Examples with Residue model.Residue used on opensource projects

Example 6 with Residue

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

the class ChainsFamilyMatching method matchFamilly.

@Override
public Coverage matchFamilly(Family family) {
    if (this.co == null)
        return null;
    this.coverage = new Coverage(co);
    FamilyChainsDB fc = this.chains.getObject(family.getJsonName());
    this.toMatch.addAll(family.getRoots());
    while (!toMatch.isEmpty()) {
        Residue res = toMatch.remove();
        List<MappedChain> mcs = null;
        List<ChainAdd> adds = fc.getAdds(res);
        // If the residue is a root
        if (adds.size() == 0) {
            Chain rootChain = fc.getRootChains().get(res);
            mcs = Isomorphism.searchAChain(rootChain, this.co, this.matchingType);
        } else // From previous mapping
        {
            mcs = new ArrayList<>();
            Residue from = adds.get(0).getFrom();
            for (MappedChain mc : mappings.get(from)) {
                try {
                    MappedChain clone = mc;
                    for (ChainAdd add : adds) clone = add.applyAndClone(mc, this.matchingType);
                    mcs.add(clone);
                } catch (Exception e) {
                }
            }
        }
        // Save results and recursive add
        if (mcs.size() > 0) {
            this.mappings.put(res, mcs);
            this.addToCoverage(family, mcs, res);
            for (Residue child : fc.getFamily().getChildrenOf(res)) {
                if (fc.getAdds(child).get(0).getFrom().equals(res)) {
                    this.toMatch.add(child);
                }
            }
        }
    }
    this.mappings.clear();
    return this.coverage;
}

Example 7 with Residue

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

the class ChainLearning method calculateMapping.

private List<MappedChain> calculateMapping(FamilyChainsDB fc, Residue res, Residue from, MappedChain mc) {
    if (this.finalChains.containsKey(res.getId())) {
        Chain chain = this.finalChains.get(res.getId());
        List<MappedChain> mappings = Isomorphism.searchAChain(chain, mc.getChemObject(), MatchingType.STRONG);
        return mappings;
    } else {
        Residue ancestor = null;
        if (!this.finalChains.containsKey(from.getId())) {
            List<ChainAdd> adds = fc.getAdds(from);
            ancestor = adds.get(0).getFrom();
        }
        List<MappedChain> newMcs = this.calculateMapping(fc, from, ancestor, mc);
        List<MappedChain> toRemove = new ArrayList<>();
        for (MappedChain newMc : newMcs) for (ChainAdd add : fc.getAdds(res)) {
            try {
                add.apply(newMc, MatchingType.STRONG);
            } catch (Exception e) {
                toRemove.add(newMc);
                break;
            }
        }
        for (MappedChain mcRem : toRemove) newMcs.remove(mcRem);
        return newMcs;
    }
}

Example 8 with Residue

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

the class ChainLearning method learnMarkovianNext.

// --------------------------------- Markovian ------------------------------------
private ResidueMappings learnMarkovianNext(ResidueMappings prevIndex) {
    ResidueMappings currentMappings = new ResidueMappings();
    // Create all extended blocs
    HashSet<Chain> blocs = new HashSet<>();
    for (Residue root : prevIndex.keySet()) {
        List<MappedChain> prevResIndex = prevIndex.get(root);
        List<MappedChain> resIndex = this.createBlocsFromPrevious(prevResIndex);
        if (resIndex.size() > 0)
            currentMappings.put(root, resIndex);
        else {
            currentMappings.put(root, prevResIndex);
            continue;
        }
        for (MappedChain mb : resIndex) blocs.add(mb.getChain());
    }
    // Filtering blocs
    for (Chain b : blocs) {
        String smiles = b.getMySmiles();
        if (!this.chains.containsKey(smiles)) {
            this.chains.put(smiles, b);
        } else {
            Chain rival = this.chains.get(smiles);
            double rivalScore = this.computeScore(rival);
            double score = this.computeScore(b);
            if (score < rivalScore) {
                this.chains.put(smiles, b);
                for (List<MappedChain> mbs : currentMappings.values()) {
                    int size = mbs.size();
                    for (int idx = size - 1; idx >= 0; idx--) if (mbs.get(idx).getChain().equals(rival))
                        mbs.remove(idx);
                }
            } else {
                for (List<MappedChain> mbs : currentMappings.values()) {
                    int size = mbs.size();
                    for (int idx = size - 1; idx >= 0; idx--) if (mbs.get(idx).getChain().equals(b))
                        mbs.remove(idx);
                }
            }
        }
        // Polymer matching and frequency computation for each new chain
        this.calculateFrequency(b);
    }
    return currentMappings;
}

Example 9 with Residue

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

the class ChainLearning method recurChildrenAdds.

private void recurChildrenAdds(FamilyChainsDB fc, Residue from, Set<Residue> children) {
    for (Residue child : children) {
        List<ChainAdd> adds = fc.getAdds(child);
        // If extensions already exist, jump to the next son.
        if (adds.size() > 0)
            continue;
        List<MappedChain> mcs = this.calculateMapping(fc, child, from, new MappedChain(child));
        // Collections.sort(mcs, new MappedChainComparator());
        MappedChain mc = mcs.get(0);
        // Hydrogen adds
        for (int atomIdx : mc.getAtomsMapping()) {
            IAtom a = mc.getChemObject().getMolecule().getAtom(atomIdx);
            int chainIdx = mc.getAtomsMapping().indexOf(atomIdx);
            Map<Integer, Integer> mapping = mc.getHydrogensMapping();
            int mappingHydrogens = mapping.containsKey(atomIdx) ? mapping.get(atomIdx) : 0;
            int molHydrogens = a.getImplicitHydrogenCount();
            if (mappingHydrogens < molHydrogens)
                adds.add(new HydrogenAdd(from, chainIdx, molHydrogens - mappingHydrogens));
        }
        // Extensions
        IMolecule resMol = mc.getChemObject().getMolecule();
        for (IBond bond : resMol.bonds()) {
            int bondIdx = resMol.getBondNumber(bond);
            if (mc.getBondsMapping().contains(bondIdx))
                continue;
            Extension ext = new Extension(bond);
            List<MappedChain> tmpMappings = Isomorphism.searchFromPreviousMapping(mc, ext, MatchingType.EXACT);
            for (MappedChain tmp : tmpMappings) if (tmp.getBondsMapping().get(tmp.getBondsMapping().size() - 1) == bondIdx) {
                Chain chain = tmp.getChain();
                BondAdd ba = new BondAdd(from, ext, chain.getPosition1(), chain.getPosition2());
                adds.add(ba);
            }
        }
        /**/
        this.recurChildrenAdds(fc, child, fc.getFamily().getChildrenOf(child));
    }
}

Example 10 with Residue

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

the class Coverage method getCorrectness.

public double getCorrectness(FamilyDB families) {
    if (!this.alreadyCalculate)
        this.calculateGreedyCoverage();
    if (this.corrects == null)
        this.calculateCorrectIncorrectNotFound(families);
    int pepAtoms = 0;
    for (@SuppressWarnings("unused") IAtom a : this.co.getMolecule().atoms()) pepAtoms++;
    int corAtoms = 0;
    for (Residue res : this.corrects.keySet()) {
        int resAtoms = res.getMolecule().getAtomCount();
        corAtoms += resAtoms * this.corrects.get(res);
    }
    double ratio = new Double(corAtoms) / new Double(pepAtoms);
    return ratio;
}