[Biopython-dev] [Bug 2948] New: _parse_pdb_header_list: bug in TITLE handling

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2948

           Summary: _parse_pdb_header_list: bug in TITLE handling
           Product: Biopython
           Version: 1.52
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: TallPaulInJax at yahoo.com


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


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