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Example 1 with SingleBondAromaticityNotSpecified

use of ambit2.smarts.SingleBondAromaticityNotSpecified 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;
}
Also used : AnyOrderQueryBond(org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond) SingleOrAromaticBond(ambit2.smarts.SingleOrAromaticBond) SingleBondAromaticityNotSpecified(ambit2.smarts.SingleBondAromaticityNotSpecified) DoubleNonAromaticBond(ambit2.smarts.DoubleNonAromaticBond) DoubleBondAromaticityNotSpecified(ambit2.smarts.DoubleBondAromaticityNotSpecified) AnyOrderQueryBond(org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond) OrderQueryBond(org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond) IQueryBond(org.openscience.cdk.isomorphism.matchers.IQueryBond) SingleNonAromaticBond(ambit2.smarts.SingleNonAromaticBond)

Aggregations

DoubleBondAromaticityNotSpecified (ambit2.smarts.DoubleBondAromaticityNotSpecified)1 DoubleNonAromaticBond (ambit2.smarts.DoubleNonAromaticBond)1 SingleBondAromaticityNotSpecified (ambit2.smarts.SingleBondAromaticityNotSpecified)1 SingleNonAromaticBond (ambit2.smarts.SingleNonAromaticBond)1 SingleOrAromaticBond (ambit2.smarts.SingleOrAromaticBond)1 IQueryBond (org.openscience.cdk.isomorphism.matchers.IQueryBond)1 AnyOrderQueryBond (org.openscience.cdk.isomorphism.matchers.smarts.AnyOrderQueryBond)1 OrderQueryBond (org.openscience.cdk.isomorphism.matchers.smarts.OrderQueryBond)1