On Tue, Feb 10, 2015 at 12:23 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > I definitely remember reading discussion where Noel was mentioning a
> limit (that at this point can't be 1k atoms) but I can't find it since
> Sourceforge seems to be down for maintenance.
>
> There is an
> I definitely remember reading discussion where Noel was mentioning a limit
> (that at this point can't be 1k atoms) but I can't find it since Sourceforge
> seems to be down for maintenance.
There is an explicit limit for InChI as defined by IUPAC. (I believe 1024
atoms.)
There was at one po
I'm confused... I just tested creating an OBMol with a PDB with ~32K atoms and
it worked.
I definitely remember reading discussion where Noel was mentioning a limit
(that at this point can't be 1k atoms) but I can't find it since Sourceforge
seems to be down for maintenance.
In any case, dealin
I have used mol2 files with many thousands of atoms. Can you explain why you
think there's a restriction or send me an example file?
Thanks very much,
-Geoff
---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geo...@pitt.edu
web: http://hutch
Hi,
I had a similar issue and my recollection is that it's a hardcoded limit in
OpenBabel. Not sure how feasible would be to remove or extend this limit, but
in the meantime I had to find workarounds to get the job done.
The best solution for me was to write a file parser to process a chain at t
Hi All,
It seems to me that there is a restriction on the number of atoms (~1000) OB
can handle when using mol2 file format. I know this is also true for SMILES and
InChI however this doesn't make much sense for mol2.
I currently do mutations/atom manipulations with large proteins with
non-sta
