Examples with SmartsToChemObject ambit2.smarts.SmartsToChemObject used on opensource projects

Example 1 with SmartsToChemObject

use of ambit2.smarts.SmartsToChemObject in project ambit-mirror by ideaconsult.

the class RuleStateBondDistribution method calcDistribution.

public void calcDistribution(IQueryAtomContainer statePattern) {
    int n = 0;
    SmartsToChemObject stco = new SmartsToChemObject(SilentChemObjectBuilder.getInstance());
    List<Integer> v2 = new ArrayList<Integer>();
    List<Integer> v3 = new ArrayList<Integer>();
    for (int i = 0; i < statePattern.getBondCount(); i++) {
        if (hasRingClosure)
            if (ringClosureBondIndex == i)
                // It is obligatory that closure bond is not registered in the distribution arrays.
                continue;
        if (statePattern.getBond(i) instanceof DoubleNonAromaticBond) {
            v2.add(new Integer(i));
            continue;
        }
        if (statePattern.getBond(i) instanceof DoubleBondAromaticityNotSpecified) {
            v2.add(new Integer(i));
            continue;
        }
        if (statePattern.getBond(i) instanceof OrderQueryBond) {
            OrderQueryBond bo = (OrderQueryBond) statePattern.getBond(i);
            if (bo.getOrder() == IBond.Order.DOUBLE)
                v2.add(new Integer(i));
            if (bo.getOrder() == IBond.Order.TRIPLE)
                v3.add(new Integer(i));
            continue;
        }
        if (statePattern.getBond(i) instanceof SmartsBondExpression) {
            IBond bo = stco.smartsExpressionToBond((SmartsBondExpression) statePattern.getBond(i));
            if (bo != null) {
                if (bo.getOrder() == IBond.Order.DOUBLE)
                    v2.add(new Integer(i));
                if (bo.getOrder() == IBond.Order.TRIPLE)
                    v3.add(new Integer(i));
            }
            continue;
        }
    }
    DBPositions = new int[v2.size()];
    for (int i = 0; i < v2.size(); i++) DBPositions[i] = v2.get(i).intValue();
    TBPositions = new int[v3.size()];
    for (int i = 0; i < v3.size(); i++) TBPositions[i] = v3.get(i).intValue();
}