Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows

[Julia W. <we...@ph...>]

Hi again,

... this is how we were able to reproduce the problem on a clean windows 7 x64 installation (only windows updates + msvc redist 2010 installed).
Are we missing something?

https://docs.google.com/file/d/0B-zHYwagUyBMQVJ4RmpldmZaUXM/edit?pli=1



Hi Greg,

thanks for your efforts in trying to solve my problem. We are running rdkit on three workstations in our office and we all have the same problem. We tried different combinations of pdb and sdf files but reading  pdb after sdf was never possible until we restarted rdkit. We have installed our python packages from Christoph Gohlke's 'Unofficial Windows Binaries for Python Extension Packages' (http://www.lfd.uci.edu/~gohlke/pythonlibs/) and I think that we all have nearly the same packages installed. We are now trying a step by step installation on a Win7 VM to narrow down our problem.
Kind regards
Julia


Von: Greg Landrum [mailto:gre...@gm...]
Gesendet: Donnerstag, 28. November 2013 04:12
An: Julia Weber
Cc: Rdk...@li...; Roger Sayle
Betreff: Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows

Hi Julia,

I just tried to reproduce the problem on my 64bit Win7 machine, but was not successful:
$ python -i
Python 2.7.3 (default, Apr 10 2012, 23:24:47) [MSC v.1500 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit import rdBase
>>> rdBase.rdkitVersion
'2013.09.1'
>>> from rdkit import Chem
>>> pdb = Chem.MolFromPDBFile('1K74.pdb')
>>> pdb is None
False
>>> m = Chem.MolFromSmiles('c1ccccc1')
>>> mb = Chem.MolToMolBlock(m)
>>> m = Chem.MolFromMolBlock(mb)
>>> pdb = Chem.MolFromPDBFile('1K74.pdb')
>>> pdb is None
False

I've tried looking for all the usual problems that would cause something like this to happen, but I haven't managed to find anything.

Is this reproducible for you with any pdb file and/or any molblock or is it just this one example?

-greg


On Mon, Nov 25, 2013 at 10:35 AM, Julia Weber <we...@ph...<mailto:we...@ph...>> wrote:
Hi Greg,

I'm using the 64bit version of the RDKit on Windows 7 Professional (64bit).

Kind regards

Julia

Von: Greg Landrum [mailto:gre...@gm...<mailto:gre...@gm...>]
Gesendet: Montag, 25. November 2013 05:11
An: Julia Weber
Cc: Rdk...@li...<mailto:Rdk...@li...>
Betreff: Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows

Hi Julia,

On Fri, Nov 22, 2013 at 11:14 AM, Julia Weber <we...@ph...<mailto:we...@ph...>> wrote:

it seems that it is not possible to read a PDB file after you have read a sdf file. I don't see this problem on Linux.

To help narrow the problem down: are you using the 32bit or 64bit version of the RDKit on windows?

Another problem is that I cannot read pdbs containing metals (e.g. 1vj5)

Is there any workaround for that problem? I hope you can help me...

That bug is reproducible on linux as well. The normal solution to this would be to skip the sanitization step that causes the error, but unfortunately it seems that also causes the PDB parser to fail. I'll take a look at fixing it.

-greg