/// <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.Instance;
InChIToStructure intostruct = factory.GetInChIToStructure(inchiString, ChemObjectBuilder.Instance);
InChIReturnCode ret = intostruct.ReturnStatus;
if (ret == InChIReturnCode.Warning) // Structure generated, but with warning message
{
warningMsg = "InChI warning: " + intostruct.Message;
}
else if (ret != InChIReturnCode.Ok) // Structure generation failed
{
errorMsg = "Structure generation failed failed: " + ret.ToString() + " [" + intostruct.Message + "]";
throw new Exception(errorMsg);
}
IAtomContainer mol = intostruct.AtomContainer;
return(mol);
}
void Main()
{
IAtomContainer container = null;
#region
// Generate factory - if native code does not load
InChIGeneratorFactory factory = new InChIGeneratorFactory();
// Get InChIGenerator
InChIGenerator gen = factory.GetInChIGenerator(container);
InChIReturnCode ret = gen.ReturnStatus;
if (ret == InChIReturnCode.Warning)
{
// InChI generated, but with warning message
Console.WriteLine($"InChI warning: {gen.Message}");
}
else if (ret != InChIReturnCode.Ok)
{
// InChI generation failed
throw new CDKException($"InChI failed: {ret.ToString()} [{gen.Message}]");
}
string inchi = gen.InChI;
string auxinfo = gen.AuxInfo;
#endregion
}
public NInchiOutput(InChIReturnCode ret, string inchi, string auxInfo, string message, string log)
{
ReturnStatus = ret;
InChI = inchi;
AuxInfo = auxInfo;
Message = message;
Log = log;
}
public void TestAuxinfo2Input()
{
// START SNIPPET: auxinfo2input
NInchiInputData data = NInchiWrapper.GetInputFromAuxInfo("AuxInfo=1/1/N:4,1,2,3,5,6/"
+ "E:(5,6)/it:im/rA:6CCNCOO/rB:s1;N1;s1;s2;d2;/rC:264,968,0;295,985,0;233,986,0;"
+ "264,932,0;326,967,0;295,1021,0;");
InChIReturnCode ret = data.ReturnStatus;
NInchiInput input = data.Input;
// END SNIPPET: auxinfo2input
}
public void TestInchi2Structure()
{
// START SNIPPET: inchi2structure
NInchiInputInchi input = new NInchiInputInchi("InChI=1/C2H6/c1-2/h1-2H3");
NInchiOutputStructure output = NInchiWrapper.GetStructureFromInchi(input);
//
InChIReturnCode retStatus = output.ReturnStatus;
int nat = output.Atoms.Count;
int nbo = output.Bonds.Count;
int nst = output.Stereos.Count;
//
NInchiAtom at0 = output.Atoms[0];
// END SNIPPET: inchi2structure
}
static void Main()
{
string inchi = "inchi";
#region
// Get InChIToStructure
InChIToStructure intostruct = InChIToStructure.FromInChI(inchi, ChemObjectBuilder.Instance);
InChIReturnCode ret = intostruct.ReturnStatus;
if (ret == InChIReturnCode.Warning)
{
// Structure generated, but with warning message
Console.WriteLine($"InChI warning: {intostruct.Message}");
}
else if (ret != InChIReturnCode.Ok)
{
// Structure generation failed
throw new CDKException($"Structure generation failed: {ret.ToString()} [{intostruct.Message}]");
}
IAtomContainer container = intostruct.AtomContainer;
#endregion
}
/// <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)
{
InChIReturnCode inchiStatus = ig.ReturnStatus;
if (inchiStatus == InChIReturnCode.Ok)
{
return(true);
}
string msg = ig.Message;
string log = ig.Log;
string auxInfo = ig.AuxInfo;
if (inchiStatus == InChIReturnCode.Warning)
{
return(true);
}
else
{
return(false);
}
}
public NInchiOutputStructure(InChIReturnCode value)
{
this.ReturnStatus = value;
}
