Examples with Family model.Family used on opensource projects

Example 11 with Family

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

the class FamilyDB method addObject.

@Override
public void addObject(String id, Family f) {
    Family prev = null;
    for (Monomer m : f.getMonomers()) if (this.database.containsKey(m.getId())) {
        prev = this.database.get(m.getId());
        break;
    }
    if (prev == null) {
        for (Monomer m : f.getMonomers()) {
            super.addObject(m.getId(), f);
            this.uniqFamilies.add(f);
        }
    } else {
        for (Monomer m : f.getMonomers()) {
            prev.addMonomer(m);
            this.database.put(m.getId(), prev);
        }
        for (Residue res : f.getResidues()) prev.addResidue(res);
        for (Link l : f.getDepandances()) prev.addDependance(l);
    }
}

Example 12 with Family

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

the class FamilyDB method areInSameFamily.

public boolean areInSameFamily(String mono1, String mono2) {
    Family family1 = null;
    Family family2 = null;
    try {
        family1 = this.getObject(mono1);
        family2 = this.getObject(mono2);
    } catch (NullPointerException e) {
        e.printStackTrace();
    }
    return family1.equals(family2);
}

Example 13 with Family

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

the class MonomericSpliting method matchAllFamilies.

/**
 * Function to match independently all families onto the polymer.
 * Can easily be parallelized
 * @param matchType Strict/Light
 */
private void matchAllFamilies(MatchingType matchType) {
    for (Family family : this.families.getFamilies()) {
        /*/ Display
			if (verbose) {
				System.out.println("In " + polName);
				System.out.println("  Family " + i++ + "/" + nbFamilies);
			}/**/
        // Time initialization
        // long time = System.currentTimeMillis();
        // Matching
        this.matcher.setAllowLightMatch(matchType);
        Coverage cov = this.matcher.matchFamilly(family);
        if (matchType.equals(MatchingType.LIGHT)) {
            for (Match match : cov.getMatches()) {
                Match transformed = DeepenMatcher.transform(match, this.coverage.getCurrentMaskedMol(), this.coverage.getChemicalObject().getMolecule());
                this.coverage.addMatch(transformed);
            }
        } else
            this.coverage.addMatches(cov);
    /*if (verbose)
				System.out.println("  Search " + matchType.getClass().getCanonicalName() +
						" for family " + family.getName() + " in " + (System.currentTimeMillis()-time) + "\n");/**/
    }
}

Example 14 with Family

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

the class ResidueCreator method createResidues.

/**
 * Create all residues from the argument monomers database according to rules entered in paramaters of the constructor.
 * @param monosDBName A monomers database.
 * @return All possible residues found.
 */
public FamilyDB createResidues(MonomersDB monosDB) {
    FamilyDB famDB = new FamilyDB();
    famDB.init(monosDB);
    for (Family family : famDB.getFamilies()) {
        this.residuesFromMonomers(family);
        for (Residue res : family.getResidues()) {
            IMolecule oldMol = res.getMolecule();
            res.setMol(new Molecule(AtomContainerManipulator.removeHydrogens(res.getMolecule())));
            IMolecule newMol = res.getMolecule();
            Map<IAtom, IAtom> conversion = new HashMap<>();
            int idx = 0;
            for (IAtom a : oldMol.atoms()) {
                if (!"H".equals(a.getSymbol())) {
                    conversion.put(a, newMol.getAtom(idx));
                    idx++;
                }
            }
            Map<IAtom, Rule> oldLinks = new HashMap<>(res.getAtomicLinks());
            res.getAtomicLinks().clear();
            for (IAtom oldA : oldLinks.keySet()) {
                Rule rule = oldLinks.get(oldA);
                res.addLink(conversion.get(oldA), rule);
            }
        }
    }
    return famDB;
}