Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

nk-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 >

Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand (Dimitri Maziuk)

I had to do something similar on 40,000 PDB files ending up using PDB_tools https://pypi.org/project/pdb-tools/ Cheers, Chris ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net

Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

nd 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] Constructing a mol object from

Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

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

Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

From: Illimar Hugo Rekand Sent: Monday, December 16, 2019 5:55:56 PM To: Paolo Tosco Subject: Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand Hey, Paolo, thanks for a good and clear example! all the best, Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department of

Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

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?

Re: [Rdkit-discuss] Constructing a mol object from a PDB ligand

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

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 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

[Rdkit-discuss] Constructing a mol object from a PDB ligand

Hello, everyone Is there a simple way to create a mol object from just the HETATM/ligand lines from a pdb-file? Would it be viable to create a function where you could create a mol object from specific lines within a pdb-file? Illimar Rekand Ph.D. candidate, Brenk-lab, Haug-lab Department