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Re: [IMP-dev] fleshing out atom.Hierarchy

The leaves of the tree don't have to be atoms. So one protein could have atoms with xyz as leaves and another domains with xyz and orientation as leaves (and it could not have atoms as leaves).

On May 24, 2009, at 2:13 PM, Friedrich Foerster <> wrote:

On Fri, May 22, 2009 at 2:19 AM, Daniel Russel <> 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?



- one must be able to determine which Particle each residue is associated
- 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 <> 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
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.


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Dr. Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried

Tel: +49 89 8578 2651
Fax: +49 89 8578 2641

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