On Wed, Nov 20, 2013 at 11:12 AM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:
> On 11/18/2013 06:56 PM, Craig James wrote:
>
> >> For L-Alanine:
> >>
> >> PC: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1
> >> PDB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1
> >> OB: InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1/i4+1
> >>
> >
> > Are you saying there is a problem, or is this just interesting for some
> > reason?
>
> I'm saying I had a bug in my script: I was not resetting the nitrogen
> after calculating N15 isotopic mass.
>
> Now if only OB stereo could do R/S and E/Z, I wouldn't have to also use
> rdkit...
>
R/S and E/Z are somewhat antiquated from a cheminformatics point of view.
While chemists find them intuitive enough, computing R/S and E/Z can
actually take an unexpectely large amount of CPU time. OpenBabel instead
uses local connectivity around a single atom or bond.
Does your application require these older designations? Or could you
instead use the atom- and bond-centric definitions that are built in to
OpenBabel?
Craig
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