ning hetatm.UpdatePropertyCache(strict=True) does not remedy this
problem. Is there a clever way I can fix this quickly without waiting for this
to be fixed in a future version?
>
>
> Illimar Rekand
> Ph.D. candidate,
> Brenk-lab, Haug-lab
> D
I had to do something similar on 40,000 PDB files ending up using PDB_tools
https://pypi.org/project/pdb-tools/
Cheers,
Chris
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example!
all the best,
Illimar Rekand
Ph.D. candidate,
Brenk-lab, Haug-lab
Department of Biomedicine
Department of Chemistry
University of Bergen
____
From: Paolo Tosco
Sent: Monday, December 16, 2019 5:52:18 PM
To: Illimar Hugo Rekand; rdkit-discuss@lists.sour
On 12/16/19 10:35 AM, Illimar Hugo Rekand wrote:
> Fair point.
>
> But when working in the 100s and 1000s range of PDB-files it would be nice to
> have some fewer steps when designing a pipeline.
But what's the selection criteria? NMR structures are usually deposited
with 20 models, do you want
n a future version?
Illimar Rekand
Ph.D. candidate,
Brenk-lab, Haug-lab
Department of Biomedicine
Department of Chemistry
University of Bergen
From: Illimar Hugo Rekand
Sent: Monday, December 16, 2019 5:55:56 PM
To: Paolo Tosco
Subject: Re: [Rdkit-discuss] Constr
Hi Illimar,
this gist:
https://gist.github.com/ptosco/2ee199b219b27e01052a7a1433b3bd22
shows a way to achieve this.
Cheers,
p.
On 16/12/2019 16:07, Illimar Hugo Rekand wrote:
Hello, everyone
Is there a simple way to create a mol object from just the HETATM/ligand lines
from a pdb-file?
W
From: Dimitri Maziuk via Rdkit-discuss
Sent: Monday, December 16, 2019 5:24:49 PM
To: rdkit-discuss@lists.sourceforge.net
Subject: Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand
On 12/16/2019 10:07 AM, Illimar Hugo Rekand wrote:
> Would it be viable to create a function wh
On 12/16/2019 10:07 AM, Illimar Hugo Rekand wrote:
Would it be viable to create a function where you could create a mol object
from specific lines within a pdb-file?
PDB file is simple text. There's any number of utilities to extract the
lines you want, incl. a plain text editor, why spend t
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