For the 26S project we currently do: get particle by name get a set of particles within a residue number range
the solution of a function that gets (key,value,container) seems like a good solution. However - it can be more complicated : 1. it can interact with the hierarchy - give me the residues range within this protein for example - so we should probably also allow for a hierarchy handle in the interface. 2. we might want to ask residue range + some other property such as have structural coverage or do not. Therefore I think that a sql type string can be more general than a list of attributes - because you do not know how they are related.
On Tue, 9 Dec 2008, Daniel Russel wrote:
> 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: > >> Hi, >> >> 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? >> >> Dina >> >> P.S. skype me, we can talk about it >> >> >> On Tue, Dec 9, 2008 at 7:03 AM, Keren Lasker kerenl@salilab.org 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, >>> Keren. >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >>> >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev