Examples with Residue model.Residue used on opensource projects

Example 31 with Residue

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

the class IsomorphismFamilyMatcher method matchFamilly.

@Override
public Coverage matchFamilly(Family family) {
    // Initialization
    Coverage cov = new Coverage(co);
    IMolecule mol = co.getMolecule();
    Set<Residue> markSet = new HashSet<>();
    Stack<Residue> searchSet = new Stack<>();
    searchSet.addAll(family.getRoots());
    // For all the nodes in the search group.
    while (!searchSet.isEmpty()) {
        Residue currentRes = searchSet.pop();
        // Search the current residue in mol.
        try {
            this.sqt.setSmarts(currentRes.getSmiles());
        } catch (CDKException e) {
            e.printStackTrace();
        }
        boolean isMatching = false;
        try {
            long time = System.currentTimeMillis();
            isMatching = this.sqt.matches(mol);
            if (verbose)
                System.out.println("    Search for " + currentRes.getName() + " in " + (System.currentTimeMillis() - time));
        } catch (CDKException e) {
            e.printStackTrace();
        }
        // If there is at least one occurrence.
        if (isMatching) {
            // Add matches to the coverage
            List<Match> matches = new ArrayList<>();
            for (List<Integer> lMatch : sqt.getMatchingAtoms()) {
                Match match = new Match(currentRes);
                for (int i : lMatch) match.addAtom(i);
                matches.add(match);
            }
            // Change to compare.
            cov.addListMatches(currentRes, matches);
            // Mark current residue to possibly add children.
            markSet.add(currentRes);
            // Add children with all parents marked
            Set<Residue> children = family.getChildrenOf(currentRes);
            for (Residue child : children) {
                boolean canBeAdded = true;
                for (Link dependance : family.getDepandances()) if (dependance.getTo().equals(child))
                    if (!markSet.contains(dependance.getFrom())) {
                        canBeAdded = false;
                        break;
                    }
                if (canBeAdded)
                    searchSet.add(child);
            }
        }
    }
    return cov;
}

Example 32 with Residue

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

the class ChainLearning method initLearn.

// -------------------------------- Initialization ----------------------------------
private void initLearn(List<Residue> roots, ResidueMappings mappings) {
    for (Residue res : roots) {
        List<MappedChain> resMappings = new ArrayList<>();
        for (IBond bond : res.getMolecule().bonds()) {
            Extension ext = new Extension(bond);
            Chain bloc = new Chain(ext);
            String smiles = bloc.getMySmiles();
            this.chains.put(smiles, bloc);
            this.frequence.put(smiles, 0);
            // Creation of residue matchings (sequences of size 1)
            for (BondMapping bm : ext.match(bond, MatchingType.EXACT)) {
                MappedChain resMap = this.createMappingFromMatch(res, bond, bloc, bm);
                resMappings.add(resMap);
            }
        }
        mappings.put(res, resMappings);
    }
    this.frequencesInit();
}

Example 33 with Residue

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

the class ChainLearning method addAddsToSons.

// -------------------------------------- Children extensions -------------------------------------
private void addAddsToSons(FamilyChainsDB fc, Family fam) {
    for (Residue root : fam.getRoots()) {
        fc.addRootChain(root, this.finalChains.get(root.getId()));
        Set<Residue> children = fam.getChildrenOf(root);
        this.recurChildrenAdds(fc, root, children);
    }
}

Example 34 with Residue

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

the class ResidueCreator method createResidue.

// Create residue when it was found
private Set<Residue> createResidue(List<RMap> match, Rule rule, Residue res) {
    Set<Residue> residues = new HashSet<>();
    // Create index
    int[] index = new int[match.size()];
    for (RMap rm : match) {
        index[rm.getId2()] = rm.getId1();
    }
    for (Replacement replace : rule.getReplacements()) {
        // Clone molecule
        Molecule oldMol = res.getMolecule();
        Molecule mol = null;
        try {
            mol = (Molecule) oldMol.clone();
        } catch (CloneNotSupportedException e) {
            e.printStackTrace();
        }
        // Save links atoms
        Map<IAtom, IAtom> convesionAtom = new HashMap<>();
        for (IAtom a : res.getAtomicLinks().keySet()) {
            int idx = oldMol.getAtomNumber(a);
            IAtom newA = mol.getAtom(idx);
            convesionAtom.put(a, newA);
        }
        // Prepare deletions
        List<IAtom> deletedAtoms = new ArrayList<>();
        List<IAtom> linkedAtoms = new ArrayList<>();
        for (int i : replace.toDelete) deletedAtoms.add(mol.getAtom(index[i]));
        for (int i : replace.toReplace) {
            IAtom atom = mol.getAtom(index[i]);
            deletedAtoms.add(atom);
            for (IAtom neighbor : mol.getConnectedAtomsList(atom)) if (!neighbor.getSymbol().equals("H") && !deletedAtoms.contains(neighbor))
                linkedAtoms.add(neighbor);
        }
        // Delete atoms
        for (IAtom a : deletedAtoms) {
            for (IBond b : mol.getConnectedBondsList(a)) mol.removeBond(b);
            mol.removeAtom(a);
        }
        String smarts = this.sg.createSMILES(mol);
        if (!Residue.existingResidue(smarts, res.getMonoName())) {
            Residue residue = Residue.constructResidue(res.getMonoName(), smarts);
            residue.setMol(mol);
            // Add old links
            for (IAtom oldA : convesionAtom.keySet()) {
                IAtom newA = convesionAtom.get(oldA);
                // int oldIdx = oldMol.getAtomNumber(oldA);
                // int newIdx = mol.getAtomNumber(newA);
                residue.getAtomicLinks().put(newA, res.getAtomicLinks().get(oldA));
            }
            // Add new Links
            for (IAtom a : linkedAtoms) residue.addLink(a, rule);
            residues.add(residue);
        } else {
            Residue residue = Residue.constructResidue(res.getMonoName(), smarts);
            residues.add(residue);
        }
    }
    return residues;
}

Example 35 with Residue

use of model.Residue 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;
}