Sounds very interesting. Regarding the stereo, I haven't done exactly that, but the general procedure is to loop over the stereo data, get the Config, change the Config, and set the Config. For tet centers, changing the Winding will do the job, while for cis/trans, changing the shape from U to Z will I think flip the stereo.
To do this exhaustively, you would need something like a recursive function, or if using Python, google tells me the following might be useful: >>> list(itertools.product([0, 1], repeat=3)) [(0, 0, 0), (0, 0, 1), (0, 1, 0), (0, 1, 1), (1, 0, 0), (1, 0, 1), (1, 1, 0), (1, 1, 1)] >>> To reduce the amount of work, it might be a good idea to consider the mirror images of the 3D structures, as these will have the tet centers with the opposite stereo already. - Noel On 5 February 2015 at 22:29, Geoffrey Hutchison <geoff.hutchi...@gmail.com> wrote: > Hi there, > > One of my current side-projects is the generation of the Pitt Quantum > Repository (http://pqr.pitt.edu/). We're producing a growing open data > repository of small molecules with systematically-derived quantum properties. > The first version of the website will go "live" sometime this summer. > > I have a good-sized chunk (~90,000 molecules) from PubChem. I'm also looking > to "grow" the database with systematic library generation and I'll be making > those tools available open source as we go. > https://github.com/pittquantum/workflows > > I'm wondering if someone already wrote a script for generating all > stereoisomers using SMILES or Open Babel already? > > Thanks, > -Geoff > > P.S. If you have a set of molecules you'd like to add to the repository, > please send me an e-mail. > P.P.S. PQR will very much be an open project, and we're open to feedback > about suggested properties, features, bugs, etc. as we go. > > --- > Prof. Geoffrey Hutchison > Department of Chemistry > University of Pittsburgh > tel: (412) 648-0492 > email: geo...@pitt.edu > web: http://hutchison.chem.pitt.edu/ > > > ------------------------------------------------------------------------------ > Dive into the World of Parallel Programming. The Go Parallel Website, > sponsored by Intel and developed in partnership with Slashdot Media, is your > hub for all things parallel software development, from weekly thought > leadership blogs to news, videos, case studies, tutorials and more. Take a > look and join the conversation now. http://goparallel.sourceforge.net/ > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel ------------------------------------------------------------------------------ Dive into the World of Parallel Programming. The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
