[Biopython-dev] [Biopython (old issues only) - Bug #2948] (Resolved) _parse_pdb_header_list: bug in TITLE handling

[redmine at redmine.open-bio.org]

Issue #2948 has been updated by Lenna Peterson.

Description updated
Status changed from New to Resolved
% Done changed from 0 to 100

Applied to master here (can't find a corresponding issue or pull request):

https://github.com/biopython/biopython/commit/cc9da03002ae90a3b8eedae69a8adae7216506b8

----------------------------------------
Bug #2948: _parse_pdb_header_list: bug in TITLE handling
https://redmine.open-bio.org/issues/2948#change-15370

* Author: Anonymous
* Status: Resolved
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: 1.52
* URL: 
----------------------------------------
parse_pdb_header.py
_parse_pdb_header_list

Hi,

1. If the TITLE in a PDB begins with a number, the parse_pdb_header_list method is stripping the prefixed number from the title, I believe because the regex written did not expect this. So the TITLE line:
TITLE     3D STRUCTURE OF ALZHEIMER'S ABETA(1-42) FIBRILS                       
becomes:
" D STRUCTURE OF ALZHEIMER'S ABETA(1-42) FIBRILS"

2. ... or it should, but it doesn't. This is because for some reason the title is converted to lower case. So it actually becomes:
" d structure of alzheimer's abeta(1-42) fibrils"

This is fixed by changing the line of code:
name=_chop_end_codes(tail).lower()
to:
name=_chop_end_codes(tail)

I don't have a solution for problem #1. Frankly, I think the (whole, or most all of the) method should be re-written to use positional stripping, ie, line[X:Y].strip().

Paul

---Files--------------------------------
bug2948.patch (914 Bytes)
0001-modified-parse_pdb_header.py.patch (1.01 KB)
0001-modified-parse_pdb_header.py.patch (1.01 KB)


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