Examples with Residue model.Residue used on opensource projects

Example 11 with Residue

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

the class Coverage method getIncorrectMonomers.

public Map<String, Integer> getIncorrectMonomers(FamilyDB families) {
    this.calculateCorrectIncorrectNotFound(families);
    Map<String, Integer> incorrects = new HashMap<>();
    for (Residue res : this.incorrects.keySet()) {
        Family fam = families.getObject(res.getMonoName());
        String name = fam.getShortName();
        int val = incorrects.containsKey(name) ? incorrects.get(name) : 0;
        incorrects.put(name, val + this.incorrects.get(res));
    }
    return incorrects;
}

Example 12 with Residue

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

the class Coverage method calculateCorrectIncorrectNotFound.

public void calculateCorrectIncorrectNotFound(FamilyDB families) {
    this.corrects = new HashMap<>();
    this.incorrects = new HashMap<>();
    this.notFound = new HashMap<>();
    List<Monomer> realMonos = new ArrayList<>();
    for (Monomer m : this.co.getGraph().nodes) realMonos.add(m);
    for (Match match : this.usedMatches) {
        Residue r = match.getResidue();
        // For each is correct ?
        boolean correct = false;
        Family fam = null;
        try {
            fam = families.getObject(r.getMonoName());
        } catch (NullPointerException e) {
            e.printStackTrace();
        }
        for (Monomer m : fam.getMonomers()) {
            if (realMonos.contains(m)) {
                correct = true;
                realMonos.remove(m);
                break;
            }
        }
        if (correct) {
            int nb = this.corrects.containsKey(r) ? this.corrects.get(r) : 0;
            this.corrects.put(r, nb + 1);
        } else {
            int nb = this.incorrects.containsKey(r) ? this.incorrects.get(r) : 0;
            this.incorrects.put(r, nb + 1);
        }
    }
    for (Monomer m : realMonos) {
        String name = null;
        try {
            Family fam = families.getObject(m.getName());
            name = fam.getShortName();
        } catch (NullPointerException e) {
            name = m.getName();
        }
        int nb = this.notFound.containsKey(name) ? this.notFound.get(name) : 0;
        this.notFound.put(name, nb + 1);
    }
}

Example 13 with Residue

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

the class Coverage method addMatch.

public void addMatch(Match match) {
    this.matches.add(match);
    Residue res = match.getResidue();
    this.residues.addObject(res.getSmiles(), res);
}

Example 14 with Residue

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

the class ResidueCreator method getResiduesWithRule.

/*
	 * Search Residues for one monomer and one rule.
	 */
private Set<Residue> getResiduesWithRule(Residue res, Rule rule) {
    Set<Residue> residues = new HashSet<>();
    IMolecule ruleMol = null;
    try {
        ruleMol = SmilesConverter.conv.transform(rule.getFormula(), false, false, true);
    } catch (InvalidSmilesException e) {
        System.err.println("Impossible to parse " + rule.getName() + " rule");
        return residues;
    }
    boolean status = false;
    try {
        status = UniversalIsomorphismTester.isSubgraph(res.getMolecule(), ruleMol);
    } catch (CDKException e) {
        e.printStackTrace();
    }
    // If rule is found
    if (status) {
        List<List<RMap>> matches = null;
        try {
            matches = UniversalIsomorphismTester.getSubgraphAtomsMaps(res.getMolecule(), ruleMol);
        } catch (CDKException e) {
            e.printStackTrace();
        }
        if (!"".equals(rule.getExclusion()))
            for (String exclusion : rule.getExclusion()) this.removeExclusions(matches, exclusion, res.getMolecule());
        for (List<RMap> match : matches) {
            Set<Residue> residuesByMatch = this.createResidue(match, rule, res);
            residues.addAll(residuesByMatch);
        }
    }
    return residues;
}

Example 15 with Residue

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

the class ResidueCreator method residuesFromMonomers.

/*
	 * Create residues from a monomer according to the rules database.
	 */
private Set<Residue> residuesFromMonomers(Family family) {
    Monomer mono = family.getMonomers().get(0);
    Set<Residue> residues = new HashSet<>();
    RulesDB rules = new RulesDB();
    rules.addDB(this.dbAlone);
    // List of residues in witch we search other residues.
    Set<Residue> searchResidues = new HashSet<>();
    IMolecule m = null;
    try {
        m = mono.getMolecule().clone();
        AtomContainerManipulator.convertImplicitToExplicitHydrogens(m);
    } catch (CloneNotSupportedException e1) {
        e1.printStackTrace();
    }
    searchResidues.add(new Residue(mono.getCode(), this.sg.createSMILES(m), true));
    boolean firstTime = true;
    while (searchResidues.size() != 0) {
        Set<Residue> nextLevelResidues = new HashSet<>();
        for (Residue res : searchResidues) {
            res.setExplicitHydrogens(true);
            Set<Residue> newResidues = new HashSet<>();
            for (Rule rule : rules.getObjects()) {
                Set<Residue> ruleResidues = this.getResiduesWithRule(res, rule);
                newResidues.addAll(ruleResidues);
                for (Residue r : ruleResidues) nextLevelResidues.add(r);
            }
            for (Residue newRes : newResidues) {
                family.addResidue(newRes);
                if (family.containsMonomer(res.getMonoName()) && res.getAtomicLinks().size() > 0)
                    family.addDependance(newRes, res);
            }
            res.setExplicitHydrogens(false);
        }
        searchResidues = nextLevelResidues;
        residues.addAll(searchResidues);
        if (firstTime) {
            firstTime = false;
            rules.addDB(this.dbNotAlone);
        }
    }
    if (residues.size() == 0) {
        String smiles = this.sg.createSMILES(m);
        Residue res = Residue.constructResidue(mono.getName(), smiles);
        family.addResidue(res);
        residues.add(res);
    }
    if (this.verbose) {
        System.out.println("Nb residues of " + mono.getCode() + " : " + residues.size());
        for (Residue res : residues) System.out.println("  " + res.getSmiles());
        System.out.println();
    }
    return residues;
}