[Biopython] a parsing error

Thu May 27 09:35:15 EDT 2010

Hi,

I developed those functions. However, I changed their names. Now, they are
called containATOMrecord and containSEQRESrecord.

If want to see them you can read in [1]. I built a test for them which is in
[2]

[1]
http://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/fcfrp/PDB.py
[2]
http://github.com/rodrigofaccioli/ContributeToBioPython/blob/master/test/test_check_pdb_file.py

Feel free for comments.

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 6:46 PM, Rodrigo Faccioli <
rodrigo_faccioli at uol.com.br> wrote:

> Hey João,
>
> Good question. We used this function with PDB database only. However, I
> think that this function can be divided into two other functions:
> isPDBFileATOMS and isPDBFileSEQRES. So, isPDBFile function call both
> function.
>
> The other functions (isPDBFileATOMS and isPDBFileSEQRES) can be to call
> separately.
>
> The code below is an example of these functions
>
> def isPDBFileATOM(pathFileName):
>     path,name = os.path.split(pathFileName)
>     FilePDB = File(path,name)
>     if FilePDB.find("ATOM"):
>         mensage = "The %s file is not a PDB File. Please, check it." %
> pathFileName
>         raise Exception(mensage)
>
> If you want, I can implement this my idea.
>
> Thanks,
>
>
> --
> 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 5:25 PM, João Rodrigues <anaryin at gmail.com> wrote:
>
>> 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/ <http://stanford.edu/%7Ejoaor/>
>>
>>
>>
>> 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
>>> > >> _______________________________________________
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>>> > >> http://lists.open-bio.org/mailman/listinfo/biopython
>>> > >>
>>> > >
>>> > >
>>> >
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>>> >
>>>
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>>
>>
>