[BioPython] Biopython to parse not only .pdb-files but also NACCESS .asa files
Ed Schofield
edschofield at gmail.com
Tue May 22 16:57:49 UTC 2007
On 21 May 2007 20:45:36 +0100, O.Doehring at cs.ucl.ac.uk
<O.Doehring at cs.ucl.ac.uk> wrote:
>
> ValueError: invalid literal for float(): 31 1.
>
> ...
>
> What do you recommend for my situation. Many thanks!
Is that a space between 31 and 1? There's your problem. My advice is to insert
import pdb
pdb.set_trace()
at line 159 in PDBParser.py and check out why the columns in your data
are misaligned with what PDBParser.py expects. A quick scan of
nac_readme.html implies that perhaps you need the -f argument to give
you the full output format?
But if you need to write your own parser for .asa files, you could use
_parse_coordinates(self, coords_trailer) as a template.
-- Ed
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