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?
Slight improvement of the proposal: - if any of the hierarchy has coordinates, all the leaves must - 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? >
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 > >
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 foerster@biochem.mpg.de wrote:
> 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 >> >> > > > > -- > -- > > Dr. Friedrich Foerster > Max-Planck Institut fuer Biochemie > Am Klopferspitz 18 > D-82152 Martinsried > > Tel: +49 89 8578 2651 > Fax: +49 89 8578 2641 > > foerster@biochem.mpg.de > > www.tomotronic.org > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
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Daniel Russel -
Friedrich Foerster