[Biopython-dev] [Bug 2948] _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


crosvera at gmail.com changed:

           What    |Removed                     |Added
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                 CC|                            |crosvera at gmail.com




------- Comment #2 from crosvera at gmail.com  2010-03-20 02:26 EST -------
Here I show an example about what Paul says:

bash-4.0$ python
Python 2.6.4 (r264:75706, Mar 10 2010, 15:54:34) 
[GCC 4.4.1 (CRUX)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.PDB import *
>>> parser=PDBParser()
>>> structure = parser.get_structure("2beg", "2BEG.pdb")
>>> structure.header.keys()
['structure_method', 'head', 'journal', 'journal_reference', 'compound',
'keywords', 'name', 'author', 'deposition_date', 'release_date', 'source',
'resolution', 'structure_reference']
>>> structure.header['head']
'protein fibril'
>>> structure.header['name']
" d structure of alzheimer's abeta(1-42) fibrils"



I made a patch, which change the regex.
From: tail=re.sub("\A\w+\s+\d*\s*","",h)
TO: tail=re.sub("\A\w+\s+\d*\s+","",h
Seems that this patch works. The result I got is this:

bash-4.0$ python
Python 2.6.4 (r264:75706, Mar 10 2010, 15:54:34) 
[GCC 4.4.1 (CRUX)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> from Bio.PDB import *
>>> parser=PDBParser()
>>> structure = parser.get_structure("2beg", "2BEG.pdb")
>>> structure.header.keys()
['structure_method', 'head', 'journal', 'journal_reference', 'compound',
'keywords', 'name', 'author', 'deposition_date', 'release_date', 'source',
'resolution', 'structure_reference']
>>> structure.header['head']
'protein fibril'
>>> structure.header['name']
" 3d structure of alzheimer's abeta(1-42) fibrils"
>>> 

I propose this patch. (my first one).


--
Carlos Ríos V.


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