On Fri, May 22, 2009 at 2:19 AM, Daniel Russel drussel@gmail.com wrote: > Slight improvement of the proposal: > - if any of the hierarchy has coordinates, all the leaves must
just one q: what about systems with different granularities; i.e., for part of a complex one might have (in fact rather often...) reasonable atomic models for some proteins or domains and not for others. for example, i sometimes have fragments, which have coordinates, and for others i can go finer in the tree. how is that solved?
thanks
frido
> - one must be able to determine which Particle each residue is associated > with > - the default "radius" attribute is used to an approximating radius- so the > radius that best approximates the sub-particles at that level of detail > - hierarchy particles can have a "bounding radius" attribute which > represents a bounding sphere. This will be used by the close pairs code and > other code and is assumed to include all relevant geometry associated with > the particle (so all geometry in the subtree). > > > On Thu, May 21, 2009 at 10:07 AM, Daniel Russel drussel@gmail.com wrote: >> >> I suggest that we impose that in an atom.Hierarchy >> - if any of the hierarchy has coordinates, all the leaves do (they can be >> at any level of the hierarchy though) >> - all residues in each molecule must be either a) explicitly represented >> as a Residue, b) part of a Domain which is a leaf (which would be expanded >> to allow non-contiguous sets of residues--or we could split off a new type >> of decorator for this) >> - any member of the hierarchy other than an Atom which has coordinates >> also has a radius. The interpretation is that this radius bounds where >> members of the (possibly elided) subtree can be. >> >> These would ensure several useful properties: >> 1) it be clear what the highest resolution representation of any hierarchy >> is >> 2) one be able to find out where in the hierarchy any residue is located >> 3) code does not need to look at the most detailed representation to get a >> rough picture of the structure, it only has to search down the tree (I'm >> from CS) to find a representation with small enough balls. >> >> Comments? > > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev > >