Are you using the dev version? If not, sounds like a problem I fixed
earlier this year - see github closed issues from that period.
- Noel
On 7 October 2015 at 20:22, Craig James <cja...@emolecules.com> wrote:
> 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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