[Biopython-dev] [BioPython] Biopython to parse not only .pdb-files but also NACCESS .asa files

[Ed Schofield]

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