[Biopython] Biopython & p3d

[Peter]

On Wed, Oct 21, 2009 at 11:31 AM, Christian Fufezan
<fufezan at uni-muenster.de> wrote:
>> This also reminds me of the SQL language for database selections, and
>> how classical SQL code with Python just used SQL statements within
>> Python strings. Have you ever used SQLAlchemy, and looked at how
>> they handle SQL statements like filters, ands, ors, etc with a clever
>> object based interface? Perhaps something like that could work for
>> a 3D structure query API.
>
> That certainly sounds very interesting. It would also allow to incorporate
> the actual pdb files into the database which would reduce loading and
> tree building times. Surveys, pattern screening could be done very fast.
> One could also imagine connecting other pdb databases, such as SCOP,
> Pfam or web services, e.g. PISCES.

I was actually suggesting having a object based API for building search
terms instead of parsing a human friendly string.

But yes, loading a PDB file into a database does have some advantages.

Peter