private static void CreateAtoms(NInchiStructure output, int numatoms, IntPtr intPtrAtoms)
{
var iatoms = (Inchi_Atom *)intPtrAtoms.ToPointer();
for (int i = 0; i < numatoms; i++)
{
Inchi_Atom iatom = iatoms[i];
var natom = new NInchiAtom(iatom.X, iatom.Y, iatom.Z, new string(iatom.elname))
{
Charge = iatom.charge,
Radical = (INCHI_RADICAL)iatom.radical,
ImplicitH = iatom.num_iso_H[0],
ImplicitProtium = iatom.num_iso_H[1],
ImplicitDeuterium = iatom.num_iso_H[2],
ImplicitTritium = iatom.num_iso_H[3],
IsotopicMass = iatom.isotopic_mass
};
output.Atoms.Add(natom);
}
}
private static void CreateBonds(NInchiStructure output, int numatoms, IntPtr intPtrAtoms)
{
var iatoms = (Inchi_Atom *)intPtrAtoms.ToPointer();
for (int i = 0; i < numatoms; i++)
{
Inchi_Atom iatom = iatoms[i];
int numbonds = iatom.num_bonds;
if (numbonds > 0)
{
var atO = output.Atoms[i];
for (int j = 0; j < numbonds; j++)
{
/* Bonds get recorded twice, so only pick one direction... */
if (iatom.neighbor[j] < i)
{
var atT = output.Atoms[iatom.neighbor[j]];
var nbond = new NInchiBond(atO, atT, (INCHI_BOND_TYPE)iatom.bond_type[j], (INCHI_BOND_STEREO)iatom.bond_stereo[j]);
output.Bonds.Add(nbond);
}
}
}
}
}
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);
}
