Examples with SMARTSBond org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond used on opensource projects

Example 1 with SMARTSBond

use of org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond in project ambit-mirror by ideaconsult.

the class SmartsParser method setDoubleBondStereoElement.

void setDoubleBondStereoElement(SMARTSBond doubleBond, IAtom atom, IAtom at0, SMARTSBond dirBond, int direction, int atomPos) {
    // Input defines a fragment of the type "a0--atom=="
    // Direction of bond "a0--atom" is defined by parameters: direction and
    // atPos
    // atomPos is the number ot 'atom' inside the CDK representation of bond
    // "a0--atom"
    // One of the bonds "atom1--at2" or "atom1--at3" must be a directional
    // bond otherwise
    // the stereo configuration is not determined.
    // 
    // The remaining part of this fragment is determined first
    // at0 at2
    // \ doubleBond /
    // atom == atom1
    // / \
    // at1 at3
    // Determining only atoms: atom1 and at2
    // atoms at1 and at3 are not needed for storing the stereo element
    // System.out.println("*** setDoubleBondStereoElement");
    IAtom atom1;
    IAtom at2 = null;
    IBond dirBond2 = null;
    if (doubleBond.getAtom(0) == atom)
        atom1 = doubleBond.getAtom(1);
    else
        atom1 = doubleBond.getAtom(0);
    java.util.List ca = container.getConnectedAtomsList(atom1);
    for (int k = 0; k < ca.size(); k++) {
        IAtom otherAt = (IAtom) ca.get(k);
        if (otherAt == atom)
            continue;
        IBond bo = container.getBond(atom1, otherAt);
        if (at2 == null) {
            if (isDirectionalBond((SMARTSBond) bo)) {
                at2 = otherAt;
                dirBond2 = bo;
                break;
            }
        }
    }
    if (at2 == null)
        // Stereo element is not complete
        return;
    // The stereo info object is created
    DoubleBondStereoInfo dbsi = new DoubleBondStereoInfo();
    dbsi.ligand1 = at0;
    dbsi.ligand2 = at2;
    // Get stored direction for the second direction bond
    int dirBond2Index = directionalBonds.indexOf(dirBond2);
    int direction2 = directions.get(dirBond2Index).intValue();
    // Get normalized directions
    int norm_dir = getNormalizedBondDirection(direction, atom, at0);
    int norm_dir2 = getNormalizedBondDirection(direction2, atom1, at2);
    boolean isUp = (norm_dir == SmartsConst.BT_UP) || (norm_dir == SmartsConst.BT_UPUNSPEC);
    boolean isUp2 = (norm_dir2 == SmartsConst.BT_UP) || (norm_dir2 == SmartsConst.BT_UPUNSPEC);
    boolean isUndefined = (norm_dir == SmartsConst.BT_UPUNSPEC) || (norm_dir == SmartsConst.BT_DOWNUNSPEC) || (norm_dir2 == SmartsConst.BT_UPUNSPEC) || (norm_dir2 == SmartsConst.BT_DOWNUNSPEC);
    if (isUp == isUp2) {
        if (isUndefined)
            dbsi.conformation = DBStereo.TOGETHER_OR_UNDEFINED;
        else
            dbsi.conformation = DBStereo.TOGETHER;
    } else {
        if (isUndefined)
            dbsi.conformation = DBStereo.OPPOSITE_OR_UNDEFINED;
        else
            dbsi.conformation = DBStereo.OPPOSITE;
    }
    if (doubleBond instanceof DoubleNonAromaticBond) {
        DoubleNonAromaticBond db = (DoubleNonAromaticBond) doubleBond;
        db.setStereoInfo(dbsi);
        processedDoubleBonds.add(doubleBond);
        processedDirBonds.add((SMARTSBond) dirBond2);
    } else {
        if (doubleBond instanceof DoubleBondAromaticityNotSpecified) {
            DoubleBondAromaticityNotSpecified db = (DoubleBondAromaticityNotSpecified) doubleBond;
            db.setStereoInfo(dbsi);
            processedDoubleBonds.add(doubleBond);
            processedDirBonds.add((SMARTSBond) dirBond2);
        } else if (doubleBond instanceof SmartsBondExpression) {
            SmartsBondExpression db = (SmartsBondExpression) doubleBond;
            db.setStereoInfo(dbsi);
            processedDoubleBonds.add(doubleBond);
            processedDirBonds.add((SMARTSBond) dirBond2);
        }
    }
}

Example 2 with SMARTSBond

use of org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond in project ambit-mirror by ideaconsult.

the class SmartsManager method getAtomMapsFromBondMaps.

/**
 * This function returns a vector of all positions (IAtoms) at which The
 * Query is matched (i.e. it first atom is matched) The full atom mapping is
 * not obtained from this function !!! This function is a helper utility for
 * the CDK isomorphism algorithm
 */
List<IAtom> getAtomMapsFromBondMaps(List bondMapping, IAtomContainer target, IAtomContainer recQuery) {
    // The query must contain at least 3 atoms and 2 bonds.
    // The first bond is always 0-1
    // Two cases are considered for the second bond:
    // a0-a1-a2 (e.g. CCC)
    // a0(-a1)-a2 (e.g. C(C)C)
    // So the common atom of bonds 0 and 1 is either atom 1 or atom 0
    // The latter assumptions are based on the way recursive SMARTS are
    // parsed
    List<IAtom> atomMaps = new ArrayList<IAtom>();
    if (recQuery.getBondCount() < 2)
        return (atomMaps);
    SMARTSBond qBond0 = (SMARTSBond) recQuery.getBond(0);
    SMARTSBond qBond1 = (SMARTSBond) recQuery.getBond(1);
    int qID0 = recQuery.getBondNumber(qBond0);
    int qID1 = recQuery.getBondNumber(qBond1);
    SMARTSAtom qAtom0 = (SMARTSAtom) recQuery.getAtom(0);
    SMARTSAtom qAtom1 = (SMARTSAtom) recQuery.getAtom(1);
    IAtom commonQAt = getBondsCommonAtom(qBond0, qBond1);
    if ((commonQAt != qAtom0) && (commonQAt != qAtom1))
        // This should never happen
        return (atomMaps);
    IBond tBond0 = null;
    IBond tBond1 = null;
    IAtom commonTAt;
    RMap map;
    List mapList;
    for (Object aList : bondMapping) {
        mapList = (List) aList;
        // Search RMaps to find the corresponding target bonds
        // (qBond0<-->tBond0, qBond1<-->tBond1)
        // Note: map.getId2 corresponds to the query; map.getId1 corresponds
        // to the target
        int found = 0;
        for (Object aMap : mapList) {
            map = (RMap) aMap;
            if (map.getId2() == qID0) {
                found++;
                tBond0 = target.getBond(map.getId1());
            }
            if (map.getId2() == qID1) {
                found++;
                tBond1 = target.getBond(map.getId1());
            }
            if (found >= 2)
                break;
        }
        if (// This should never happen
        found < 2)
            continue;
        commonTAt = getBondsCommonAtom(tBond0, tBond1);
        if (commonQAt == qAtom0)
            atomMaps.add(commonTAt);
        else {
            // So the other atom (not commonTAt) must be added to atomMaps
            if (commonTAt == tBond0.getAtom(0))
                atomMaps.add(tBond0.getAtom(1));
            else
                atomMaps.add(tBond0.getAtom(0));
        }
    }
    return (atomMaps);
}

Example 3 with SMARTSBond

use of org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond in project ambit-mirror by ideaconsult.

the class SmartsManager method getFirstPosAtomMappingsFor2AtomQuery.

List<IAtom> getFirstPosAtomMappingsFor2AtomQuery(IAtomContainer target, IAtomContainer recQuery) {
    List<IAtom> atomMaps = new ArrayList<IAtom>();
    if (recQuery.getBondCount() == 0)
        // The two atoms must be connected otherwise
        return (atomMaps);
    // substr. search returns no matches
    SMARTSAtom qAtom0 = (SMARTSAtom) recQuery.getAtom(0);
    SMARTSAtom qAtom1 = (SMARTSAtom) recQuery.getAtom(1);
    SMARTSBond qBond = (SMARTSBond) recQuery.getBond(0);
    for (int i = 0; i < target.getAtomCount(); i++) {
        IAtom at = target.getAtom(i);
        if (qAtom0.matches(at)) {
            List ca = target.getConnectedAtomsList(at);
            for (int j = 0; j < ca.size(); j++) if (qAtom1.matches((IAtom) ca.get(j))) {
                IBond bo = target.getBond(at, (IAtom) ca.get(j));
                if (bo != null)
                    if (qBond.matches(bo)) {
                        atomMaps.add(at);
                        // for j-cycle
                        break;
                    }
            }
        }
    }
    return (atomMaps);
}

Example 4 with SMARTSBond

use of org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond in project cdk by cdk.

the class SmartsQueryVisitor method visit.

public Object visit(ASTSmarts node, Object data) {
    SMARTSAtom atom;
    SMARTSBond bond = null;
    ASTAtom first = (ASTAtom) node.jjtGetChild(0);
    atom = (SMARTSAtom) first.jjtAccept(this, null);
    if (data != null) {
        // this is a sub smarts
        bond = (SMARTSBond) ((Object[]) data)[1];
        IAtom prev = (SMARTSAtom) ((Object[]) data)[0];
        if (bond == null) {
            // since no bond was specified it could be aromatic or single
            bond = new AromaticOrSingleQueryBond(builder);
            bond.setAtoms(new IAtom[] { prev, atom });
        } else {
            bond.setAtoms(new IAtom[] { prev, atom });
        }
        if (neighbors.containsKey(prev)) {
            neighbors.get(prev).add(atom);
        }
        query.addBond(bond);
        bond = null;
    }
    // first ATOM in expresion
    query.addAtom(atom);
    if (tetrahedral.get(query.getAtomCount() - 1)) {
        List<IAtom> localNeighbors = new ArrayList<>(query.getConnectedAtomsList(atom));
        localNeighbors.add(atom);
        neighbors.put(atom, localNeighbors);
    }
    // now process the rest of the bonds/atoms
    for (int i = 1; i < node.jjtGetNumChildren(); i++) {
        Node child = node.jjtGetChild(i);
        if (child instanceof ASTLowAndBond) {
            bond = (SMARTSBond) child.jjtAccept(this, data);
        } else if (child instanceof ASTAtom) {
            SMARTSAtom newAtom = (SMARTSAtom) child.jjtAccept(this, null);
            if (bond == null) {
                // since no bond was specified it could be aromatic or single
                bond = new AromaticOrSingleQueryBond(builder);
            }
            bond.setAtoms(new IAtom[] { atom, newAtom });
            query.addBond(bond);
            query.addAtom(newAtom);
            if (neighbors.containsKey(atom)) {
                neighbors.get(atom).add(newAtom);
            }
            if (tetrahedral.get(query.getAtomCount() - 1)) {
                List<IAtom> localNeighbors = new ArrayList<>(query.getConnectedAtomsList(newAtom));
                localNeighbors.add(newAtom);
                neighbors.put(newAtom, localNeighbors);
            }
            atom = newAtom;
            bond = null;
        } else if (child instanceof ASTSmarts) {
            // another smarts
            child.jjtAccept(this, new Object[] { atom, bond });
            bond = null;
        } else if (child instanceof ASTRingIdentifier) {
            handleRingClosure(atom, (ASTRingIdentifier) child);
        } else {
            throw new IllegalStateException("Unhandled node type: " + child.getClass());
        }
    }
    return query;
}

Example 5 with SMARTSBond

use of org.openscience.cdk.isomorphism.matchers.smarts.SMARTSBond in project ambit-mirror by ideaconsult.

the class SmartsParser method getNeighborDoubleBond.

SMARTSBond getNeighborDoubleBond(SMARTSBond bond, int atNum) {
    // bond is a directional single bond
    // the neighbor double is search among the "atNum" neighbors
    IAtom at = bond.getAtom(atNum);
    java.util.List ca = container.getConnectedAtomsList(at);
    for (int k = 0; k < ca.size(); k++) {
        IBond bo = container.getBond(at, (IAtom) ca.get(k));
        if (bo != bond) {
            if (bo instanceof DoubleNonAromaticBond)
                return (SMARTSBond) bo;
            if (bo instanceof DoubleBondAromaticityNotSpecified)
                return (SMARTSBond) bo;
            if (bo instanceof SmartsBondExpression) {
                SmartsToChemObject stco = new SmartsToChemObject(SilentChemObjectBuilder.getInstance());
                IBond bondFromExpr = stco.smartsExpressionToBond((SmartsBondExpression) bo);
                if (bondFromExpr != null)
                    if (bondFromExpr.getOrder() == IBond.Order.DOUBLE)
                        return (SMARTSBond) bo;
            }
        }
    }
    return (null);
}