[Open Babel] Cis-trans streochemistry lost on upgrading to 2.3.0?

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

Re: [Open Babel] Cis-trans streochemistry lost on upgrading to 2.3.0?

Sure. I am attaching the same file of the example in my message. I have seen the same behaviour with many other files. Miguel. El mar, 09-11-2010 a las 14:08 +0100, Noel O'Boyle escribió: Can you provide an example cif file for testing? - Noel 2010/11/9 Miguel Quirós Olozábal mqui

Re: [Open Babel] Cis-trans streochemistry lost on upgrading to 2.3.0?

it's a general problem. All of my test cases for stereochemistry use the SDF format which, naturally, works fine. I'll file a bug and chase it up. - Noel 2010/11/9 Miguel Quirós Olozábal mqui...@ugr.es: Sure. I am attaching the same file of the example in my message. I have seen

Re: [Open Babel] Wrong bond orders, aromaticity, hydrogens, ... when dealing with coordination chemistry compounds

in the cheminformatic world. In inorganic chemistry, the valence of nitrogen is in many cases _4_ , not 3. Thanks again. Best wishes, Miguel Quirós -- Miguel Quirós Olozábal Departamento de Química Inorgánica. Facultad de Ciencias. Universidad de Granada. 18071 Granada. SPAIN. email: mquirosatugrdotes

Re: [Open Babel] Wrong bond orders, aromaticity, hydrogens, ... when dealing with coordination chemistry compounds

El vie, 01-07-2011 a las 14:13 +0100, Noel O'Boyle escribió: 2011/7/1 Miguel Quirós Olozábal mqui...@ugr.es: El vie, 01-07-2011 a las 10:08 +0200, Pascal Muller escribió: Dear Miguel, Hello. I posted the attached long message a couple of weeks ago and I have

Re: [Open Babel] Converting CIF to XYZ - various errors commandline or program call

first line are comment inside the file they should be preceded by a #. Also symmetry operators are not present (not sure it they are neccessary for the conversion, perhaps no). Also I would try put the element symbols without charges (i.e. La instead of La+3). Good luck. -- Miguel Quirós

Re: [Open Babel] Smiles conversion problems with Ion and Zwitterion

/logmein_12329d2d ___ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Miguel Quirós Olozábal Departamento de Química Inorgánica. Facultad de Ciencias. Universidad

Re: [Open Babel] Converting CIFs to mols using OpenBabel

://lists.sourceforge.net/lists/listinfo/openbabel-discuss -- Miguel Quirós Olozábal Departamento de Química Inorgánica. Facultad de Ciencias. Universidad de Granada. 18071 Granada. SPAIN. email: mquirosatugrdotes mquirosarrobaugrpuntoes

Re: [Open Babel] Converting CIFs to mols using OpenBabel

belonging to each of the most oustanding inorganic families to use as a test bench. Thanks again. Best wishes, Miguel Quirós -- Miguel Quirós Olozábal Departamento de Química Inorgánica. Facultad de Ciencias. Universidad de Granada. 18071 Granada. SPAIN. email: mquirosatugrdotes

Re: [Open Babel] Converting CIFs to mols using OpenBabel

+0100, Miguel Quirós Olozábal escribió: Thanks a lot for your message. It probably will take some time to prepare such set. I would like to include files containing a single different problem each one, with compounds as simple as possible and without purely crystallographic problems

[Open Babel] OpenSMARTS specification (?)

of proposal??) but I am not able to find it now. Thanks a lot for any reply, Miguel Quirós -- Miguel Quirós Olozábal Departamento de Química Inorgánica. Facultad de Ciencias. Universidad de Granada. 18071 Granada. SPAIN. email: mquirosugres mquirosugres

[Open Babel] Error Writer.hpp not found

any reply. Best wishes, Miguel. -- Miguel Quirós Olozábal Departamento de Química Inorgánica. Facultad de Ciencias. Universidad de Granada. 18071 Granada. SPAIN. email: mquirosugres mquirosugres ___ OpenBabel-discuss mailing list OpenBab