[Biopython] a parsing error

[João Rodrigues]

Hello,

I usually get that error when the parser finds an empty PDB file.

Try outputting the name of the file you're currently parsing so you know
when it breaks.

Best

João [...] Rodrigues
@ http://stanford.edu/~joaor/



On Tue, May 25, 2010 at 9:29 AM, Bala subramanian <bala.biophysics at gmail.com
> wrote:

> Friends,
>
> The following code takes all the pdb's in the current directory and creates
> a matrix. I get a parsing error. Pls write what is going wrong.
>
> from numpy import zeros,savetxt,matrix
> from Bio.PDB import *
> import glob
> donor=[ 'ARG','ASN', 'GLN', 'LYS', 'TRP' ]
> ali=['ALA', 'ARG', 'CYS', 'ILE', 'LEU', 'LYS', 'MET', 'PRO', 'THR', 'VAL' ]
> parser=PDBParser()
> X5_MAT=matrix(zeros((34,34),int))
> files=glob.glob('*.pdb')
> for i in range(len(files)):
>    strng=str(i)
>    structure=parser.get_structure(strng,files[i])
>    res=Selection.unfold_entities(structure,'R')
>
>    for x in range(len(res)):
>        for y in range(len(res)):
>            if x <> y :
>                if not res[x].get_resname() in donor: continue
>
>                else:
>                    if res[y].get_resname() in ali:
>                        X5_MAT[x,y] = X5_MAT[x,y] + 1
>
>            else: pass
>
>
> savetxt('myfile.txt', matrix(X5_MAT), fmt='%d')
>
>
> *The error is pasted below*
>
> Traceback (most recent call last):
>  File "un_don_ali.py", line 14, in <module>
>    structure=parser.get_structure(' ',files[i])
>  File "/usr/lib/python2.5/site-packages/Bio/PDB/PDBParser.py", line 64, in
> get_structure
>    self._parse(file.readlines())
>  File "/usr/lib/python2.5/site-packages/Bio/PDB/PDBParser.py", line 82, in
> _parse
>    self.header, coords_trailer=self._get_header(header_coords_trailer)
>  File "/usr/lib/python2.5/site-packages/Bio/PDB/PDBParser.py", line 95, in
> _get_header
>    header=header_coords_trailer[0:i]
> UnboundLocalError: local variable 'i' referenced before assignment
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