On Dec 9, 2008, at 9:53 AM, Dina Schneidman wrote:
> I think IndexModel is the best solution, but in C++. having python and > c++ is more than enough, we don't want to support something else. I > suggested extending the Model because of the update reason, in this > case you can update the indexing when you add/remove particles. I don't understand what you mean.
> > > On Tue, Dec 9, 2008 at 9:29 AM, Keren Lasker kerenl@salilab.org > wrote: >> 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 >> >> _______________________________________________ >> 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