/// <summary>
/// <para>Converts an InChI into an InChI for validation purposes (the same as the -InChI2InChI option).</para>
/// <para>This method may also be used to filter out specific layers. For instance, /Snon would remove the
/// stereochemical layer; Omitting /FixedH and/or /RecMet would remove Fixed-H or Reconnected layers.
/// In order to keep all InChI layers use options string "/FixedH /RecMet"; option /InChI2InChI is not needed.</para>
/// </summary>
/// <param name="input"></param>
/// <returns></returns>
public static NInchiOutput GetInchiFromInchi(NInchiInputInchi input)
{
if (input == null)
{
throw new ArgumentNullException(nameof(input), "Null input");
}
var native_input = new Inchi_InputINCHI();
var szInChI = Marshal.StringToHGlobalAnsi(input.Inchi);
var szOptions = Marshal.StringToHGlobalAnsi(input.Options);
try
{
native_input.szInChI = szInChI;
native_input.szOptions = szOptions;
var native_output = new Inchi_Output();
var ret = GetINCHIfromINCHI(ref native_input, out native_output);
NInchiOutput oo = ToInchiOutput(ret, native_output);
FreeStdINCHI(ref native_output);
return(oo);
}
finally
{
Marshal.FreeHGlobal(szOptions);
Marshal.FreeHGlobal(szInChI);
}
}
public void TestGetOptions()
{
NInchiInputInchi input = new NInchiInputInchi("InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H");
input.Options = NInchiWrapper.FlagChar + "compress";
Assert.AreEqual(NInchiWrapper.FlagChar + "compress", input.Options);
}
/// <summary>
/// Constructor. Generates CMLMolecule from InChI.
/// </summary>
/// <param name="inchi"></param>
/// <param name="builder"></param>
/// <param name="options"></param>
internal InChIToStructure(string inchi, IChemObjectBuilder builder, string options)
{
try
{
input = new NInchiInputInchi(inchi, options);
}
catch (NInchiException jie)
{
throw new CDKException("Failed to convert InChI to molecule: " + jie.Message, jie);
}
GenerateAtomContainerFromInChI(builder);
}
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
}
/// <summary>
/// Constructor. Generates CMLMolecule from InChI.
/// </summary>
/// <param name="inchi"></param>
/// <param name="builder"></param>
/// <param name="options"></param>
internal InChIToStructure(string inchi, IChemObjectBuilder builder, IEnumerable <string> options)
{
if (options == null)
{
throw new ArgumentNullException(nameof(options));
}
try
{
input = new NInchiInputInchi(inchi, options.Select(n => InChIOption.ValueOfIgnoreCase(n)));
}
catch (NInchiException jie)
{
throw new CDKException("Failed to convert InChI to molecule: " + jie.Message);
}
GenerateAtomContainerFromInChI(builder);
}
/// <summary>
/// Generated 0D structure from an InChI string.
/// </summary>
/// <param name="input"></param>
/// <returns></returns>
public static NInchiOutputStructure GetStructureFromInchi(NInchiInputInchi input)
{
if (input == null)
{
throw new ArgumentNullException(nameof(input), "Null input");
}
var native_input = new Inchi_InputINCHI();
var szInChI = Marshal.StringToHGlobalAnsi(input.Inchi);
var szOptions = Marshal.StringToHGlobalAnsi(input.Options);
try
{
native_input.szInChI = szInChI;
native_input.szOptions = szOptions;
var native_output = new Inchi_OutputStruct();
var ret = GetStructFromINCHI(ref native_input, out native_output);
NInchiOutputStructure output = new NInchiOutputStructure(ret,
Marshal.PtrToStringAnsi(native_output.szMessage),
Marshal.PtrToStringAnsi(native_output.szLog),
native_output.WarningFlags[0], native_output.WarningFlags[1],
native_output.WarningFlags[2], native_output.WarningFlags[3]);
CreateAtoms(output, native_output.num_atoms, native_output.atom);
CreateBonds(output, native_output.num_atoms, native_output.atom);
CreateStereos(output, native_output.num_stereo0D, native_output.stereo0D);
FreeStructFromINCHI(ref native_output);
return(output);
}
finally
{
Marshal.FreeHGlobal(szOptions);
Marshal.FreeHGlobal(szInChI);
}
}
public void TestGetInchi()
{
NInchiInputInchi input = new NInchiInputInchi("InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H");
Assert.AreEqual("InChI=1/C6H6/c1-2-4-6-5-3-1/h1-6H", input.Inchi);
}
