Re: [Rdkit-discuss] SDF and stereo config

2014-09-30 Thread Greg Landrum
Hi Dimitri, On Tue, Sep 30, 2014 at 1:48 AM, Dimitri Maziuk dmaz...@bmrb.wisc.edu wrote: Hi guys, could someone who knows chemistry (I don't) tell me if I'm completely off the mark here? Attached sdf is D-alanine downloaded from pubchem. Also from pubchem, copied from the same cid 71080

Re: [Rdkit-discuss] SDF and stereo config

2014-09-30 Thread Dimitri Maziuk
On 09/30/2014 08:29 AM, Greg Landrum wrote: ... If you'd like to see the R/S tags, you can do something like this: In [*2*]: m = Chem.MolFromMolFile('./71080.sdf') In [*3*]: Chem.FindMolChiralCenters(m) Out[*3*]: [(3, 'R')] If you want more detail about the CW/CCW thing, let me know and

[Rdkit-discuss] SDF and stereo config

2014-09-29 Thread Dimitri Maziuk
Hi guys, could someone who knows chemistry (I don't) tell me if I'm completely off the mark here? Attached sdf is D-alanine downloaded from pubchem. Also from pubchem, copied from the same cid 71080 page is the inchi string: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1 (it's also