biopython/biopython — pull request #196 by matsu3shiro (2013-07-02 11:42:21+00:00)
Title: Fixing a bug in SeqIO.PdbIO in parsing pdb-atom sequence

Fixing a problem that SeqIO.PdbIO outputs erroneous amino acid sequence
if the ATOM record has more than one missing segments.

SeqIO.PdbIO includes a bug in parsing amino acid sequences
from PDB ATOM records (pdb-atom).
It outputs erroneous amino acid sequence
if the ATOM record has more than one missing segments.

The original code trys to insert 'X's for each gap position,
but it adds the C-terminal sequence from the gap
each time it fills a gap in addition to the 'X's.
In contrast, the insertion of C-terminal sequence is only required
at the final gap position.
Thus, this code outputs an amino acid sequence
in which C-terminal sequence is erroneously repeated
if the coordinate file includes more than one gap positions.

I fixed this bug by moving lines 173-174 out of the FOR loop
starting from line 166.