public void TestExampleStructure2InchiAlanine()
{
// START SNIPPET: structure2inchi-alanine
// Example input - 0D D-Alanine
NInchiInput input = new NInchiInput();
//
// Generate atoms
NInchiAtom a1 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "C"));
NInchiAtom a2 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "C"));
NInchiAtom a3 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "N"));
NInchiAtom a4 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "C"));
NInchiAtom a5 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "O"));
NInchiAtom a6 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "O"));
NInchiAtom a7 = input.Add(new NInchiAtom(0.0, 0.0, 0.0, "H"));
a3.ImplicitH = 2;
a4.ImplicitH = 3;
a5.ImplicitH = 1;
//
// Add bonds
input.Add(new NInchiBond(a1, a2, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a1, a3, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a1, a4, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a2, a5, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a2, a6, INCHI_BOND_TYPE.Double));
input.Add(new NInchiBond(a1, a7, INCHI_BOND_TYPE.Single));
//
// Add stereo parities
input.Stereos.Add(NInchiStereo0D
.CreateNewTetrahedralStereo0D(a1, a3, a4, a7, a2, INCHI_PARITY.Even));
//
NInchiOutput output = NInchiWrapper.GetInchi(input);
// END SNIPPET: structure2inchi-alanine
}
/// <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 TestInchi2InchiHydrogen()
{
// START SNIPPET: inchi2inchi-hydrogen
// Input InChI with fixed-hydrogen layer
string inchiIn = "InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/"
+ "t2-/m0/s1/f/h5H";
//
NInchiOutput output = NInchiWrapper.GetInchiFromInchi(
new NInchiInputInchi(inchiIn));
string inchiOut = output.InChI;
// Output InChI:
// InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1
// END SNIPPET: inchi2inchi-hydrogen
}
public void TestInchi2InchiCompress()
{
// START SNIPPET: inchi2inchi-compress
string inchi = "InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)";
//
// Compress InChI
NInchiOutput cout = NInchiWrapper.GetInchiFromInchi(
new NInchiInputInchi(inchi, "-compress"));
string compressedInchi = cout.InChI;
// compressedInchi = InChI=1/C3H7NO2/cABBCC/hB1D2A3,1EF
//
// Uncompress InChI
NInchiOutput ucout = NInchiWrapper.GetInchiFromInchi(
new NInchiInputInchi(compressedInchi));
string uncompressedInchi = ucout.InChI;
// uncompressedInchi = InChI=1/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)
// END SNIPPET: inchi2inchi-compress
}
public void TestExampleStructure2InchiDiChloroethene()
{
// START SNIPPET: structure2inchi-dichloroethene
// Example input - 2D E-1,2-dichloroethene
NInchiInput input = new NInchiInput();
//
// Generate atoms
NInchiAtom a1 = input.Add(new NInchiAtom(2.866, -0.250, 0.000, "C"));
NInchiAtom a2 = input.Add(new NInchiAtom(3.732, 0.250, 0.000, "C"));
NInchiAtom a3 = input.Add(new NInchiAtom(2.000, 2.500, 0.000, "Cl"));
NInchiAtom a4 = input.Add(new NInchiAtom(4.598, -0.250, 0.000, "Cl"));
a1.ImplicitH = 1;
a2.ImplicitH = 1;
//
// Add bond
input.Add(new NInchiBond(a1, a2, INCHI_BOND_TYPE.Double));
input.Add(new NInchiBond(a1, a3, INCHI_BOND_TYPE.Single));
input.Add(new NInchiBond(a2, a4, INCHI_BOND_TYPE.Single));
NInchiOutput output = NInchiWrapper.GetInchi(input);
//END SNIPPET: structure2inchi - dichloroethene
}
/// <summary>
/// <para>Calculates the Standard InChI string for a chemical structure.</para>
/// <para>The only valid structure perception options are NEWPSOFF/DoNotAddH/SNon. In any other structural
/// perception options are specified then the calculation will fail.</para>
/// </summary>
/// <param name="input"></param>
/// <returns></returns>
public static NInchiOutput GetStdInchi(NInchiInput input)
{
if (input == null)
{
throw new ArgumentNullException(nameof(input), "Null input");
}
var prep = InitInchiInput(input);
fixed(Inchi_Atom *atoms = prep.atoms)
fixed(Inchi_Stereo0D * stereos = prep.stereos)
{
Inchi_Input native_input = new Inchi_Input();
Inchi_Output native_output = new Inchi_Output();
native_input.atom = new IntPtr(atoms);
native_input.num_atoms = (Int16)input.Atoms.Count;
native_input.stereo0D = new IntPtr(stereos);
native_input.num_stereo0D = (Int16)input.Stereos.Count;
var szOptions = Marshal.StringToHGlobalAnsi(input.Options);
try
{
native_input.szOptions = szOptions;
var ret = GetStdINCHI(ref native_input, out native_output);
NInchiOutput oo = ToInchiOutput(ret, native_output);
FreeStdINCHI(ref native_output);
return(oo);
}
finally
{
Marshal.FreeHGlobal(szOptions);
}
}
}
public void TestGetLog()
{
NInchiOutput output = new NInchiOutput(InChIReturnCode.Unknown, null, null, null, "Test log");
Assert.AreEqual("Test log", output.Log);
}
public void TestGetMessage()
{
NInchiOutput output = new NInchiOutput(InChIReturnCode.Unknown, null, null, "Test message", null);
Assert.AreEqual("Test message", output.Message);
}
public void TestGetAuxInfo()
{
NInchiOutput output = new NInchiOutput(InChIReturnCode.Unknown, null, "AuxInfo=1/0/N:1,2,6,3,5,4/E:(1,2,3,4,5,6)/rA:6nCCCCCC/rB:d1;s2;d3;s4;s1d5;/rC:-.7145,.4125,0;-.7145,-.4125,0;0,-.825,0;.7145,-.4125,0;.7145,.4125,0;0,.825,0;", null, null);
Assert.AreEqual("AuxInfo=1/0/N:1,2,6,3,5,4/E:(1,2,3,4,5,6)/rA:6nCCCCCC/rB:d1;s2;d3;s4;s1d5;/rC:-.7145,.4125,0;-.7145,-.4125,0;0,-.825,0;.7145,-.4125,0;.7145,.4125,0;0,.825,0;", output.AuxInfo);
}
public void TestGetInchi()
{
NInchiOutput output = new NInchiOutput(InChIReturnCode.Unknown, "Inchi=1/C6H6/c1-2-4-6-5-3-1/h1-6H", null, null, null);
Assert.AreEqual("Inchi=1/C6H6/c1-2-4-6-5-3-1/h1-6H", output.InChI);
}
public void TestGetReturnStatus()
{
NInchiOutput output = new NInchiOutput(InChIReturnCode.Ok, null, null, null, null);
Assert.AreEqual(InChIReturnCode.Ok, output.ReturnStatus);
}
