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
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 <>
Frido and I find ourselves many times need to query particles based
Few such examples: a protein with a specific name, particles with a
I think that it would be very useful to have something similar to
queries on the particles DB.
Bret might had something similar implemented - but it is probably
IMP.Atom will probably need such functionality as well.
has anyone took a look at that before ?
IMP-dev mailing list