests/peps.json");
    RulesDB rules = RulesJsonLoader.loader.loadFile("data_tests/rules.json");
    ResidueCreator rc = new ResidueCreator(rules);
    FamilyDB families = rc.createResidues(monos);
    ChainLearning cl = new ChainLearning(peps);
    cl.setMarkovianSize(3);
    cl.learn(families);
    ChainsDB chains = cl.getDb();
    MonomericSpliting ms = new MonomericSpliting(families, chains, 2, 2, 3);
    Polymer pol = peps.getObject("633");
    ms.computeCoverage(pol);
    this.coverage = ms.getCoverage();
    this.coverage.calculateGreedyCoverage();
    this.contractedGraph = new ContractedGraph(coverage);
}

Example 12 with MonomersDB

use of db.MonomersDB in project Smiles2Monomers by yoann-dufresne.

the class TreeWidthTests method setUp.

@Before
public void setUp() throws Exception {
    String pepDBname = "data_tests/peps.json";
    // Loading databases
    MonomersDB monoDB = new MonomersDB();
    PolymersJsonLoader pcl = new PolymersJsonLoader(monoDB);
    this.pepDB = pcl.loadFile(pepDBname);
}