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

Example 1 with IAtom

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

the class SmilesGenerator method isStartOfDoubleBond.

/**
 *  Says if an atom is the start of a double bond configuration
 *
 *@param  a                        The atom which is the start of configuration
 *@param  container                The atomContainer the atom is in
 *@param  parent                   The atom we came from
 *@param  doubleBondConfiguration  The array indicating where double bond
 *      configurations are specified (this method ensures that there is
 *      actually the possibility of a double bond configuration)
 *@return                          false=is not start of configuration, true=is
 */
private boolean isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, boolean[] doubleBondConfiguration) {
    // TO-DO: We make the silent assumption of unset hydrogen count equals zero hydrogen count here.
    int lengthAtom = container.getConnectedAtomsCount(a) + ((a.getImplicitHydrogenCount() == CDKConstants.UNSET) ? 0 : a.getImplicitHydrogenCount());
    if (lengthAtom != 3 && (lengthAtom != 2 && !a.getSymbol().equals("N"))) {
        return (false);
    }
    List<IAtom> atoms = container.getConnectedAtomsList(a);
    IAtom one = null;
    IAtom two = null;
    boolean doubleBond = false;
    IAtom nextAtom = null;
    for (IAtom atomi : atoms) {
        if (atomi != parent && container.getBond(atomi, a).getOrder() == CDKConstants.BONDORDER_DOUBLE && isEndOfDoubleBond(container, atomi, a, doubleBondConfiguration)) {
            doubleBond = true;
            nextAtom = atomi;
        }
        if (atomi != nextAtom && one == null) {
            one = atomi;
        } else if (atomi != nextAtom && one != null) {
            two = atomi;
        }
    }
    String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
    if (one != null && ((!a.getSymbol().equals("N") && two != null && !morgannumbers[container.getAtomNumber(one)].equals(morgannumbers[container.getAtomNumber(two)]) && doubleBond && doubleBondConfiguration[container.getBondNumber(a, nextAtom)]) || (doubleBond && a.getSymbol().equals("N") && Math.abs(BondTools.giveAngleBothMethods(nextAtom, a, parent, true)) > Math.PI / 10))) {
        return (true);
    } else {
        return (false);
    }
}

Example 2 with IAtom

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

the class SmilesGenerator method createDFSTree.

/**
 *  Recursively perform a DFS search on the <code>container</code> placing
 *  atoms and branches in the vector <code>tree</code>.
 *
 *@param  a          the atom being visited.
 *@param  tree       vector holding the tree.
 *@param  parent     the atom we came from.
 *@param  container  the AtomContainer that we are parsing.
 */
private void createDFSTree(IAtom a, List<Object> tree, IAtom parent, IAtomContainer container) {
    tree.add(a);
    List<IAtom> neighbours = new ArrayList<IAtom>(getCanNeigh(a, container));
    neighbours.remove(parent);
    IAtom next;
    a.setFlag(CDKConstants.VISITED, true);
    // logger.debug("Starting with DFSTree and AtomContainer of size " + container.getAtomCount());
    // logger.debug("Current Atom has " + neighbours.size() + " neighbours");
    Iterator<IAtom> iter = neighbours.iterator();
    while (iter.hasNext()) {
        next = (IAtom) iter.next();
        if (!next.getFlag(CDKConstants.VISITED)) {
            if (!iter.hasNext()) {
                // Last neighbour therefore in this chain
                createDFSTree(next, tree, a, container);
            } else {
                List<Object> branch = new Vector<Object>();
                tree.add(branch);
                // logger.debug("adding branch");
                createDFSTree(next, branch, a, container);
            }
        } else {
            // Found ring closure between next and a
            // logger.debug("found ringclosure in DFTTreeCreation");
            ringMarker++;
            BrokenBond bond = new BrokenBond(a, next, ringMarker);
            if (!brokenBonds.contains(bond)) {
                brokenBonds.add(bond);
            } else {
                ringMarker--;
            }
        }
    }
}

Example 3 with IAtom

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

the class SmilesGenerator method parseChain.

/**
 *  Parse a branch
 */
@SuppressWarnings("unchecked")
private void parseChain(List<Object> v, StringBuffer buffer, IAtomContainer container, IAtom parent, boolean chiral, boolean[] doubleBondConfiguration, List<IAtom> atomsInOrderOfSmiles, boolean useAromaticity) {
    int positionInVector = 0;
    IAtom atom;
    // logger.debug("in parse chain. Size of tree: " + v.size());
    for (int h = 0; h < v.size(); h++) {
        Object o = v.get(h);
        if (o instanceof IAtom) {
            atom = (IAtom) o;
            if (parent != null) {
                parseBond(buffer, atom, parent, container, useAromaticity);
            } else {
                if (chiral && BondTools.isStereo(container, atom)) {
                    parent = (IAtom) ((List<?>) v.get(1)).get(0);
                }
            }
            parseAtom(atom, buffer, container, chiral, doubleBondConfiguration, parent, atomsInOrderOfSmiles, v, useAromaticity);
            /*
				 *  The principle of making chiral smiles is quite simple, although the code is
				 *  pretty uggly. The Atoms connected to the chiral center are put in sorted[] in the
				 *  order they have to appear in the smiles. Then the Vector v is rearranged according
				 *  to sorted[]
				 */
            if (chiral && BondTools.isStereo(container, atom) && container.getBond(parent, atom) != null) {
                // logger.debug("in parseChain in isChiral");
                IAtom[] sorted = null;
                List<?> chiralNeighbours = container.getConnectedAtomsList(atom);
                if (BondTools.isTetrahedral(container, atom, false) > 0) {
                    sorted = new IAtom[3];
                }
                if (BondTools.isTetrahedral(container, atom, false) == 1) {
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.DOWN) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if ((container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if ((container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.UP) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if ((container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                                if ((container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == CDKConstants.UNSET || container.getBond(parent, atom).getStereo() == IBond.Stereo.NONE) {
                        boolean normalBindingIsLeft = false;
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) {
                                    if (BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom)) {
                                        normalBindingIsLeft = true;
                                        break;
                                    }
                                }
                            }
                        }
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (normalBindingIsLeft) {
                                    if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) {
                                        sorted[0] = (IAtom) chiralNeighbours.get(i);
                                    }
                                    if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP) {
                                        sorted[2] = (IAtom) chiralNeighbours.get(i);
                                    }
                                    if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN) {
                                        sorted[1] = (IAtom) chiralNeighbours.get(i);
                                    }
                                } else {
                                    if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP) {
                                        sorted[1] = (IAtom) chiralNeighbours.get(i);
                                    }
                                    if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) {
                                        sorted[0] = (IAtom) chiralNeighbours.get(i);
                                    }
                                    if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN) {
                                        sorted[2] = (IAtom) chiralNeighbours.get(i);
                                    }
                                }
                            }
                        }
                    }
                }
                if (BondTools.isTetrahedral(container, atom, false) == 2) {
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.UP) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.DOWN) {
                        double angle1 = 0;
                        double angle2 = 0;
                        IAtom atom1 = null;
                        IAtom atom2 = null;
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    if (angle1 == 0) {
                                        angle1 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
                                        atom1 = (IAtom) chiralNeighbours.get(i);
                                    } else {
                                        angle2 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
                                        atom2 = (IAtom) chiralNeighbours.get(i);
                                    }
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                        if (angle1 < angle2) {
                            sorted[0] = atom2;
                            sorted[2] = atom1;
                        } else {
                            sorted[0] = atom1;
                            sorted[2] = atom2;
                        }
                    }
                }
                if (BondTools.isTetrahedral(container, atom, false) == 3) {
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.UP) {
                        TreeMap<Double, Integer> hm = new TreeMap<Double, Integer>();
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), Integer.valueOf(i));
                            }
                        }
                        Object[] ohere = hm.values().toArray();
                        for (int i = ohere.length - 1; i > -1; i--) {
                            sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == null || container.getBond(parent, atom).getStereo() == IBond.Stereo.NONE) {
                        double angle1 = 0;
                        double angle2 = 0;
                        IAtom atom1 = null;
                        IAtom atom2 = null;
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if ((container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    if (angle1 == 0) {
                                        angle1 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
                                        atom1 = (IAtom) chiralNeighbours.get(i);
                                    } else {
                                        angle2 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
                                        atom2 = (IAtom) chiralNeighbours.get(i);
                                    }
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                        if (angle1 < angle2) {
                            sorted[1] = atom2;
                            sorted[2] = atom1;
                        } else {
                            sorted[1] = atom1;
                            sorted[2] = atom2;
                        }
                    }
                }
                if (BondTools.isTetrahedral(container, atom, false) == 4) {
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.DOWN) {
                        TreeMap<Double, Integer> hm = new TreeMap<Double, Integer>();
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), Integer.valueOf(i));
                            }
                        }
                        Object[] ohere = hm.values().toArray();
                        for (int i = ohere.length - 1; i > -1; i--) {
                            sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == null || container.getBond(parent, atom).getStereo() == IBond.Stereo.NONE) {
                        double angle1 = 0;
                        double angle2 = 0;
                        IAtom atom1 = null;
                        IAtom atom2 = null;
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if ((container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    if (angle1 == 0) {
                                        angle1 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
                                        atom1 = (IAtom) chiralNeighbours.get(i);
                                    } else {
                                        angle2 = BondTools.giveAngle(atom, parent, (IAtom) chiralNeighbours.get(i));
                                        atom2 = (IAtom) chiralNeighbours.get(i);
                                    }
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                        if (angle1 < angle2) {
                            sorted[1] = atom2;
                            sorted[0] = atom1;
                        } else {
                            sorted[1] = atom1;
                            sorted[0] = atom2;
                        }
                    }
                }
                if (BondTools.isTetrahedral(container, atom, false) == 5) {
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.DOWN) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.UP) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == CDKConstants.UNSET || container.getBond(parent, atom).getStereo() == IBond.Stereo.NONE) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                }
                if (BondTools.isTetrahedral(container, atom, false) == 6) {
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.UP) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.DOWN) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == null || container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.NONE) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == CDKConstants.UNSET || container.getBond(parent, atom).getStereo() == IBond.Stereo.NONE) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[2] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.UP && !BondTools.isLeft(((IAtom) chiralNeighbours.get(i)), parent, atom) && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond((IAtom) chiralNeighbours.get(i), atom).getStereo() == IBond.Stereo.DOWN) {
                                    sorted[1] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                    }
                }
                if (BondTools.isSquarePlanar(container, atom)) {
                    sorted = new IAtom[3];
                    // This produces a U=SP1 order in every case
                    TreeMap<Double, Integer> hm = new TreeMap<Double, Integer>();
                    for (int i = 0; i < chiralNeighbours.size(); i++) {
                        if (chiralNeighbours.get(i) != parent && !isBondBroken((IAtom) chiralNeighbours.get(i), atom)) {
                            hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), Integer.valueOf(i));
                        }
                    }
                    Object[] ohere = hm.values().toArray();
                    for (int i = 0; i < ohere.length; i++) {
                        sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
                    }
                }
                if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom) != 0) {
                    sorted = new IAtom[container.getConnectedAtomsCount(atom) - 1];
                    TreeMap<Double, Integer> hm = new TreeMap<Double, Integer>();
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.UP) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == null || container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == IBond.Stereo.NONE) {
                                hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), Integer.valueOf(i));
                            }
                            if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == IBond.Stereo.DOWN) {
                                sorted[sorted.length - 1] = (IAtom) chiralNeighbours.get(i);
                            }
                        }
                        Object[] ohere = hm.values().toArray();
                        for (int i = 0; i < ohere.length; i++) {
                            sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == IBond.Stereo.DOWN) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == null || container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == IBond.Stereo.NONE) {
                                hm.put(new Double(BondTools.giveAngle(atom, parent, ((IAtom) chiralNeighbours.get(i)))), Integer.valueOf(i));
                            }
                            if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == IBond.Stereo.UP) {
                                sorted[sorted.length - 1] = (IAtom) chiralNeighbours.get(i);
                            }
                        }
                        Object[] ohere = hm.values().toArray();
                        for (int i = 0; i < ohere.length; i++) {
                            sorted[i] = ((IAtom) chiralNeighbours.get(((Integer) ohere[i]).intValue()));
                        }
                    }
                    if (container.getBond(parent, atom).getStereo() == null || container.getBond(parent, atom).getStereo() == IBond.Stereo.NONE) {
                        for (int i = 0; i < chiralNeighbours.size(); i++) {
                            if (chiralNeighbours.get(i) != parent) {
                                if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == null || container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == IBond.Stereo.NONE) {
                                    hm.put(new Double((BondTools.giveAngleFromMiddle(atom, parent, ((IAtom) chiralNeighbours.get(i))))), Integer.valueOf(i));
                                }
                                if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == IBond.Stereo.UP) {
                                    sorted[0] = (IAtom) chiralNeighbours.get(i);
                                }
                                if (container.getBond(atom, (IAtom) chiralNeighbours.get(i)).getStereo() == IBond.Stereo.DOWN) {
                                    sorted[sorted.length - 2] = (IAtom) chiralNeighbours.get(i);
                                }
                            }
                        }
                        Object[] ohere = hm.values().toArray();
                        sorted[sorted.length - 1] = ((IAtom) chiralNeighbours.get(((Integer) ohere[ohere.length - 1]).intValue()));
                        if (ohere.length == 2) {
                            sorted[sorted.length - 3] = ((IAtom) chiralNeighbours.get(((Integer) ohere[0]).intValue()));
                            if (BondTools.giveAngleFromMiddle(atom, parent, ((IAtom) chiralNeighbours.get(((Integer) ohere[1]).intValue()))) < 0) {
                                IAtom dummy = sorted[sorted.length - 2];
                                sorted[sorted.length - 2] = sorted[0];
                                sorted[0] = dummy;
                            }
                        }
                        if (ohere.length == 3) {
                            sorted[sorted.length - 3] = sorted[sorted.length - 2];
                            sorted[sorted.length - 2] = ((IAtom) chiralNeighbours.get(((Integer) ohere[ohere.length - 2]).intValue()));
                            sorted[sorted.length - 4] = ((IAtom) chiralNeighbours.get(((Integer) ohere[ohere.length - 3]).intValue()));
                        }
                    }
                }
                // This builds an onew[] containing the objects after the center of the chirality in the order given by sorted[]
                if (sorted != null) {
                    int numberOfAtoms = 3;
                    if (BondTools.isTrigonalBipyramidalOrOctahedral(container, atom) != 0) {
                        numberOfAtoms = container.getConnectedAtomsCount(atom) - 1;
                    }
                    Object[] omy = new Object[numberOfAtoms];
                    Object[] onew = new Object[numberOfAtoms];
                    for (int k = getRingOpenings(atom, null).size(); k < numberOfAtoms; k++) {
                        if (positionInVector + 1 + k - getRingOpenings(atom, null).size() < v.size()) {
                            omy[k] = v.get(positionInVector + 1 + k - getRingOpenings(atom, null).size());
                        }
                    }
                    for (int k = 0; k < sorted.length; k++) {
                        if (sorted[k] != null) {
                            for (int m = 0; m < omy.length; m++) {
                                if (omy[m] instanceof IAtom) {
                                    if (omy[m] == sorted[k]) {
                                        onew[k] = omy[m];
                                    }
                                } else {
                                    if (omy[m] == null) {
                                        onew[k] = null;
                                    } else {
                                        if (((List<?>) omy[m]).get(0) == sorted[k]) {
                                            onew[k] = omy[m];
                                        }
                                    }
                                }
                            }
                        } else {
                            onew[k] = null;
                        }
                    }
                    // This is a workaround for 3624.MOL.2 I don't have a better solution currently
                    boolean doubleentry = false;
                    for (int m = 0; m < onew.length; m++) {
                        for (int k = 0; k < onew.length; k++) {
                            if (m != k && onew[k] == onew[m]) {
                                doubleentry = true;
                            }
                        }
                    }
                    if (!doubleentry) {
                        // Make sure that the first atom in onew is the first one in the original smiles order. This is important to have a canonical smiles.
                        if (positionInVector + 1 < v.size()) {
                            Object atomAfterCenterInOriginalSmiles = v.get(positionInVector + 1);
                            int l = 0;
                            while (onew[0] != atomAfterCenterInOriginalSmiles) {
                                Object placeholder = onew[onew.length - 1];
                                for (int k = onew.length - 2; k > -1; k--) {
                                    onew[k + 1] = onew[k];
                                }
                                onew[0] = placeholder;
                                l++;
                                if (l > onew.length) {
                                    break;
                                }
                            }
                        }
                        // This cares about ring openings. Here the ring closure (represendted by a figure) must be the first atom. In onew the closure is null.
                        if (getRingOpenings(atom, null).size() > 0) {
                            int l = 0;
                            while (onew[0] != null) {
                                Object placeholder = onew[0];
                                for (int k = 1; k < onew.length; k++) {
                                    onew[k - 1] = onew[k];
                                }
                                onew[onew.length - 1] = placeholder;
                                l++;
                                if (l > onew.length) {
                                    break;
                                }
                            }
                        }
                        // The last in onew is a vector: This means we need to exchange the rest of the original smiles with the rest of this vector.
                        if (onew[numberOfAtoms - 1] instanceof List) {
                            for (int i = 0; i < numberOfAtoms; i++) {
                                if (onew[i] instanceof IAtom) {
                                    List<Object> vtemp = new Vector<Object>();
                                    vtemp.add(onew[i]);
                                    for (int k = positionInVector + 1 + numberOfAtoms; k < v.size(); k++) {
                                        vtemp.add(v.get(k));
                                    }
                                    onew[i] = vtemp;
                                    for (int k = v.size() - 1; k > positionInVector + 1 + numberOfAtoms - 1; k--) {
                                        v.remove(k);
                                    }
                                    for (int k = 1; k < ((List<?>) onew[numberOfAtoms - 1]).size(); k++) {
                                        v.add(((List<?>) onew[numberOfAtoms - 1]).get(k));
                                    }
                                    onew[numberOfAtoms - 1] = ((List<?>) onew[numberOfAtoms - 1]).get(0);
                                    break;
                                }
                            }
                        }
                        // Put the onew objects in the original Vector
                        int k = 0;
                        for (int m = 0; m < onew.length; m++) {
                            if (onew[m] != null) {
                                v.set(positionInVector + 1 + k, onew[m]);
                                k++;
                            }
                        }
                    }
                }
            }
            parent = atom;
        } else {
            // Have Vector
            // logger.debug("in parseChain after else");
            boolean brackets = true;
            List<IAtom> result = new Vector<IAtom>();
            addAtoms((List<?>) o, result);
            IAtom prevAtom;
            /*				
				 * Got to find last atom that was processed.
				 * This is to check the relative position of the current atom/chain with respect to its parent
				*/
            prevAtom = (IAtom) ((Vector<IAtom>) atomsInOrderOfSmiles).lastElement();
            int maxConnectedBondCount = 4;
            /**
             * If the parent atom of this new chain is the very first atom in the SMILES string and this chain is placed
             * immediately after the parent atom then the max connected bond count for the parent should be 3 instead of 4.
             */
            if (atomsInOrderOfSmiles.indexOf(parent) == 0 && prevAtom == parent) {
                maxConnectedBondCount = 3;
            }
            if (isRingOpening(parent, result) && container.getConnectedBondsCount(parent) < maxConnectedBondCount) {
                brackets = false;
            }
            if (brackets) {
                buffer.append('(');
            }
            parseChain((List<Object>) o, buffer, container, parent, chiral, doubleBondConfiguration, atomsInOrderOfSmiles, useAromaticity);
            if (brackets) {
                buffer.append(')');
            }
        }
        positionInVector++;
    // logger.debug("in parseChain after positionVector++");
    }
}

Example 4 with IAtom

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

the class SmilesGenerator method isEndOfDoubleBond.

/**
 *  Says if an atom is the end of a double bond configuration
 *
 *@param  atom                     The atom which is the end of configuration
 *@param  container                The atomContainer the atom is in
 *@param  parent                   The atom we came from
 *@param  doubleBondConfiguration  The array indicating where double bond
 *      configurations are specified (this method ensures that there is
 *      actually the possibility of a double bond configuration)
 *@return                          false=is not end of configuration, true=is
 */
private boolean isEndOfDoubleBond(IAtomContainer container, IAtom atom, IAtom parent, boolean[] doubleBondConfiguration) {
    if (container.getBondNumber(atom, parent) == -1 || doubleBondConfiguration.length <= container.getBondNumber(atom, parent) || !doubleBondConfiguration[container.getBondNumber(atom, parent)]) {
        return false;
    }
    // TO-DO: We make the silent assumption of unset hydrogen count equals zero hydrogen count here.
    int lengthAtom = container.getConnectedAtomsCount(atom) + ((atom.getImplicitHydrogenCount() == CDKConstants.UNSET) ? 0 : atom.getImplicitHydrogenCount());
    // TO-DO: We make the silent assumption of unset hydrogen count equals zero hydrogen count here.
    int lengthParent = container.getConnectedAtomsCount(parent) + ((parent.getImplicitHydrogenCount() == CDKConstants.UNSET) ? 0 : parent.getImplicitHydrogenCount());
    if (container.getBond(atom, parent) != null) {
        if (container.getBond(atom, parent).getOrder() == CDKConstants.BONDORDER_DOUBLE && (lengthAtom == 3 || (lengthAtom == 2 && atom.getSymbol().equals("N"))) && (lengthParent == 3 || (lengthParent == 2 && parent.getSymbol().equals("N")))) {
            List<IAtom> atoms = container.getConnectedAtomsList(atom);
            IAtom one = null;
            IAtom two = null;
            IAtom atomi = null;
            for (int i = 0; i < atoms.size(); i++) {
                atomi = (IAtom) container.getAtom(i);
                if (atomi != parent && one == null) {
                    one = atomi;
                } else if (atomi != parent && one != null) {
                    two = atomi;
                }
            }
            String[] morgannumbers = MorganNumbersTools.getMorganNumbersWithElementSymbol(container);
            if ((one != null && two == null && atom.getSymbol().equals("N") && Math.abs(BondTools.giveAngleBothMethods(parent, atom, one, true)) > Math.PI / 10) || (!atom.getSymbol().equals("N") && one != null && two != null && !morgannumbers[container.getAtomNumber(one)].equals(morgannumbers[container.getAtomNumber(two)]))) {
                return (true);
            } else {
                return (false);
            }
        }
    }
    return (false);
}

Example 5 with IAtom

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

the class BlocsTests method setUp.

@Before
public void setUp() throws Exception {
    this.sc = SmilesConverter.conv;
    // String smiles = "C(C(=O)O)C(=O)N";
    IAtom a1;
    IAtom a2;
    a1 = new Atom("C");
    a1.setFlag(CDKConstants.ISAROMATIC, true);
    a2 = new Atom("N");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // NC
    this.ext1 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a2 = new Atom("O");
    // NC=O
    this.ext2 = new Extension(new Bond(a1, a2, Order.DOUBLE));
    a2 = new Atom("C");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // NC(C)=O
    this.ext3 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a1 = new Atom("C");
    a1.setFlag(CDKConstants.ISAROMATIC, true);
    // NC(CC)=O
    this.ext4 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a2 = new Atom("C");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // NC(CCC)=O
    this.ext5 = new Extension(new Bond(a1, a2, Order.SINGLE));
    a1 = new Atom("C");
    a1.setFlag(CDKConstants.ISAROMATIC, true);
    a2 = new Atom("N");
    a2.setFlag(CDKConstants.ISAROMATIC, true);
    // N1C(CCC1)=O
    this.ext6 = new Extension(new Bond(a1, a2, Order.SINGLE));
    // NC
    this.blc1 = new Chain(null, ext1, -1, -1);
    // NC=O
    this.blc2 = new Chain(blc1, ext2, -1, 0);
    // NC(C)=O
    this.blc3 = new Chain(blc2, ext3, 0, -1);
    // NC(CC)=O
    this.blc4 = new Chain(blc3, ext4, 3, -1);
    // NC(CCC)=O
    this.blc5 = new Chain(blc4, ext5, 4, -1);
    // N1C(CC1)=O
    this.blc6 = new Chain(blc5, ext6, 5, 1);
}