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Re: [IMP-dev] query particles

In general, I think having queries on the whole collection of particles in the model is not a good idea (since other people's code, restraints or states can add particles to the model and you can never be sure what those look like).

There is already functionality to search a Hierarchy (although it is more aimed at C++-- we could use a python interface which takes takes a python lambda function to make it more convenient to use in python). And python has all sorts of features for searching a list (and C++ has a few). It is not clear to me that we could provide an interface that is general and much more concise.

As a slight simplification for python users, we could provide a function which takes a list of key, value pairs (with keys of arbitrary type) and a container. It is a bit messier to provide this interface in C++ as we would have to have a separate list per type.

Another thing to simplify such search would be a "DefaultValuesDecorator" which wraps a particle and pretend it has all attributes, just providing default values for missing ones. This would obviate the need to check for an attribute before matching against it.

What sort of queries do you all do?

On Dec 9, 2008, at 8:43 AM, 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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