Examples with EdgeToBondMap org.openscience.cdk.graph.GraphUtil.EdgeToBondMap used on opensource projects

Example 1 with EdgeToBondMap

use of org.openscience.cdk.graph.GraphUtil.EdgeToBondMap in project cdk by cdk.

the class Ullmann method matchAll.

@Override
public Mappings matchAll(IAtomContainer target) {
    EdgeToBondMap bonds2 = EdgeToBondMap.withSpaceFor(target);
    int[][] g2 = GraphUtil.toAdjList(target, bonds2);
    Iterable<int[]> iterable = new UllmannIterable(query, target, g1, g2, bonds1, bonds2, atomMatcher, bondMatcher);
    Mappings mappings = new Mappings(query, target, iterable);
    return filter(mappings, query, target);
}

Example 2 with EdgeToBondMap

use of org.openscience.cdk.graph.GraphUtil.EdgeToBondMap in project cdk by cdk.

the class VentoFoggia method matchAll.

/**
 *{@inheritDoc}
 */
@Override
public Mappings matchAll(final IAtomContainer target) {
    final EdgeToBondMap bonds2;
    final int[][] g2;
    AdjListCache cached = target.getProperty(AdjListCache.class.getName());
    if (cached == null || !cached.validate(target)) {
        cached = new AdjListCache(target);
        target.setProperty(AdjListCache.class.getName(), cached);
    }
    bonds2 = cached.bmap;
    g2 = cached.g;
    Iterable<int[]> iterable = new VFIterable(query, target, g1, g2, bonds1, bonds2, atomMatcher, bondMatcher, subgraph);
    Mappings mappings = new Mappings(query, target, iterable);
    return filter(mappings, query, target);
}

Example 3 with EdgeToBondMap

use of org.openscience.cdk.graph.GraphUtil.EdgeToBondMap in project cdk by cdk.

the class StereoElementFactory method using3DCoordinates.

/**
 * Create a stereo element factory for creating stereo elements using 3D
 * coordinates and depiction labels (up/down, wedge/hatch).
 *
 * @param container the structure to create the factory for
 * @return the factory instance
 */
public static StereoElementFactory using3DCoordinates(IAtomContainer container) {
    EdgeToBondMap bondMap = EdgeToBondMap.withSpaceFor(container);
    int[][] graph = GraphUtil.toAdjList(container, bondMap);
    return new StereoElementFactory3D(container, graph, bondMap).checkSymmetry(true);
}

Example 4 with EdgeToBondMap

use of org.openscience.cdk.graph.GraphUtil.EdgeToBondMap in project cdk by cdk.

the class AllRingsFinder method findAllRingsInIsolatedRingSystem.

/**
 * Compute all rings up to an including the {@literal maxRingSize}. No
 * pre-processing is done on the container.
 *
 * @param atomContainer the molecule to be searched for rings
 * @param maxRingSize   Maximum ring size to consider. Provides a possible
 *                      breakout from recursion for complex compounds.
 * @return a RingSet containing the rings in molecule
 * @throws CDKException An exception thrown if the threshold was exceeded
 */
public IRingSet findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer, int maxRingSize) throws CDKException {
    final EdgeToBondMap edges = EdgeToBondMap.withSpaceFor(atomContainer);
    final int[][] graph = GraphUtil.toAdjList(atomContainer, edges);
    AllCycles ac = new AllCycles(graph, maxRingSize, threshold.value);
    if (!ac.completed())
        throw new CDKException("Threshold exceeded for AllRingsFinder");
    IRingSet ringSet = atomContainer.getBuilder().newInstance(IRingSet.class);
    for (int[] path : ac.paths()) {
        ringSet.addAtomContainer(toRing(atomContainer, edges, path));
    }
    return ringSet;
}

Example 5 with EdgeToBondMap

use of org.openscience.cdk.graph.GraphUtil.EdgeToBondMap in project cdk by cdk.

the class FischerRecognitionTest method recogniseRightHandedGlyceraldehydeWithImplicitHydrogen.

/**
 * @cdk.inchi InChI=1/C3H6O3/c4-1-3(6)2-5/h1,3,5-6H,2H2/t3-/s2
 */
@Test
public void recogniseRightHandedGlyceraldehydeWithImplicitHydrogen() throws Exception {
    IAtomContainer m = new AtomContainer(8, 7, 0, 0);
    m.addAtom(atom("C", 0, 0.80d, 1.24d));
    m.addAtom(atom("C", 1, 0.80d, 0.42d));
    m.addAtom(atom("O", 1, 0.09d, 1.66d));
    m.addAtom(atom("O", 0, 1.52d, 1.66d));
    m.addAtom(atom("O", 1, 1.63d, 0.42d));
    m.addAtom(atom("C", 2, 0.80d, -0.41d));
    m.addAtom(atom("O", 1, 1.52d, -0.82d));
    m.addBond(0, 1, IBond.Order.SINGLE);
    m.addBond(0, 2, IBond.Order.SINGLE);
    m.addBond(0, 3, IBond.Order.DOUBLE, IBond.Stereo.E_Z_BY_COORDINATES);
    m.addBond(1, 4, IBond.Order.SINGLE);
    m.addBond(1, 5, IBond.Order.SINGLE);
    m.addBond(5, 6, IBond.Order.SINGLE);
    EdgeToBondMap bondMap = EdgeToBondMap.withSpaceFor(m);
    int[][] graph = GraphUtil.toAdjList(m, bondMap);
    FischerRecognition recogniser = new FischerRecognition(m, graph, bondMap, Stereocenters.of(m));
    List<IStereoElement> elements = recogniser.recognise(Collections.singleton(Projection.Fischer));
    org.hamcrest.MatcherAssert.assertThat(elements.size(), is(1));
    assertTetrahedralCenter(elements.get(0), m.getAtom(1), ANTI_CLOCKWISE, m.getAtom(0), m.getAtom(4), m.getAtom(5), m.getAtom(1));
}