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Re: [IMP-dev] query particles

Why use SQL over python or C++ logic?

On Dec 9, 2008, at 9:15 AM, Keren Lasker wrote:

we do the same - but this is an ad hoc solution.
Agreed, but it might be one of those things (like storing the whole model, restraints and all) where there is unlikely to be a general solution that adds any benefit as the general case is very complex and the ad hoc solution is quite simple.

It should not be part of Model I think but an external IndexModel class maybe or a IndexDecorator.
Again, I think having it act on a whole model is a really bad idea (the IMP equivalent of using global variables :-)

I suggested SQL because your query can be complex containing often more than one attribute.
Why not just use python or C++ rather than add another language to learn? There are a few operations which are more concise in SQL, but I don't know that we want to support them or that they make sense in our case (where would presumably have to return whole particles).

Ben - you will need it in IMP.Atom - have you already started working on that?
How come? I think I am missing some use case :-)

On Tue, 9 Dec 2008, Dina Schneidman wrote:


I need this too (surprisingly). Usually I do it with mapping between
the particle and the attribute.
It is simple. however it is unclear where should we put such a
mapping. Putting it in a model
could be the best, however not everyone needs it. So it means
somewhere else or extending the Model to ProteinModel?


P.S. skype me, we can talk about it

On Tue, Dec 9, 2008 at 7:03 AM, Keren Lasker <> wrote:
hi all,

Frido and I find ourselves many times need to query particles based on
attribute values.
Few such examples: a protein with a specific name, particles with a specific
residue range.

I think that it would be very useful to have something similar to SQL
queries on the particles DB.
Bret might had something similar implemented - but it is probably obsolete.
IMP.Atom will probably need such functionality as well.

has anyone took a look at that before ?

thank you,
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