[Tutor] Basic web form interaction with http://propka.ki.ku.dk/

[Mateusz Koryciński]

Hi,

IMHO, first of all you should check if server admins allow automatic
connection outside web browser. Maybe they do and there a simple way to
connect and they will tell you how (for example how query should look like
as a command for software installed on server). I just check and they have
link to source code and some scripts - check this out, maybe there are
scripts for sending query?

About libraries - I don't really know how it looks like in Windows, but in
Linux (I am working mostly with it) you can download libraries to home
folder and import them to script directly from directory. Or you can export
new path to show python where it should look for libraries. In this case you
don't need root privileges.

If it's bioinformatics classes you should ask department admin to install
biopython. It have libraries to handle pdb files so it could be very
helpful.

Cheers,
Mateusz

2011/8/6 Troels Emtekær Linnet <tlinnet at gmail.com>

> Hi Mateus.
>
> No, I was certainly not aware of BioPython. What a nice project. I will
> check it out.
>
> No, the script should not download a .pdb file.
> The idea is, that a "researcher/student" sits with his/hers favorite
> protein in pymol and would like to know the pKa value
> of his/hers favorite amino acids.
>
> The student "probably" has only pymol installed, and would not like to
> install to many other python packages.
> Maybe the student can't, because it is a university computer.
>
> With this web-interaction script, the students activate the script, with:
> get_pka Molecule, residue
>
> The script saves the molecule to a .pdb file. Interact with the propka web
> site, send the file, wait 1 minute, grep for the line
> with the amino acid, and parse it back to pymol, so the student can see the
> pKa.
>
> To big benefit with this, is that the student does not have to handle to
> hard installations of scripts/programs or the manual way.
> And the student knows, that the pKa prediction is from the newest software
> available.
> If the student get greedy, he/she starts writing a pymol script that alter
> the pdb structure in pymol, and receive the new pKa value for each
> structural change.
> The downside, is of course the "waiting" time for the server response.
>
> Best
> Troels
>
>
>
> Troels Emtekær Linnet
> Karl-Liebknecht-Straße 53, 2 RE <http://maps.google.dk/>
> 04107 Leipzig, Tyskland
> Mobil: +49 1577-8944752
>
>
>
> 2011/8/6 Mateusz Koryciński <mat.korycinski at gmail.com>
>
>> Hi,
>>
>> Have You tried something similar to interface used in BioPython? I think U
>> could get solution by reading code for connection with databases like
>> Entrez. Maybe this will give you some ideas.
>>
>> Do you want your script to download pdb file from PDB database? Or you
>> want only sending and receiving from propka?
>>
>>
>> Cheers,
>> Mateusz
>>
>> 2011/8/6 Troels Emtekær Linnet <tlinnet at gmail.com>
>>
>>> Dear Python users.
>>>
>>> I am an semi-experienced in python, but totally new on the web
>>> interactions.
>>> I have been working with scripts o the protein program Pymol, which can
>>> be extended with python script.
>>>
>>>
>>> I hope that some of you can help me with an interaction script to
>>> http://propka.ki.ku.dk/.
>>> I hope that some of you can show be a basic python script to load the
>>> suitable python modules and interacting
>>> with the web form.
>>>
>>> The main idea is, to load a protein structure in pymol.
>>> Then writing a pymol/python script that saves the stucture of the protein
>>> into a .pdb file.
>>> Then open http://propka.ki.ku.dk/, send the .pdb file, wait 1-2 minutes
>>> for the result, and capture the result.
>>>
>>> I hope that some of you can show be the basics steps, to interact with
>>> the web form.
>>>
>>> Best
>>> Troels
>>>
>>> _______________________________________________
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>>>
>>
>>
>> --
>> Pozdrawiam,
>> Mateusz Koryciński
>>
>
>


-- 
Pozdrawiam,
Mateusz Koryciński
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