public void TestGetOptions()
{
NInchiInput input = new NInchiInput();
input.Options = NInchiWrapper.FlagChar + "compress";
Assert.AreEqual(NInchiWrapper.FlagChar + "compress", input.Options);
}
public static NInchiInputData GetInputFromAuxInfo(string auxInfo)
{
if (auxInfo == null)
{
throw new ArgumentNullException(nameof(auxInfo), "Null AuxInfo");
}
var native_output = new InchiInpData();
var iiii = Marshal.AllocHGlobal(Marshal.SizeOf(typeof(Inchi_Input)));
try
{
native_output.pInp = iiii;
int ret;
ret = Get_inchi_Input_FromAuxInfo(auxInfo, 0, 0, out native_output);
NInchiInput oos = new NInchiInput();
Inchi_Input *pii = (Inchi_Input *)native_output.pInp.ToPointer();
{
CreateAtoms(oos, pii->num_atoms, pii->atom);
CreateBonds(oos, pii->num_atoms, pii->atom);
CreateStereos(oos, pii->num_stereo0D, pii->stereo0D);
}
var oo = new NInchiInputData(ret, oos, native_output.bChiral, new string(native_output.szErrMsg));
return(oo);
}
finally
{
Free_inchi_Input((Inchi_Input *)iiii.ToPointer());
}
}
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
}
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 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);
}
}
}
static Set_inchi_Input_ InitInchiInput(NInchiInput input)
{
var natoms = input.Atoms.Count;
var nstereo = input.Stereos.Count;
var nbonds = input.Bonds.Count;
if (natoms > MAX_ATOMS)
{
throw new ArgumentException("Too many atoms");
}
var atoms = new Inchi_Atom[natoms];
{
for (int i = 0; i < natoms; i++)
{
var atom = input.Atoms[i];
Inchi_Atom iatom = new Inchi_Atom();
{
var elname = Encoding.ASCII.GetBytes(atom.ElementType);
for (int n = 0; n < elname.Length; n++)
{
iatom.elname[n] = (sbyte)elname[n];
}
iatom.elname[elname.Length] = 0;
}
iatom.X = atom.X;
iatom.Y = atom.Y;
iatom.Z = atom.Z;
iatom.charge = (SByte)atom.Charge;
iatom.radical = (SByte)atom.Radical;
iatom.num_iso_H[0] = (SByte)atom.ImplicitH;
iatom.num_iso_H[1] = (SByte)atom.ImplicitProtium;
iatom.num_iso_H[2] = (SByte)atom.ImplicitDeuterium;
iatom.num_iso_H[3] = (SByte)atom.ImplicitTritium;
iatom.isotopic_mass = (Int16)atom.IsotopicMass;
iatom.num_bonds = 0;
atoms[i] = iatom;
}
}
{
for (int i = 0; i < nbonds; i++)
{
var bond = input.Bonds[i];
var atomO = bond.OriginAtom;
var atomT = bond.TargetAtom;
var bondType = bond.BondType;
var bondStereo = bond.BondStereo;
var iaO = input.Atoms.IndexOf(atomO);
var iaT = input.Atoms.IndexOf(atomT);
var iatom = atoms[iaO];
int numbonds = atoms[iaO].num_bonds;
if (numbonds == MAXVAL)
{
throw new ArgumentException("Too many bonds from one atom; maximum: " + MAXVAL);
}
iatom.neighbor[numbonds] = (Int16)iaT;
iatom.bond_type[numbonds] = (SByte)bondType;
iatom.bond_stereo[numbonds] = (SByte)bondStereo;
iatom.num_bonds++;
atoms[iaO] = iatom;
}
}
var stereos = new Inchi_Stereo0D[nstereo];
{
for (var i = 0; i < input.Stereos.Count; i++)
{
var stereo = input.Stereos[i];
var istereo = stereos[i];
var cat = stereo.CentralAtom;
var nat0 = stereo.Neighbors[0];
var nat1 = stereo.Neighbors[1];
var nat2 = stereo.Neighbors[2];
var nat3 = stereo.Neighbors[3];
istereo.central_atom = (Int16)input.Atoms.IndexOf(cat);
istereo.neighbor[0] = (Int16)input.Atoms.IndexOf(nat0);
istereo.neighbor[1] = (Int16)input.Atoms.IndexOf(nat1);
istereo.neighbor[2] = (Int16)input.Atoms.IndexOf(nat2);
istereo.neighbor[3] = (Int16)input.Atoms.IndexOf(nat3);
istereo.type = (SByte)stereo.StereoType;
istereo.parity = (SByte)stereo.Parity;
stereos[i] = istereo;
}
}
var pre = new Set_inchi_Input_
{
atoms = atoms,
stereos = stereos
};
return(pre);
}
