Re: [Open Babel] stereo config

2013-11-16 Thread Dimitri Maziuk
On 2013-11-16 03:27, Noel O'Boyle wrote: > Can you be a bit more specific with your question? After reading your > email twice I can't figure out exactly what the problem is. > > (I note in passing that PDB files are the worst possible way of > storing chemical data as they typically do not contain

Re: [Open Babel] stereo config

2013-11-16 Thread Dimitri Maziuk
On 2013-11-16 10:21, David Hall wrote: ... > Of those strings, only "SMILES_CANONICAL CACTVS" specify two > stereochemical centers. The ones without canonical in their name don't > specify any stereochemistry at all. I'm pretty sure those never specify > any stereochemistry in the entire ligand exp

[Open Babel] Announcement - R interface for OpenBabel

2013-11-16 Thread Thomas Girke
Dear List, As suggested by Noel O'Boyle on the OpenBabel-devel list, I would like to announce the release of a new OpenBabel R package called ChemmineOB that is now available on the Bioconductor site: http://bioconductor.org/packages/devel/bioc/html/ChemmineOB.html Currently, ChemmineOB provides

Re: [Open Babel] stereo config

2013-11-16 Thread Noel O'Boyle
Can you be a bit more specific with your question? After reading your email twice I can't figure out exactly what the problem is. (I note in passing that PDB files are the worst possible way of storing chemical data as they typically do not contain bond orders.) - Noel On 15 November 2013 22:47,