On 1 March 2010 22:34, Craig A. James <cja...@emolecules.com> wrote:
> Noel O'Boyle wrote:
>>
>> Does anyone have any ideas about how to stop inchi complaining about
>> undefined stereocenters? We know it's undefined - we don't need to
>> hear all about it.
>>
>>>>> pybel.readstring("smi", "FC(Br)(Cl)I").write("inchi")
>>
>> ==============================
>> *** Open Babel Warning in InChI code
>> #0 :Omitted undefined stereo
>> 'InChI=1S/CBrClFI/c2-1(3,4)5\n'
>
> Are you sure it's InChI? I had to take a line out of the smilesformat.cpp
> code because of this very problem.
I'm sure. But can you provide a test case for this patch so I can look into it.
> Craig
>
> svn diff smilesformat.cpp Index: smilesformat.cpp
> ===================================================================
> --- smilesformat.cpp (revision 3495)
> +++ smilesformat.cpp (working copy)
> @@ -682,7 +682,10 @@
> if (ChiralSearch != _tetrahedralMap.end() && ChiralSearch->second !=
> NULL)
> {
> int insertpos = NumConnections(ChiralSearch->first) - 2;
> - if (insertpos < 0) {
> + if (insertpos > 2) {
> + obErrorLog.ThrowError(__FUNCTION__, "Warning: Tetrahedral center
> with > 4 bonds.", obWarning);
> + }
> + else if (insertpos < 0) {
> if (ChiralSearch->second->from != OBStereo::NoRef)
> obErrorLog.ThrowError(__FUNCTION__, "Error: Overwriting previous
> from reference id.", obError);
>
>
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