use of ambit2.smarts.DoubleBondAromaticityNotSpecified in project ambit-mirror by ideaconsult.
the class SLN2ChemObject method slnBondToQueryBond.
/*
* Converts only the bond type/expression info
* connected atoms info is not handled
*/
public IQueryBond slnBondToQueryBond(SLNBond slnBo) {
currentConversionError = null;
currentConversionWarning = null;
if (slnBo == null) {
currentConversionError = "Bond is null";
return null;
}
if (slnBo.bondType == 0) {
if (slnBo.bondExpression == null)
return new AnyOrderQueryBond(SilentChemObjectBuilder.getInstance());
// TODO handle bond expression
} else {
if (slnBo.bondExpression == null) {
IQueryBond bond = null;
switch(slnBo.bondType) {
case 1:
if (conversionConfig.FlagSLNSingleBondToSingleOrAromaticBond)
bond = new SingleOrAromaticBond(SilentChemObjectBuilder.getInstance());
else if (conversionConfig.FlagSupportSingleBondAromaticityNotSpecified)
bond = new SingleBondAromaticityNotSpecified(SilentChemObjectBuilder.getInstance());
else
bond = new SingleNonAromaticBond(SilentChemObjectBuilder.getInstance());
break;
case 2:
if (conversionConfig.FlagSupportDoubleBondAromaticityNotSpecified)
bond = new DoubleBondAromaticityNotSpecified(SilentChemObjectBuilder.getInstance());
else
bond = new DoubleNonAromaticBond(SilentChemObjectBuilder.getInstance());
break;
case 3:
bond = new OrderQueryBond(IBond.Order.TRIPLE, SilentChemObjectBuilder.getInstance());
break;
}
return bond;
}
// TODO handle bond expression
}
return null;
}
use of ambit2.smarts.DoubleBondAromaticityNotSpecified 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();
}
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