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

[Lukas P. <lp...@eb...>]

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

--------------------------
Lukas Pravda, Ph.D.
Bioinformatician/Scientific Programmer
 
Protein Data Bank in Europe (PDBe)
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
United Kingdom
 


On 25/02/2019, 10:11, "Illimar Hugo Rekand" <Ill...@ui...> wrote:

    Hello,
    
    
    I am currently trying to access the xyz-coordinates for specific atoms (in a loop) from a .PDB-file. Is there an easy way to do this without creating a conformer of the molecule?
    
    
    all the best,
    
    
    Illimar Rekand
    
    Ph.D. Candidate
    
    Department of Biomedicine
    
    University of Bergen
    
    
    _______________________________________________
    Rdkit-discuss mailing list
    Rdk...@li...
    https://lists.sourceforge.net/lists/listinfo/rdkit-discuss