[Biopython] a parsing error

[João Rodrigues]

Hey Rodrigo,

About that isPDB function of yours. What if the protein is a result of a
webserver that outputs only ATOM records?

Best!

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



On Tue, May 25, 2010 at 12:56 PM, Rodrigo Faccioli <
rodrigo_faccioli at uol.com.br> wrote:

> 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/> <
> > 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
> > >> _______________________________________________
> > >> Biopython mailing list  -  Biopython at lists.open-bio.org
> > >> http://lists.open-bio.org/mailman/listinfo/biopython
> > >>
> > >
> > >
> >
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>
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