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

Example 6 with IAtom

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

the class BonbMatchingTests method setUp.

@Before
public void setUp() throws Exception {
    // cNH
    IAtom a2 = new Atom("C");
    a2.setImplicitHydrogenCount(0);
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    IAtom a1 = new Atom("N");
    a1.setImplicitHydrogenCount(1);
    this.bond1 = new Bond(a1, a2, Order.DOUBLE);
}

Example 7 with IAtom

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

the class ResidueJsonLoader method objectFromJson.

@Override
protected Family objectFromJson(JSONObject obj) {
    Residue res = new Residue((String) obj.get("mono"), (String) obj.get("smarts"), true);
    res.setIdx(((Number) obj.get("id")).intValue());
    JSONArray array = (JSONArray) obj.get("links");
    for (Object o : array) {
        JSONObject jso = (JSONObject) o;
        String name = (String) jso.get("name");
        Rule rule = null;
        try {
            rule = this.rules.getObject(name);
        } catch (NullPointerException e) {
            System.err.println("Unknown link " + name);
        }
        int idx = ((Number) jso.get("atom")).intValue();
        IAtom ia = res.getMolecule().getAtom(idx);
        res.addLink(ia, rule);
    }
    // Family construction
    Family fam = new Family();
    try {
        for (String name : ((String) obj.get("family")).split("€")) {
            Monomer m = this.monos.getObject(name);
            fam.addMonomer(m);
        }
    } catch (NullPointerException e) {
        System.err.println("Unloaded residue " + res.getMonoName());
    }
    fam.addResidue(res);
    for (Object jso : (JSONArray) obj.get("depandances")) {
        int idx = ((Number) jso).intValue();
        fam.addDependance(idx, new Integer(res.getId()));
    }
    return fam;
}

Example 8 with IAtom

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

the class MonomersSerialization method deserializeObject.

private void deserializeObject(Monomer mono, ObjectInputStream ois) {
    try {
        int nbAtoms = ois.readInt();
        if (nbAtoms != mono.getMolecule().getAtomCount()) {
            System.err.println("Bad serialized value for atom count in " + mono.getCode());
        }
        for (IAtom a : mono.getMolecule().atoms()) {
            Point2d p = new Point2d(ois.readDouble(), ois.readDouble());
            a.setPoint2d(p);
        }
    } catch (IOException e) {
        e.printStackTrace();
    }
}

Example 9 with IAtom

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

the class MySMILES method createDFS.

private void createDFS(DFS dfs, AtomNode current, AtomNode from) {
    current.state = State.CHECK;
    dfs.path.add(current);
    List<AtomNode> toExplore = new ArrayList<MySMILES.AtomNode>();
    // For all neighbors save enighbors to explore
    for (IAtom a : dfs.mol.getConnectedAtomsList(current.atom)) {
        AtomNode nei = dfs.nodes.get(a);
        if (from != null && nei.atom == from.atom)
            continue;
        switch(nei.state) {
            case FREE:
                toExplore.add(nei);
                nei.state = State.TOEXPLORE;
            case TOEXPLORE:
                // TODO better smiles with less () and cycles first
                break;
            default:
                if (nei.rings == null)
                    nei.rings = new ArrayList<Integer>();
                nei.rings.add(dfs.ringNumber);
                if (current.rings == null)
                    current.rings = new ArrayList<Integer>();
                current.rings.add(dfs.ringNumber++);
                break;
        }
    }
    if (toExplore.size() == 0)
        return;
    // Sort neighbors to explore.
    List<List<AtomNode>> sortedNeighbors = dfs.sort(toExplore, current, dfs.mol);
    for (List<AtomNode> similar : sortedNeighbors) {
        HashMap<List<AtomNode>, DFS> clones = new HashMap<>();
        // Clone if there are most than one possibility
        List<List<AtomNode>> alternatives = this.getAllAlternatives(similar);
        for (List<AtomNode> alt : alternatives) clones.put(alt, dfs.clone());
        // Explore all alternatives for equivalent nodes
        DFS bestClone = null;
        for (List<AtomNode> alternative : alternatives) {
            DFS clone = clones.get(alternative);
            for (AtomNode node : alternative) {
                node = clone.nodes.get(node.atom);
                // To avoid 2 usages of same node if there are rings
                if (node.state != State.TOEXPLORE) {
                    clones.remove(node);
                    continue;
                }
                clone.path.add(new TextNode("("));
                this.createDFS(clone, node, current);
                clone.path.add(new TextNode(")"));
            }
            // Select best clone
            if (bestClone == null)
                bestClone = clone;
            else if (bestClone.toString().compareTo(clone.toString()) > 0)
                bestClone = clone;
        }
        // Transformation of the current DFS with the best clone extensions.
        for (int idx = dfs.path.size(); idx < bestClone.path.size(); idx++) {
            Node node = bestClone.path.get(idx);
            if (node instanceof AtomNode) {
                AtomNode cloneNode = (AtomNode) node;
                IAtom atom = cloneNode.atom;
                AtomNode an = dfs.nodes.get(atom);
                an.state = cloneNode.state;
                an.rings = cloneNode.rings;
                an.sortLink = cloneNode.sortLink;
                dfs.path.add(an);
            } else {
                dfs.path.add(new TextNode(((TextNode) node).txt));
            }
        }
        dfs.ringNumber = bestClone.ringNumber;
    }
}

Example 10 with IAtom

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

the class IsomorphismTests method initMappingTest.

@Test
public void initMappingTest() {
    List<MappedChain> mbs = Isomorphism.searchFromPreviousMapping(this.mb0, this.ext1, MatchingType.STRONG);
    if (mbs.size() != 2)
        fail("2 matches needed");
    boolean isGood = true;
    for (MappedChain mb : mbs) {
        IMolecule mol = mb.getChemObject().getMolecule();
        IAtom a1 = (mol.getAtom(mb.getAtomsMapping().get(0)));
        IAtom a2 = (mol.getAtom(mb.getAtomsMapping().get(1)));
        if (!((a1.getSymbol().equals("C") && a2.getSymbol().equals("S")) || (a1.getSymbol().equals("S") && a2.getSymbol().equals("C"))))
            isGood = false;
    }
    Assert.assertTrue(isGood);
}