[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [IMP-dev] query particles



Daniel - I am sorry I was a way for a few hours - but in the end I did not really follow from this thread what type of queries would be possible.

On Tue, 9 Dec 2008, Daniel Russel wrote:

True, but is our only current hook for keeping things up to date. One alternative would be to add hooks to monitor attribute changes, but that would be tricky to make not expensive. You don't have to add states to a model though, so you could update it manually if you want.



On Dec 9, 2008, at 11:08 AM, "Dina Schneidman" <> wrote:

but you don't always want to update you indexing before/after scoring

On Tue, Dec 9, 2008 at 11:06 AM, Daniel Russel <> wrote:
Score states don't have anything to do with scoring either :-) they are just
updated before scoring since that is when things can change during
optimization. They used to just be called States which is perhaps clearer.



On Dec 9, 2008, at 10:56 AM, "Dina Schneidman" <> wrote:

maybe it's a simple solution in order to have it in a model, but
conceptually this indexing has nothing to do with scoring

On Tue, Dec 9, 2008 at 10:42 AM, Daniel Russel <> wrote:

From what I understand, what you want is a way of specifying what indexes
we
want build (not a way of specifying queries). We could easily provide
ScoreStates for indexes based on:
- set of discrete valued attributes
- D-dimensional interval queries on float values


On Dec 9, 2008, at 9:55 AM, Keren Lasker wrote:

Daniel - we all know how to run for loops ;)
I just thought it make sense to have something more efficient :)

On Tue, 9 Dec 2008, Daniel Russel wrote:


On Dec 9, 2008, at 9:29 AM, Keren Lasker wrote:

For the 26S project we currently do:
get particle by name

How could we beat something like:
[x for x in myparticles if x.has_attribute(name) and x.get_value(name)
==
"myname"]
with an SQL query?

get a set of particles within a residue number range

again, some variant on:
[x for x in molecular_hierarchy_get_by_type(root,
MolecularHierarchyDecorator.RESIDUE) if
ResidueDecorator(x).get_index() > lb and
ResidueDecorator(x).get_index()
<ub]

or C++, something like
BOOST_FOREACH(Particle *p, molecular_hierarchy_get_by_type(root,
MolecularHierarchyDecorator.RESIDUE)) {
if (ResidueDecorator(p).get_index() > lb and
ResidueDecorator(p).get_index() <ub) {
// do something
}
}

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.

But the added complication is why I would suggest sticking with C++ or
python. Lambda functions or list comprehensions support very general
logic
(more so than SQL) and allow you to leverage existing code. SQL would
make
it really hard to use any of the existing functionality and require
lots of
things be exposed in another language. For example, try to find all
particles close to a point in SQL? It is kind of ugly.

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 <>
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

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev

_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev
_______________________________________________
IMP-dev mailing list

https://salilab.org/mailman/listinfo/imp-dev