/// <summary>
/// Convert an InChI string to an IAtomContainer
/// </summary>
/// <param name="inchiString"></param>
/// <returns></returns>
public static IAtomContainer InChIToAtomContainer(string inchiString)
{
string warningMsg, errorMsg;
InChIGeneratorFactory factory = InChIGeneratorFactory.getInstance();
InChIToStructure intostruct = factory.getInChIToStructure(inchiString, DefaultChemObjectBuilder);
INCHI_RET ret = intostruct.getReturnStatus();
if (ret == INCHI_RET.WARNING) // Structure generated, but with warning message
{
warningMsg = "InChI warning: " + intostruct.getMessage();
}
else if (ret != INCHI_RET.OKAY) // Structure generation failed
{
errorMsg = "Structure generation failed failed: " + ret.toString() + " [" + intostruct.getMessage() + "]";
throw new Exception(errorMsg);
}
IAtomContainer mol = intostruct.getAtomContainer();
return(mol);
}
/// <summary>
/// SimplifyMolfileForInChIGeneration
/// </summary>
/// <param name="molfile"></param>
/// <returns></returns>
//static string SimplifyMolfileForInChIGeneration(string molfile)
//{
// string smiles = CdkMol.StructureConverter.MolfileStringToSmilesString(molfile); // convert to smiles
// string molfile2 = CdkMol.StructureConverter.SmilesStringToMolfileString(smiles); // and back to V2000 molfile without Sgroups
// return molfile2;
//}
/// <summary>
/// IsAcceptableInchiStatus
/// </summary>
/// <param name="ig"></param>
/// <returns></returns>
static bool IsAcceptableInchiStatus(InChIGenerator ig)
{
INCHI_RET inchiStatus = ig.getReturnStatus();
if (inchiStatus == INCHI_RET.OKAY)
{
return(true);
}
string msg = ig.getMessage();
string log = ig.getLog();
string auxInfo = ig.getAuxInfo();
if (inchiStatus == INCHI_RET.WARNING)
{
return(true);
}
else
{
return(false);
}
}
