Hi Illimar,
When reading a PDB file that has multiple models, the RDKit PDB Parser
creates a separate conformer for each model, it shouldn't be creating
additional atoms.
Here's a little demo:
>>> from rdkit import Chem
>>> import rdkit
>>> print(rdkit.__version__)
2019.03.2
>>> !grep -c '^ATOM
On 5/29/19 3:31 PM, David Cosgrove wrote:
> Biopython is excellent for extracting particular models from a PDB file. As
> Dimitri suggests, you can then pass the result into your processing script.
> It is quite straightforward to write the relevant PDB model to a string in
> PDB format and parse
Biopython is excellent for extracting particular models from a PDB file. As
Dimitri suggests, you can then pass the result into your processing script.
It is quite straightforward to write the relevant PDB model to a string in
PDB format and parse with RDKit’s PDB reader, for example.
Dave
On
On 5/29/19 8:19 AM, Illimar Hugo Rekand wrote:
> Hey, RDKitters!
>
>
> I am currently trying to figure out how to only read in the first model of a
> pdb-file. I've designed a script that performs calculations on a per-atom
> basis, and this is very slow when it tries to account for multiple
Hey, RDKitters!
I am currently trying to figure out how to only read in the first model of a
pdb-file. I've designed a script that performs calculations on a per-atom
basis, and this is very slow when it tries to account for multiple models, for
example with a NMR-structure.
my code is
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