Hello.
When getting SMILES from CIF files, it seems that the stereochemistry
around double bonds is no longer indicated in the output after upgrading
to 2.3.0.
For example, with a CIF file containing such a double bond, I get with
version 2.3.0:
$ babel 2005910.cif -osmi
OC(=O)C=Cc1c(cc(cc1)N(=O)=O)N(=O)=O C9 H6 N2 O6
1 molecule converted
34 audit log messages 1 debugging messages
whereas for version 2.2.3, I used to get:
$ babel 2005910.cif -osmi
OC(=O)/C=C/c1c(cc(cc1)N(=O)=O)N(=O)=O C9 H6 N2 O6
1 molecule converted
1 info messages 30 audit log messages 1 debugging messages
As you can see, the cis-trans geometry does not appear after upgrading
openbabel. Is this a regression or there is an option (run-time or
compilation) that needs to be set to get the stereochemistry?
Thanks for any reply,
Miguel Quirós
--
Miguel Quirós Olozábal
Departamento de Química Inorgánica. Facultad de Ciencias.
Universidad de Granada. 18071 Granada. SPAIN.
email: mquiros<at>ugr<dot>es
mquiros<arroba>ugr<punto>es
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