[Biopython] Bio.PDB and Bio.SeqIO.PdbIO

[João Rodrigues]

Hi Tiago,

The header records are very chaotic... some of them are well documented and
populated by programs, e.g. SEQRES, HELIX, SHEET, etc. These would be easy
to add to the parser (check the parse_pdb_header functions in Bio.PDB) but
they are not there at the moment.

Cheers,

João

Tiago Antao <tra at popgen.net> escreveu no dia Fri Feb 20 2015 at 3:33:33 PM:

> Hi,
>
> I am trying to get around the relationship between Bio.PDB and
> Bio.SeqIO.PdbIO, lets see if I got this right:
>
> 1. Bio.PDB is quite limited in terms of what records it can parse. For
> example I cannot get to SEQRES or anything related to secondary
> structure (SHEET, HELIX)?
>
> 2. PdbIO allows to extract the protein sequences from SEQRES
>
>
> Or, to put it another way, a generic PDB file is not completely
> accessible from inside Biopython in the sense that we cannot access
> some of the records (SHEET and HELIX being the examples here). Or is
> there a way to get to them via Bio.PDB?
>
> Many thanks for your help,
> T
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