Fwd: [chimera-dev] database access

[Daniel Greenblatt]

Hi Lars

Currently, Chimera does not have any functionality that interfaces 
directly with MySQL-type relational databases, although this will 
eventually be implemented as part of another project (but not for a 
while still:-). However, Python *does* have several modules devoted to 
accessing databases, and one could write an extension to Chimera to 
accomplish this. We would certainly be willing to assist you in the 
Chimera-side development of such an extension if this is the approach 
you ultimately decide to take.  See here for more information:

     http://www.python.org/topics/database/modules.html

  I think that all three approaches you detail are very reasonable.

There are generally two ways to create a model in Chimera. The first is 
by reading in a known file format (such as PDB  or mol2), and the 
second is by manually building the model from raw information.

It seems that your (1) and (3) take the first approach - the server 
side (i.e. your database) is responsible for processing the raw 
information and giving Chimera a file in a format it understands.

Your method (2) takes the other approach, by supplying Chimera with raw 
information, which it then builds into a model. This is also possible 
in Chimera, although this all happens in the C++ code, which is not 
distributed with Chimera. We don't currently have any examples 
illustrating this in our Programmers Guide, but if you decided to 
pursue this route, we could provide you with some instructional 
examples on how to do this.

It is hard to say which one of these approaches is best, because it 
depends on your aims -  speed/efficiency?  ease of implementation?

Dan Greenblatt
Computer Graphics Lab
University of California, San Francisco
dan at cgl.ucsf.edu

> first)
>
> My plugin accesses the db and creates a temporary file - then it tells
> chimera to load it.
> Advantage chimera can use it native (and probably fast) reading
> routines...
>
>
> second)
>
> The plugin fetches the data form the db and builds up the molecule in
> chimera by use of the python-interface...
>
>
> third()
>
> I tell chimera to access the database X, use password Y, and run 
> select /
> or  call a stored procedure.
> the stored-procedure or (for older mysql a linked extension function)
> could build up an input-format chimera understands from the actual 
> data.
> the select-version would be a bit ugly cause we would need several of 
> them
> or place some file-blobs in the bd.
>
>
> I hope your are interested to do some thing about approach three...
>
> Sincerely
> Lars
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