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

Example 1 with AromaticOrSingleQueryBond

use of org.openscience.cdk.isomorphism.matchers.smarts.AromaticOrSingleQueryBond 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;
}