Re: [Rdkit-discuss] molecule standardization in cartridge search

2015-09-25 Thread Abhik Seal
Hi Long time back I used PL python with RDKit cartridge inside postgres i have made a blog post here is the link might be of help http://data2quest.blogspot.com/2014/07/converting-inchi-to-mol-using-plpython.html Abhik Seal Indiana University Bloomington School of Informatics and Computing

Re: [Rdkit-discuss] Generation of stereo-isomers

2015-09-25 Thread Soren Wacker
Hi all, I opened an issue at rdkit-github for that matter. https://github.com/rdkit/rdkit/issues/626 Thanks to your comments! If you want look at the code snippet I posted. At the moment, simply all stereo-isomers are generated. regards Soren On Fri, Sep 25, 2015 at 12:19 AM, Axel Pahl

Re: [Rdkit-discuss] Generation of stereo-isomers

2015-09-25 Thread Axel Pahl
Hi Soren, maybe this function which enumerates racemates with one stereocenter into the corresponding enantiomers might help: def enum_racemates(sdf_list_or_file, find_only=True, mol_id="molid"): """returns: result_sdf::list, racemic_molids::list find_only==True: return new sdf as

Re: [Rdkit-discuss] molecule standardization in cartridge search

2015-09-25 Thread Jan Holst Jensen
On 2015-09-24 16:22, Tim Dudgeon wrote: > I'm trying to get to grips with using the RDKit cartridge, and so far > its going well. > One thing I'm concerned about is molecule standardization, along the > lines of the ChemAxon Standardizer that allows substructure searches to > be done is a way that

Re: [Rdkit-discuss] molecule standardization in cartridge search

2015-09-25 Thread Tim Dudgeon
Jan, thanks for that. I'll give it a try. Are there any examples of writing RDKit functions and procedures for postgres in python? I see this general postgres docs: http://www.postgresql.org/docs/9.4/static/plpython.html but wondered if there are any RDKit specific examples anywhere? Tim On

Re: [Rdkit-discuss] molecule standardization in cartridge search

2015-09-25 Thread TJ O'Donnell
Tim, I have a set of postgres python (PL/Python) functions using rdkit. It is available at https://github.com/tjod/rdchord and some docs at https://github.com/tjod/rdchord/wiki TJ O'Donnell On Fri, Sep 25, 2015 at 6:54 AM, Tim Dudgeon wrote: > Jan, > > thanks for that.