Re: [Rdkit-discuss] Atom coordinates from PDB-file

[Jose M. G. <jos...@gm...>]

Hi Illimar,

if you are familiar with pandas DataFrames, then I would also recommend 
BioPandas for this:

https://github.com/rasbt/biopandas

Cheers,
Jose Manuel

On 26.02.19 00:05, Stéphane Téletchéa wrote:
> Hi all,
>
> Le 25/02/2019 à 12:38, Lukas Pravda a écrit :
>> Hi Illimar,
>>
>> If you need to access coordinates without creating conformer object 
>> do you really need to use rdkit I the first place? PDB file is column 
>> based format, so extracting coordinates for atoms for example with 
>> python is very straightforward.
>>
>> Lukas
>
> To pick certains atoms on a PDB file, I'd go for biopython's Bio.PDB ->
>
> https://biopython.org/wiki/The_Biopython_Structural_Bioinformatics_FAQ
>
> HTH,
>
> Stéphane
>