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

[Greg L. <gre...@gm...>]

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...> 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...]
> *Gesendet:* Montag, 25. November 2013 05:11
> *An:* Julia Weber
> *Cc:* 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...> 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
>
>
>