On Jan 25, 2010, at 3:33 PM, Keren Lasker wrote:
> thanks Daniel.
> Is there a function for each of those ?
Of course :-) And many more. And refiners for most of them (which is more useful, since that is what rigid body taking methods use to do the mapping).
> if so it would be useful to explicitly have it in the documentation.
Most of the methods have to do with atom::Hierarchies and are documented there, since the same considerations hold whether or not the particle happens to be a rigid body (eg, any time you are doing collision detection with a hierarchy, you have to decide what sort of representation to use, all atoms, coarse grained, residues etc). It would be good to have a more thorough introduction to molecular hierarchies, but my thought has been to rip that out of the paper. I could use the current text top start producing something.
The rigid body docs says very general things about members vs other sets you might be interested in. I'll improve the text there, but it can't really be too specific to molecular hierarchies.
> and specifically for my current requirement - what is the function for getting the set of particles which defines the highest resolution description of the shape, if the rigid body is not defined by atom::Hierarchy.
> ?
There is no way to have a general purpose function for that since it would involve mind reading :-) The rigid body usage methods all take refiners which map from the rigid body to the set of particles you are interested in for that usage. You just have to provide the right refiner to produce your desired representation.
Why aren't the set of particles a molecular hierarchy (assuming it is representing a molecule)?
> On Jan 26, 2010, at 1:27 AM, Daniel Russel wrote:
>
>> On Jan 25, 2010, at 3:20 PM, Keren Lasker wrote:
>>
>>> To get the particles within a rigid body, it is better using IMP::core::get_leaves or get_members,
>> Maybe :-) They do different things (that might happen to have the same result sometimes).
>>
>>
>>> i.e.: does get_members return the leaves or the children of the RigidBody ?
>> neither, it returns all particles which move rigidly with the rigid body.
>>
>> Basically, when you have a shape that happens to be rigid, there are many sets of particles associated with it
>> - all particles which movie rigidly with the shape (the rigid members)
>> - the set of particles which defines the highest resolution description of the shape (which, if the rigid body is created from a molecular hierarchy, would be the leaves)
>> - the set of particles which defines the coarsest description of the shape. Typically this is just the rigid body particle itself with a radius
>> - the set of particles defining the residues in the rigid body
>> - the particles defining the sphere hierarchy used for collision detection between that rigid hierarchy and another rigid hierarchy (which would be members, if they existed)
>> etc.
>>
>> Depending on what you want to do, you will need different ones of these sets.
>>
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