Can anyone shed some light on this? If I use Gen2D and then try to write
out an InChI, the stereo layer is wiped out.
#include <string>
#include <sstream>
#include <openbabel/mol.h>
#include <openbabel/obconversion.h>
#include <openbabel/op.h>
using namespace std;
using namespace OpenBabel;
/*----------------------------------------------------------------------
* FUNCTION: emol_mk_init
* Initialize some static variables.
----------------------------------------------------------------------*/
int main(int argc, char **argv)
{
char *smiles;
int smilen;
OBConversion *pconv_smi = new OBConversion();
OBConversion *pconv_ich = new OBConversion();
pconv_smi->SetInAndOutFormats("smi", "can");
pconv_ich->SetOutFormat("inchi");
OBMol *pmol = new OBMol;;
pconv_smi->ReadString(pmol, "C[C@H](Br)Cl");
cout << pconv_ich->WriteString(pmol, true) << "\n";
cout << pconv_smi->WriteString(pmol, true) << "\n";
OBOp* pOp = OBOp::FindType("gen2D");
pOp->Do(pmol);
cout << pconv_ich->WriteString(pmol, true) << "\n";
cout << pconv_smi->WriteString(pmol, true) << "\n";
}
The output is:
InChI=1S/C2H4BrCl/c1-2(3)4/h2H,1H3/t2-/m1/s1
C[C@H](Br)Cl
==============================
*** Open Babel Warning in InChI code
#0 :Omitted undefined stereo
InChI=1S/C2H4BrCl/c1-2(3)4/h2H,1H3
C[C@H](Br)Cl
Notice that the stereo layer "/t2-/m1/s1" of the InChI is gone after
applying Gen2D to it. I would have imagined that Gen2D would add
coordinates, but not actually alter the molecule itself. But the chiral
center is still OK in the SMILES string.
I can only guess that some stereo flag is getting reset, and InChI pays
attention while SMILES ignores it.
Thanks!
Craig
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