[Biopython] a parsing error

[Rodrigo Faccioli]

Hi,

In this way, we developed a method which check if the file is a valid PDB
format. The method is called isPDBFile. You can see it at [1]. If you want
I'll create a new code for you.

I hope this message can help in something.

[1]
http://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/fcfrp/PDB.py

Thanks in advance,

--
Rodrigo Antonio Faccioli
Ph.D Student in Electrical Engineering
University of Sao Paulo - USP
Engineering School of Sao Carlos - EESC
Department of Electrical Engineering - SEL
Intelligent System in Structure Bioinformatics
http://laips.sel.eesc.usp.br
Phone: 55 (16) 3373-9366 Ext 229
Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
Public Profile - http://br.linkedin.com/pub/rodrigo-faccioli/7/589/a5


On Tue, May 25, 2010 at 1:47 PM, Bala subramanian <bala.biophysics at gmail.com
> wrote:

> Hi,
> Thank you very much. I just checked and in fact one of the files was a
> corrupted one.
>
> Thank you,
> Bala
>
> On Tue, May 25, 2010 at 6:41 PM, João Rodrigues <anaryin at gmail.com> wrote:
>
> > 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/ <http://stanford.edu/%7Ejoaor/> <
> http://stanford.edu/%7Ejoaor/>
> >
> >
> >
> > 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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> >> http://lists.open-bio.org/mailman/listinfo/biopython
> >>
> >
> >
>
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