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.
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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