biopython/biopython — pull request #75 by etal (2012-10-05 04:38:07+00:00)
Title: Add a "pdb-atom" parser to SeqIO (via PdbIO)

Here's an implementation of the "pdb-atom" format for SeqIO. I've been using this code for my own work for a little while now, and it seems reliable.

Relevant bug report:
https://redmine.open-bio.org/issues/3295

At some point we left off with a concern over the handling of some weird, out-of-order residues at the end of the PDB structure 3BEG. This handles them correctly, i.e. the result is consistent with the "pdb-seqres" output and a reasonable understanding of the crystallographers' intentions.

As before, disordered residues are treated as unknown ("X") rather than gaps ("-").