[BioPython] PDB parser

[Catherine Letondal]

Hi,

Many thanks for all the answers! I haven't tried all the parsers, but
the ones I have tried are very useful and work fine.  
My question is: how is it planned to integrate this work in Bio.PDB? 
The next question is: is there a Structure class planned for BioPython?
Is the Bio.PDB module going to have a Bio.PDB.parse_file() as the Clustalw 
module (or a default parser with an optional consumer or a scanner to be used
by a user-defined parser, etc... according to the consumer/parser model)  
but all this creating a Structure - or StrutureRecord - instance ?

Thanks!

Thomas Hamelryck wrote:
> 
> Hi Catherine,
> 
> I've attached a PDBParser class that you can probably use. An example of its 
> use can be found in the file test.py.
> 
> PDBParser uses an aggregated StructureBuilder class, which you are supposed 
> to implement for your specific purpose (it's easy). This class needs to have 
> a set of standard methods (init_atom, init_residue, init_chain, 
> init_model,...) that are called each time a new atom, residue, chain, model, 
> etc. is encountered. 
> 
> Cheers,
>  
> ---
> Thomas Hamelryck      Vrije Universiteit Brussel (VUB)
> Intitute for Molecular Biology            ULTR Department
> Paardenstraat 65    1640 Sint-Gensius-Rode, Belgium
>                 http://ultr.vub.ac.be/~thomas

Michael George Lerner wrote:
>
> I don't know about other such projects (official or not), but I'm working
> on a PDB parser.  Like Andrew Dalke's UPDB, it reads in format definition
> files and spits out parsers.  Mine uses biopython's Consumer/Parser model
> (I think that didn't exist when Andrew Dalke wrote UPDB).  It seems to
> work fairly well, except for the fact that it's really slow.  Once I can
> speed it up a bit, I'm planning on giving it back to biopython.  Actually,
> I suppose I'll give it back to biopython either way .. but people are more
> likely to actually _want_ it if it runs at a reasonable speed :).
>
> I guess this message should provide some more motivation for me to get
> back to work on my PDB parser ..
>
> -michael
>
> p.s. writing this thing has been a lot of fun.
>
> --
> This isn't a democracy;|                        _  |Michael Lerner
>  it's a cheer-ocracy.  | ASCII ribbon campaign ( ) |   Michigan
> -Torrence,  Bring It On|  - against HTML email  X  |  Biophysics
>                        |                       / \ | mlerner@umich

Iddo Friedberg wrote:
>
> There's Konrad Hinsen's PDB parser, linked from Biopython's script
> central. Not an official part of Biopython, and does not use the
> consumer/parser module.
>
> Iddo
>
Jeffrey Chang wrote:
> Biopython's missing a PDB parser right now, so anything you have would
> probably be useful to someone.  :)
>
> One way to speed it up would be to have it output Martel expressions.
> I don't know how large of a change that will be to the code, but
> Martel is quite fast.  The end user can choose which parts of the file
> she wants to receive, which speeds things up by reducing python function
> calls.
>
>
> Jeff
"Cayte" wrote:
> Under Bio.Crystal I have a class called Hetero for 3 letter pdb codes. We
> may want to use it or replace it with your solution to avoid duplication.
>

--
Catherine Letondal -- Pasteur Institute Computing Center