Examples with IAtom org.openscience.cdk.interfaces.IAtom used on opensource projects

Example 31 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class SmilesConverter method transform.

public Molecule transform(String smiles, boolean addHydrogens, boolean calculateCoordinate, boolean expliciteHydrogens) throws InvalidSmilesException {
    Molecule imol = null;
    try {
        imol = new Molecule(sp.parseSmiles(smiles));
        // Add hydrogens
        if (addHydrogens) {
            CDKHydrogenAdder adder = CDKHydrogenAdder.getInstance(imol.getBuilder());
            try {
                adder.addImplicitHydrogens(imol);
                if (expliciteHydrogens)
                    AtomContainerManipulator.convertImplicitToExplicitHydrogens(imol);
            } catch (CDKException e) {
                e.printStackTrace();
            }
        } else {
            for (IAtom a : imol.atoms()) a.setImplicitHydrogenCount(0);
            if (!expliciteHydrogens)
                imol = new Molecule(AtomContainerManipulator.removeHydrogens(imol));
        }
        if (calculateCoordinate) {
            StructureDiagramGenerator sdg = new StructureDiagramGenerator(imol);
            try {
                sdg.generateCoordinates();
            } catch (CDKException e) {
                System.err.println(smiles);
                e.printStackTrace();
            }
            imol = new Molecule(sdg.getMolecule());
        }
    } catch (InvalidSmilesException e) {
        throw e;
    }
    return imol;
}

Example 32 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class Coverage method getCoverageRatio.

public double getCoverageRatio() {
    if (!this.alreadyCalculate)
        this.calculateGreedyCoverage();
    int coveredAtoms = 0;
    for (Match match : this.usedMatches) coveredAtoms += match.getAtoms().size();
    int pepAtoms = 0;
    for (@SuppressWarnings("unused") IAtom a : this.co.getMolecule().atoms()) pepAtoms++;
    double ratio = new Double(coveredAtoms) / new Double(pepAtoms);
    return ratio;
}

Example 33 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class IsomorphismTests method MappingTest.

@Test
public void MappingTest() {
    List<MappedChain> mbs = Isomorphism.searchFromPreviousMapping(this.mb0, this.ext1, MatchingType.STRONG);
    boolean isGood = true;
    for (MappedChain mb : mbs) {
        List<MappedChain> extendedMbs = Isomorphism.searchFromPreviousMapping(mb, this.ext2, MatchingType.STRONG);
        MappedChain newMb = extendedMbs.get(0);
        IMolecule mol = mb.getChemObject().getMolecule();
        IAtom newA = (mol.getAtom(newMb.getAtomsMapping().get(2)));
        if (!(// Same first atom
        (newMb.getAtomsMapping().get(0) == mb.getAtomsMapping().get(0)) && // Same second atom
        (newMb.getAtomsMapping().get(1) == mb.getAtomsMapping().get(1)) && // Extended by C atom
        (newA.getSymbol().equals("C"))))
            isGood = false;
    }
    Assert.assertTrue(isGood);
}

Example 34 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class ContractedGraph method addUncoveredVerticies.

// Create nodes not covered
private void addUncoveredVerticies(IMolecule mol) {
    for (IAtom atom : mol.atoms()) {
        int idx = mol.getAtomNumber(atom);
        if (!this.verticiesOfatoms.keySet().contains(idx)) {
            Vertex v = new Vertex();
            v.id = "?";
            v.vertices.add(idx);
            this.addVertex(v);
            this.verticiesOfatoms.put(idx, v);
        }
    }
}

Example 35 with IAtom

use of org.openscience.cdk.interfaces.IAtom in project Smiles2Monomers by yoann-dufresne.

the class ContractedGraph method createLinks.

// Create links between contracted and unknown nodes
private void createLinks(IMolecule mol) {
    this.removeAllEdges(this.edgeSet());
    for (Object o : this.vertexSet()) {
        Vertex v = (Vertex) o;
        for (int idx : v.vertices) {
            IAtom a = mol.getAtom(idx);
            List<IAtom> neighbors = mol.getConnectedAtomsList(a);
            for (IAtom n : neighbors) {
                int aIdx = mol.getAtomNumber(n);
                if (!v.vertices.contains(aIdx)) {
                    // Base edge
                    Vertex vOa = this.verticiesOfatoms.get(aIdx);
                    String l0 = "";
                    String l1 = "";
                    // Labels
                    if (v.kind.containsKey(idx))
                        l0 = v.kind.get(idx).getName();
                    if (vOa.kind.containsKey(aIdx))
                        l1 = vOa.kind.get(aIdx).getName();
                    LabeledEdge edge = new LabeledEdge(v, vOa, l0, l1);
                    this.addEdge(edge);
                }
            }
        }
    }
}