Examples with TetrahedralChirality org.openscience.cdk.stereo.TetrahedralChirality used on opensource projects

Example 1 with TetrahedralChirality

use of org.openscience.cdk.stereo.TetrahedralChirality in project ambit-mirror by ideaconsult.

the class SMIRKSManager method getCloneStructure.

IAtomContainer getCloneStructure(IAtomContainer target) throws Exception {
    IAtomContainer mol = new AtomContainer();
    IAtom[] newAtoms = new IAtom[target.getAtomCount()];
    IBond[] newBonds = new IBond[target.getBondCount()];
    // Clone atoms
    for (int i = 0; i < target.getAtomCount(); i++) {
        IAtom a = target.getAtom(i);
        IAtom a1 = cloneAtom(a);
        mol.addAtom(a1);
        newAtoms[i] = a1;
    }
    // Clone bonds
    for (int i = 0; i < target.getBondCount(); i++) {
        IBond b = target.getBond(i);
        IBond b1 = MoleculeTools.newBond(target.getBuilder());
        IAtom[] a01 = new IAtom[2];
        int ind0 = target.getAtomNumber(b.getAtom(0));
        int ind1 = target.getAtomNumber(b.getAtom(1));
        a01[0] = mol.getAtom(ind0);
        a01[1] = mol.getAtom(ind1);
        b1.setAtoms(a01);
        b1.setOrder(b.getOrder());
        boolean FlagArom = b.getFlag(CDKConstants.ISAROMATIC);
        b1.setFlag(CDKConstants.ISAROMATIC, FlagArom);
        mol.addBond(b1);
        newBonds[i] = b1;
    }
    // Clone stereo elements
    for (IStereoElement element : target.stereoElements()) {
        if (element instanceof DoubleBondStereochemistry) {
            DoubleBondStereochemistry dbs0 = (DoubleBondStereochemistry) element;
            DoubleBondStereochemistry dbs = StereoChemUtils.cloneDoubleBondStereochemistry(dbs0, target, mol, newAtoms, newBonds);
            if (dbs != null)
                mol.addStereoElement(dbs);
            continue;
        }
        if (element instanceof TetrahedralChirality) {
            TetrahedralChirality thc0 = (TetrahedralChirality) element;
            TetrahedralChirality thc = StereoChemUtils.cloneTetrahedralChirality(thc0, target, mol, newAtoms);
            if (thc != null)
                mol.addStereoElement(thc);
            continue;
        }
    // TODO handle ExtendedTetrahedral (... allene like chiral centers)
    }
    return mol;
}

Example 2 with TetrahedralChirality

use of org.openscience.cdk.stereo.TetrahedralChirality in project ambit-mirror by ideaconsult.

the class IsomorphismTester method getTargetChiralAtomStereo.

int getTargetChiralAtomStereo(SmartsAtomExpression atom, Node node) {
    int queryChiralCenter_index = query.getAtomNumber(atom);
    IAtom targetCenter = node.atoms[queryChiralCenter_index];
    if (atom.extChirInfo == null) {
        // Handle chiral stereo center
        TetrahedralChirality thc = findTargetChiralStereoElement(targetCenter);
        if (thc == null)
            return SmartsConst.ChC_Unspec;
        IAtom[] targetMatchedLigands = new IAtom[atom.stereoLigands.size()];
        for (int i = 0; i < targetMatchedLigands.length; i++) {
            int query_index = query.getAtomNumber(atom.stereoLigands.get(i));
            targetMatchedLigands[i] = node.atoms[query_index];
        }
        if (atom.hasImplicitHStereoLigand) {
            // The targetCenter must be within target ligands
            boolean FlagOK = false;
            for (int i = 0; i < targetMatchedLigands.length; i++) {
                if (targetMatchedLigands[i] == targetCenter) {
                    FlagOK = true;
                    break;
                }
            }
            if (!FlagOK)
                // This case should not occur if target stereo element is OK
                return SmartsConst.ChC_Unspec;
        }
        // ligands as defined in the target molecule.
        IAtom[] targetOriginalLigands = thc.getLigands();
        // (additional checks are done below as well)
        if (targetOriginalLigands == null)
            return SmartsConst.ChC_Unspec;
        if (targetOriginalLigands.length != 4)
            return SmartsConst.ChC_Unspec;
        // Determining the target ligands permutation as well as
        // checking the correctness of the target stereo element (there is a chance that
        // the target stereo element is no correct - in this case the result is
        // ChC_Unspec)
        // The query ligands order is considered to be the basic permutation (0,1,2,3)
        int[] targetPerm = new int[4];
        for (int i = 0; i < targetMatchedLigands.length; i++) {
            int pos = getLigandIndex(targetMatchedLigands[i], targetOriginalLigands);
            if (pos == -1)
                return SmartsConst.ChC_Unspec;
            // This means incorrect target ligands in the stereo element.
            // Neighbor to the targer center is matched which is not within
            // The stereo element ligang list.
            // This error should not appear but if present it is due to
            // incorrect target AtomContainer object
            targetPerm[i] = pos;
        }
        int nSwitches = ChiralPermutations.getNumOfPairSwitches(ChiralPermutations.basic4Permutation, targetPerm);
        if ((nSwitches % 2) == 0) {
            // relative stereo configurations are the same
            if (thc.getStereo() == ITetrahedralChirality.Stereo.ANTI_CLOCKWISE)
                return SmartsConst.ChC_AntiClock;
            else
                return SmartsConst.ChC_Clock;
        } else {
            // relative stereo configurations are different
            if (thc.getStereo() == ITetrahedralChirality.Stereo.ANTI_CLOCKWISE)
                return SmartsConst.ChC_Clock;
            else
                return SmartsConst.ChC_AntiClock;
        }
    } else {
        // Handle extended chirality
        ExtendedTetrahedral exth = findTargetExtendedTetrahedralElement(targetCenter);
        if (exth == null)
            return SmartsConst.ChC_Unspec;
        IAtom[] targetMatchedLigands = new IAtom[atom.stereoLigands.size()];
        for (int i = 0; i < targetMatchedLigands.length; i++) {
            int query_index = query.getAtomNumber(atom.stereoLigands.get(i));
            targetMatchedLigands[i] = node.atoms[query_index];
        }
        // peripherals (ligands) as defined in the target molecule.
        IAtom[] targetOriginalLigands = exth.peripherals();
        // (additional checks are done below as well)
        if (targetOriginalLigands == null)
            return SmartsConst.ChC_Unspec;
        if (targetOriginalLigands.length != 4)
            return SmartsConst.ChC_Unspec;
        // Determining the target ligands permutation as well as
        // checking the correctness of the target stereo element (there is a chance that
        // the target stereo element is no correct - in this case the result is
        // ChC_Unspec)
        // The query ligands order is considered to be the basic permutation (0,1,2,3)
        int[] targetPerm = new int[4];
        for (int i = 0; i < targetMatchedLigands.length; i++) {
            int pos = getLigandIndex(targetMatchedLigands[i], targetOriginalLigands);
            if (pos == -1)
                return SmartsConst.ChC_Unspec;
            // This means incorrect target ligands in the stereo element.
            // Neighbor to the targer center is matched which is not within
            // The stereo element ligang list.
            // This error should not appear but if present it is due to
            // incorrect target IAtomContainer object
            targetPerm[i] = pos;
        }
        int nSwitches = ChiralPermutations.getNumOfPairSwitches(ChiralPermutations.basic4Permutation, targetPerm);
        if ((nSwitches % 2) == 0) {
            // relative stereo configurations are the same
            if (exth.winding() == ITetrahedralChirality.Stereo.ANTI_CLOCKWISE)
                return SmartsConst.ChC_AntiClock;
            else
                return SmartsConst.ChC_Clock;
        } else {
            // relative stereo configurations are different
            if (exth.winding() == ITetrahedralChirality.Stereo.ANTI_CLOCKWISE)
                return SmartsConst.ChC_Clock;
            else
                return SmartsConst.ChC_AntiClock;
        }
    }
}

Example 3 with TetrahedralChirality

use of org.openscience.cdk.stereo.TetrahedralChirality in project ambit-mirror by ideaconsult.

the class StereoChemUtils method getAllStereoElementsStatus.

public static String getAllStereoElementsStatus(IAtomContainer mol, List<IStereoElement> invElements) {
    StringBuffer sb = new StringBuffer();
    sb.append(" Normal elements \n");
    for (IStereoElement element : mol.stereoElements()) {
        if (element instanceof DoubleBondStereochemistry) {
            int status = checkDoubleBondStereochemistry((DoubleBondStereochemistry) element, mol);
            sb.append("    DBStereo status = " + status + "   " + doubleBondStereochemistry2String((DoubleBondStereochemistry) element, mol) + "\n");
            continue;
        }
        if (element instanceof TetrahedralChirality) {
            int status = checkTetrahedralChirality((TetrahedralChirality) element, mol);
            sb.append("    Chiral atom status = " + status + "   " + tetrahedralChirality2String((TetrahedralChirality) element, mol) + "\n");
            continue;
        }
    // TODO handle ExtendedTetrahedral stereo elements
    }
    sb.append(" Invalidated elements \n");
    for (IStereoElement element : invElements) {
        if (element instanceof DoubleBondStereochemistry) {
            int status = checkDoubleBondStereochemistry((DoubleBondStereochemistry) element, mol);
            sb.append("   DBStereo status = " + status + "   " + doubleBondStereochemistry2String((DoubleBondStereochemistry) element, mol) + "\n");
            continue;
        }
        if (element instanceof TetrahedralChirality) {
            int status = checkTetrahedralChirality((TetrahedralChirality) element, mol);
            sb.append("   Chiral atom status = " + status + "   " + tetrahedralChirality2String((TetrahedralChirality) element, mol) + "\n");
            continue;
        }
    // TODO handle ExtendedTetrahedral stereo elements
    }
    return sb.toString();
}

Example 4 with TetrahedralChirality

use of org.openscience.cdk.stereo.TetrahedralChirality in project ambit-mirror by ideaconsult.

the class StereoChemUtils method cloneTetrahedralChirality.

/*
	 * Cloning based on presumption that atom/bond indices define 
	 * the atom mapping between original and clone molecule 
	 */
public static TetrahedralChirality cloneTetrahedralChirality(TetrahedralChirality originalTHC, IAtomContainer originalMol, IAtomContainer cloneMol) {
    IAtom chiralAtom = originalTHC.getChiralAtom();
    if (chiralAtom == null)
        return null;
    int chiralAtomNum = originalMol.getAtomNumber(chiralAtom);
    IAtom[] ligands0 = originalTHC.getLigands();
    if (ligands0 == null)
        return null;
    IAtom[] ligands = new IAtom[ligands0.length];
    for (int i = 0; i < ligands0.length; i++) {
        int atNum = originalMol.getAtomNumber(ligands0[i]);
        ligands[i] = cloneMol.getAtom(atNum);
    }
    TetrahedralChirality thc = new TetrahedralChirality(cloneMol.getAtom(chiralAtomNum), ligands, originalTHC.getStereo());
    return thc;
}

Example 5 with TetrahedralChirality

use of org.openscience.cdk.stereo.TetrahedralChirality in project ambit-mirror by ideaconsult.

the class StereoChemUtils method getStereoElementsStatus.

public static String getStereoElementsStatus(IAtomContainer mol) {
    StringBuffer sb = new StringBuffer();
    List<IStereoElement> okElements = new ArrayList<IStereoElement>();
    for (IStereoElement element : mol.stereoElements()) {
        if (element instanceof DoubleBondStereochemistry) {
            int status = checkDoubleBondStereochemistry((DoubleBondStereochemistry) element, mol);
            sb.append("DBStereo status = " + status + "   " + doubleBondStereochemistry2String((DoubleBondStereochemistry) element, mol) + "\n");
            continue;
        }
        if (element instanceof TetrahedralChirality) {
            int status = checkTetrahedralChirality((TetrahedralChirality) element, mol);
            sb.append("Chiral atom status = " + status + "   " + tetrahedralChirality2String((TetrahedralChirality) element, mol) + "\n");
            continue;
        }
    // TODO handle ExtendedTetrahedral stereo elements
    }
    return sb.toString();
}