[Biopython-dev] [Biopython - Feature #3295] (New) SeqIO read support for the PDB format

[redmine at redmine.open-bio.org]

Issue #3295 has been reported by Eric Talevich.

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Feature #3295: SeqIO read support for the PDB format
https://redmine.open-bio.org/issues/3295

Author: Eric Talevich
Status: New
Priority: Normal
Assignee: 
Category: 
Target version: 
URL: 


It's useful to be able to retrieve primary sequences from a PDB file. I propose an implementation in SeqIO that uses PDBParser and PPBuilder to extract the peptide sequences from a given structure and yield each one as a SeqRecord.

Basically:

<pre>
>>> struct = PDB.PDBParser().get_structure(pdb_id, fname)
>>> for peptide in PDB.PPBuilder().build_peptides(struct):
...     yield SeqRecord(Seq(peptide.get_sequence(), generic_protein),
...                     id=pdb_id+chain_id)
</pre>

but with proper metadata.

This will be read-only support, of course.

Sound good?


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