[Biopython-dev] [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

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

More information about the Biopython-dev mailing list