Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows
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:greg.land...@gmail.com]
Gesendet: Donnerstag, 28. November 2013 04:12
An: Julia Weber
Cc: Rdkit-discuss@lists.sourceforge.net; 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('c1c1')
>>> 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
mailto:we...@pharmchem.uni-frankfurt.de>>
wrote:
Hi Greg,
I'm using the 64bit version of the RDKit on Windows 7 Professional (64bit).
Kind regards
Julia
Von: Greg Landrum [mailto:greg.land...@gmail.com<mailto:greg.land...@gmail.com>]
Gesendet: Montag, 25. November 2013 05:11
An: Julia Weber
Cc:
Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net>
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
mailto:we...@pharmchem.uni-frankfurt.de>>
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
--
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Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows
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:greg.land...@gmail.com]
Gesendet: Donnerstag, 28. November 2013 04:12
An: Julia Weber
Cc: Rdkit-discuss@lists.sourceforge.net; 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('c1c1')
>>> 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
mailto:we...@pharmchem.uni-frankfurt.de>>
wrote:
Hi Greg,
I'm using the 64bit version of the RDKit on Windows 7 Professional (64bit).
Kind regards
Julia
Von: Greg Landrum [mailto:greg.land...@gmail.com<mailto:greg.land...@gmail.com>]
Gesendet: Montag, 25. November 2013 05:11
An: Julia Weber
Cc:
Rdkit-discuss@lists.sourceforge.net<mailto:Rdkit-discuss@lists.sourceforge.net>
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
mailto:we...@pharmchem.uni-frankfurt.de>>
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
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
http://pubads.g.doubleclick.net/gampad/clk?id=84349351&iu=/4140/ostg.clktrk___
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https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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('c1c1')
>>> 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...@pharmchem.uni-frankfurt.de> wrote:
> Hi Greg,
>
>
>
> I‘m using the 64bit version of the RDKit on Windows 7 Professional (64bit).
>
>
>
> Kind regards
>
>
>
> Julia
>
>
>
> *Von:* Greg Landrum [mailto:greg.land...@gmail.com]
> *Gesendet:* Montag, 25. November 2013 05:11
> *An:* Julia Weber
> *Cc:* Rdkit-discuss@lists.sourceforge.net
> *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...@pharmchem.uni-frankfurt.de> 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
>
>
>
--
Rapidly troubleshoot problems before they affect your business. Most IT
organizations don't have a clear picture of how application performance
affects their revenue. With AppDynamics, you get 100% visibility into your
Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro!
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Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows
Hi Greg, I'm using the 64bit version of the RDKit on Windows 7 Professional (64bit). Kind regards Julia Von: Greg Landrum [mailto:greg.land...@gmail.com] Gesendet: Montag, 25. November 2013 05:11 An: Julia Weber Cc: Rdkit-discuss@lists.sourceforge.net 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 mailto:we...@pharmchem.uni-frankfurt.de>> 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows
Hello Greg, Multiple bonds from metal ions (Ca, Mg, etc.) are not unusual in the PDB. And from what I remember, it is not even consistent in the sense that metal ions do not always have multiple bonds. Do forcefields have parameters for bonds involving metal ions? If not, perhaps you could simply disregard all bonds involving metal ions? Ling > > From: Greg Landrum >To: "Rdkit-discuss@lists.sourceforge.net" > >Cc: Roger Sayle >Sent: Sunday, November 24, 2013 9:51 PM >Subject: Re: [Rdkit-discuss] reading PDB file failed after reading sdf on >Windows > > > > > >On Mon, Nov 25, 2013 at 5:10 AM, Greg Landrum wrote: > > >>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. > > >I've now fixed the problem with not being able to skip sanitization, but I am >still stuck on this particular protein. >1VJ5 has a Mg atom (#4333) with CONECT records to six other atoms. This leads >to a valence on Mg that is higher than the RDKit normally accepts. > > > >How should this type of situation be handled by the PDB parser? > > >The irony of a PDB file wth *too many* CONECT records is killing me. :-) > > >-greg > > > >-- >Shape the Mobile Experience: Free Subscription >Software experts and developers: Be at the forefront of tech innovation. >Intel(R) Software Adrenaline delivers strategic insight and game-changing >conversations that shape the rapidly evolving mobile landscape. Sign up now. >http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk > >___ >Rdkit-discuss mailing list >Rdkit-discuss@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > >-- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] reading PDB file failed after reading sdf on Windows
On Mon, Nov 25, 2013 at 5:10 AM, Greg Landrum wrote: > > >> 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. > I've now fixed the problem with not being able to skip sanitization, but I am still stuck on this particular protein. 1VJ5 has a Mg atom (#4333) with CONECT records to six other atoms. This leads to a valence on Mg that is higher than the RDKit normally accepts. How should this type of situation be handled by the PDB parser? The irony of a PDB file wth *too many* CONECT records is killing me. :-) -greg -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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...@pharmchem.uni-frankfurt.de> 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
