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

Example 21 with IAtom

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

the class Extension method createBond.

private void createBond(String name0, int h0, boolean arom0, String name1, int h1, boolean arom1, Order ord) {
    if (arom0)
        name0 = name0.toLowerCase();
    if (arom1)
        name1 = name1.toLowerCase();
    List<String> names = new ArrayList<>();
    names.add(name0 + ":" + h0);
    names.add(name1 + ":" + h1);
    Collections.sort(names);
    // this.inverted = !names.get(0).equals(name0 + ":" + h0);
    IAtom c0 = null;
    String n0 = names.get(0);
    if (Extension.savedAtoms.containsKey(n0))
        c0 = Extension.savedAtoms.get(n0);
    else {
        String[] split = n0.split(":");
        char first = Character.toUpperCase(split[0].charAt(0));
        String name = first + split[0].substring(1);
        c0 = new Atom(name);
        c0.setFlag(CDKConstants.ISAROMATIC, Character.isLowerCase(split[0].charAt(0)));
        c0.setImplicitHydrogenCount(new Integer(split[1]));
        Extension.savedAtoms.put(n0, c0);
    }
    IAtom c1 = null;
    String n1 = names.get(1);
    if (Extension.savedAtoms.containsKey(n1))
        c1 = Extension.savedAtoms.get(n1);
    else {
        String[] split = n1.split(":");
        char first = Character.toUpperCase(split[0].charAt(0));
        String name = first + split[0].substring(1);
        c1 = new Atom(name);
        c1.setFlag(CDKConstants.ISAROMATIC, Character.isLowerCase(split[0].charAt(0)));
        c1.setImplicitHydrogenCount(new Integer(split[1]));
        Extension.savedAtoms.put(n1, c1);
    }
    String key = names.get(0) + ord + names.get(1);
    if (Extension.savedBonds.containsKey(key)) {
        this.bond = Extension.savedBonds.get(key);
    } else {
        this.bond = new Bond(c0, c1, ord);
        Extension.savedBonds.put(key, this.bond);
    }
}

Example 22 with IAtom

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

the class DeepenMatcher method transform.

/**
 * Transformation of mappings from tmp molecule to entire molecule.
 */
public static Match transform(Match match, IMolecule sub, IMolecule entire) {
    Match transformed = new Match(match.getResidue());
    // Atoms & Hydrogens
    for (int idx : match.getAtoms()) {
        IAtom a = sub.getAtom(idx);
        int realIdx = entire.getAtomNumber(a);
        transformed.addAtom(realIdx);
        transformed.addHydrogens(realIdx, match.getHydrogensFrom(idx));
    }
    // Bonds
    for (int idx : match.getBonds()) {
        IBond b = sub.getBond(idx);
        transformed.addBond(entire.getBondNumber(b));
    }
    return transformed;
}

Example 23 with IAtom

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

the class PictureGenerator method transform.

/**/
public Molecule transform(String smiles) throws InvalidSmilesException {
    Molecule imol = null;
    imol = new Molecule(this.sp.parseSmiles(smiles));
    for (IAtom a : imol.atoms()) a.setImplicitHydrogenCount(0);
    StructureDiagramGenerator sdg = new StructureDiagramGenerator(imol);
    try {
        sdg.generateCoordinates();
    } catch (CDKException e) {
        System.err.println(smiles);
        e.printStackTrace();
    }
    imol = new Molecule(sdg.getMolecule());
    return imol;
}

Example 24 with IAtom

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

the class SmilesGenerator method isValidDoubleBondConfiguration.

/**
 *  Tells if a certain bond is center of a valid double bond configuration.
 *
 *@param  container  The atomcontainer.
 *@param  bond       The bond.
 *@return            true=is a potential configuration, false=is not.
 */
public boolean isValidDoubleBondConfiguration(IAtomContainer container, IBond bond) {
    IAtom atom0 = bond.getAtom(0);
    IAtom atom1 = bond.getAtom(1);
    List<IAtom> connectedAtoms = container.getConnectedAtomsList(atom0);
    IAtom from = null;
    for (IAtom connectedAtom : connectedAtoms) {
        if (connectedAtom != atom1) {
            from = connectedAtom;
        }
    }
    boolean[] array = new boolean[container.getBondCount()];
    for (int i = 0; i < array.length; i++) {
        array[i] = true;
    }
    if (isStartOfDoubleBond(container, atom0, from, array) && isEndOfDoubleBond(container, atom1, atom0, array) && !bond.getFlag(CDKConstants.ISAROMATIC)) {
        return (true);
    } else {
        return (false);
    }
}

Example 25 with IAtom

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

the class SmilesGenerator method createSMILESWithoutCheckForMultipleMolecules.

/**
 *  Generate canonical SMILES from the <code>molecule</code>. This method
 *  canonicaly lables the molecule but dose not perform any checks on the
 *  chemical validity of the molecule. Does not care about multiple molecules.
 *  IMPORTANT: A precomputed Set of All Rings (SAR) can be passed to this
 *  SmilesGenerator in order to avoid recomputing it. Use setRings() to
 *  assign the SAR.
 *
 * @param  molecule                 The molecule to evaluate.
 * @param  chiral                   true=SMILES will be chiral, false=SMILES
 *      will not be chiral.
 * @param  doubleBondConfiguration  Should E/Z configurations be read at these positions? If the flag at position X is set to true,
 *                                  an E/Z configuration will be written from coordinates around bond X, if false, it will be ignored.
 *                                  If flag is true for a bond which does not constitute a valid double bond configuration, it will be
 *                                  ignored (meaning setting all to true will create E/Z indication will be pu in the smiles wherever
 *                                  possible, but note the coordinates might be arbitrary).
 * @exception  CDKException         At least one atom has no Point2D;
 *      coordinates are needed for creating the chiral smiles. This excpetion
 *      can only be thrown if chiral smiles is created, ignore it if you want a
 *      non-chiral smiles (createSMILES(AtomContainer) does not throw an
 *      exception).
 *@see                             org.openscience.cdk.graph.invariant.CanonicalLabeler#canonLabel(IAtomContainer)
 * @return the SMILES representation of the molecule
 */
@TestMethod("testCreateSMILESWithoutCheckForMultipleMolecules_withDetectAromaticity,testCreateSMILESWithoutCheckForMultipleMolecules_withoutDetectAromaticity")
public synchronized String createSMILESWithoutCheckForMultipleMolecules(IAtomContainer molecule, boolean chiral, boolean[] doubleBondConfiguration) throws CDKException {
    if (molecule.getAtomCount() == 0) {
        return "";
    }
    canLabler.canonLabel(molecule);
    brokenBonds.clear();
    ringMarker = 0;
    IAtom start = null;
    for (int i = 0; i < molecule.getAtomCount(); i++) {
        IAtom atom = molecule.getAtom(i);
        if (chiral && atom.getPoint2d() == null) {
            throw new CDKException("Atom number " + i + " has no 2D coordinates, but 2D coordinates are needed for creating chiral smiles");
        }
        // logger.debug("Setting all VISITED flags to false");
        atom.setFlag(CDKConstants.VISITED, false);
        if ((Long) atom.getProperty("CanonicalLable") == 1) {
            start = atom;
        }
    }
    // detect aromaticity
    if (useAromaticityFlag || chiral) {
        if (rings == null) {
            if (ringFinder == null) {
                ringFinder = new AllRingsFinder();
            }
            rings = ringFinder.findAllRings(molecule);
        }
        AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(molecule);
        CDKHueckelAromaticityDetector.detectAromaticity(molecule);
    }
    if (chiral && rings.getAtomContainerCount() > 0) {
        List<?> v = RingPartitioner.partitionRings(rings);
        // logger.debug("RingSystems: " + v.size());
        for (int i = 0; i < v.size(); i++) {
            int counter = 0;
            Iterator<IAtomContainer> containers = RingSetManipulator.getAllAtomContainers((IRingSet) v.get(i)).iterator();
            while (containers.hasNext()) {
                IAtomContainer allrings = (IAtomContainer) containers.next();
                for (int k = 0; k < allrings.getAtomCount(); k++) {
                    if (!BondTools.isStereo(molecule, allrings.getAtom(k)) && hasWedges(molecule, allrings.getAtom(k)) != null) {
                        IBond bond = molecule.getBond(allrings.getAtom(k), hasWedges(molecule, allrings.getAtom(k)));
                        if (bond.getStereo() == IBond.Stereo.UP) {
                            allrings.getAtom(k).setProperty(RING_CONFIG, UP);
                        } else {
                            allrings.getAtom(k).setProperty(RING_CONFIG, DOWN);
                        }
                        counter++;
                    }
                }
                if (counter == 1) {
                    for (int k = 0; k < allrings.getAtomCount(); k++) {
                        IBond bond = molecule.getBond(allrings.getAtom(k), hasWedges(molecule, allrings.getAtom(k)));
                        if (bond != null) {
                            if (bond.getStereo() == IBond.Stereo.UP) {
                                allrings.getAtom(k).setProperty(RING_CONFIG, UP);
                            } else {
                                allrings.getAtom(k).setProperty(RING_CONFIG, DOWN);
                            }
                        }
                    }
                }
            }
        }
    }
    StringBuffer l = new StringBuffer();
    createSMILES(start, l, molecule, chiral, doubleBondConfiguration, useAromaticityFlag);
    rings = null;
    // remove all CanonicalLable/InvariancePair props
    for (int k = 0; k < molecule.getAtomCount(); k++) {
        molecule.getAtom(k).removeProperty("CanonicalLable");
        molecule.getAtom(k).removeProperty("InvariancePair");
    }
    return l.toString();
}