Examples with SLNAtom ambit2.sln.SLNAtom used on opensource projects

Example 16 with SLNAtom

use of ambit2.sln.SLNAtom in project ambit-mirror by ideaconsult.

the class SLN2ChemObject method QueryAtomContainerToSLNContainer.

public SLNContainer QueryAtomContainerToSLNContainer(IQueryAtomContainer query) {
    clearAllErrorsAndWarnings();
    SLNContainer slnCon = new SLNContainer(SilentChemObjectBuilder.getInstance());
    for (int i = 0; i < query.getAtomCount(); i++) {
        // SLNAtom slnAtom = (SLNAtom) slnContainer.getAtom(i);
        // IQueryAtom atom = slnAtomToQueryAtom(slnAtom);
        IQueryAtom atom = (IQueryAtom) query.getAtom(i);
        SLNAtom slnAtom = queryAtomToSLNAtom(atom);
        if (currentConversionWarning != null)
            conversionWarnings.add(currentConversionWarning + " for atom: " + (i + 1));
        if (slnAtom == null) {
            conversionErrors.add(currentConversionError + " for atom: " + (i + 1));
            continue;
        }
        slnCon.addAtom(slnAtom);
    // convertedAtoms.put(slnAtom, atom);
    }
    return slnCon;
}