Java Code Examples for org.openscience.cdk.interfaces.IAtomContainer#setProperty()

/**
 * Copy the input container and suppress any explicit hydrogens. Only
 * hydrogens that can be represented as a hydrogen count value on the atom
 * are suppressed. If a copy is not needed please use {@link
 * #suppressHydrogens}.
 *
 * @param org the container from which to remove hydrogens
 * @return a copy of the input with suppressed hydrogens
 * @see #suppressHydrogens
 */
public static IAtomContainer copyAndSuppressedHydrogens(IAtomContainer org) {
    /*
     * Remove the CTAB_SGROUPS flag as CDK 2.2 complains
     */
    org.setProperty(CDKConstants.CTAB_SGROUPS, null);
    /*
     * @ASAD: IMP STEP to avoid unset Hydrogen arror:
     * Set implicit Hydrogen count
     */
    try {
        IAtomContainer clone = org.clone();
        clone.setID(org.getID());
        for (int i = 0; i < org.getAtomCount(); i++) {
            int implicitHydrogenCount = getImplicitHydrogenCount(clone.getAtom(i));
            clone.getAtom(i).setImplicitHydrogenCount(implicitHydrogenCount);
            clone.getAtom(i).setProperties(org.getAtom(i).getProperties());
            clone.getAtom(i).setFlags(org.getAtom(i).getFlags());
        }
        return suppressHydrogens(clone);
    } catch (CloneNotSupportedException e) {
        throw new IllegalStateException("atom container could not be cloned");
    }
}
 

/**
 * {@inheritDoc}
 */
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);
    return new Mappings(query, target, iterable);
}
 

private void setReactantMolecule(IReaction IR, Collection<IAtomContainer> metabolites) {
//
//        System.out.println("-------------------");
//        System.out.println("Reactants");
//        System.out.println("-------------------");

        Iterator<IAtomContainer> it = metabolites.iterator();
        //System.out.println("Stoic Map Size: " + stoichiometryMap.size());

        while (it.hasNext()) {
            IAtomContainer mol = it.next();
//            System.out.println("Insertion: " + mol.getID() + ", " + stoichiometryMap.get(mol.getID()));
            mol.setProperty("STOICHIOMETRY", stoichiometryMap.get(mol.getID()));
            IR.addReactant(mol, stoichiometryMap.get(mol.getID()));
            //IR.setReactantCoefficient(mol,wt);
//            System.out.println("Reaction: " + mol.getID() + ", " + standardizedReaction.getProductCoefficient(mol));
        }

        metabolites.clear();
        stoichiometryMap.clear();
    }
 

private void setProductMolecule(IReaction IR, Collection<IAtomContainer> metabolites) {

//        System.out.println("-------------------");
//        System.out.println("Products");
//        System.out.println("-------------------");
        Iterator<IAtomContainer> it = metabolites.iterator();
        while (it.hasNext()) {
            IAtomContainer mol = it.next();
//
//            System.out.println("Insertion: " + mol.getID() + ", " + stoichiometryMap.get(mol.getID()));
            mol.setProperty("STOICHIOMETRY", stoichiometryMap.get(mol.getID()));
            IR.addProduct(mol, stoichiometryMap.get(mol.getID()));
//         standardizedReaction.setProductCoefficient(mol,stoichiometryMap.get(mol.getID()));
        }

        metabolites.clear();
        stoichiometryMap.clear();
    }
 

private void writeChemFile(IChemFile file) throws Exception {
    IAtomContainer bigPile = file.getBuilder().newInstance(IAtomContainer.class);
    for (IAtomContainer container : ChemFileManipulator.getAllAtomContainers(file)) {
        bigPile.add(container);
        if (container.getTitle() != null) {
            if (bigPile.getTitle() != null) {
                bigPile.setTitle(bigPile.getTitle() + "; " + container.getTitle());
            } else {
                bigPile.setTitle(container.getTitle());
            }
        }
        if (container.getProperty(CDKConstants.REMARK) != null) {
            if (bigPile.getProperty(CDKConstants.REMARK) != null) {
                bigPile.setProperty(CDKConstants.REMARK, bigPile.getProperty(CDKConstants.REMARK) + "; "
                        + container.getProperty(CDKConstants.REMARK));
            } else {
                bigPile.setProperty(CDKConstants.REMARK, container.getProperty(CDKConstants.REMARK));
            }
        }
    }
    writeMolecule(bigPile);
}
 

/**
 *
 * @param ac
 */
public void invert(IAtomContainer ac) {
    if (shouldInvert && 
            ac.getProperty(INVERTED) == null ||
            !((Boolean)ac.getProperty(INVERTED))) {
        for (IAtom atom : ac.atoms()) {
            atom.getPoint2d().y *= - 1;
        }
        ac.setProperty(INVERTED, TRUE);
    }
    shouldInvert = false;
}
 

/**
 * Read non-structural data from input and store as properties the provided
 * 'container'. Non-structural data appears in a structure data file (SDF)
 * after an Molfile and before the record deliminator ('$$$$'). The data
 * consists of one or more Data Header and Data blocks, an example is seen
 * below.
 *
 * <pre>{@code
 * > 29 <DENSITY>
 * 0.9132 - 20.0
 *
 * > 29 <BOILING.POINT>
 * 63.0 (737 MM)
 * 79.0 (42 MM)
 *
 * > 29 <ALTERNATE.NAMES>
 * SYLVAN
 *
 * > 29 <DATE>
 * 09-23-1980
 *
 * > 29 <CRC.NUMBER>
 * F-0213
 *
 * }</pre>
 *
 *
 * @param input input source
 * @param container the container
 * @throws IOException an error occur whilst reading the input
 */
static void readNonStructuralData(final BufferedReader input, final IAtomContainer container) throws IOException {

    String line, header = null;
    boolean wrap = false;

    final StringBuilder data = new StringBuilder(80);

    while (!endOfRecord(line = input.readLine())) {

        final String newHeader = dataHeader(line);

        if (newHeader != null) {

            if (header != null) {
                container.setProperty(header, data.toString());
            }

            header = newHeader;
            wrap = false;
            data.setLength(0);

        } else {

            if (data.length() > 0 || !line.equals(" ")) {
                line = line.trim();
            }

            if (line.isEmpty()) {
                continue;
            }

            if (!wrap && data.length() > 0) {
                data.append(NEW_LINE);
            }
            data.append(line);

            wrap = line.length() == 80;
        }
    }

    if (header != null) {
        container.setProperty(header, data.toString());
    }
}