I am not sure I entirely understand you message. Would you consider it
an improvement to be able to do the following:
# a,b,c are Particles which are MolecularHierarchyDecorator roots for
the proteins
# they can have arbitrary levels
# the identifier for the equivalence class hierarchy
traits= HiearchyDecoratorTraits("equivlanence_class")
abp= Particle()
m.add_particle(abp)
cp= Particle()
m.add_particle(cp)
# create a new hierarchy to define which proteins can be equivalently
connected
abh= HierarchyDecorator.create(abp, traits)
abh.add_child(HierarchyDecorator.create(a, traits))
abh.add_child(HierarchyDecorator.create(b, traits))
# nothing else has the same type as c
ch= HierarchyDecorator.create(cp, traits)
ch.add_child(HierarchyDecorator.create(c, traits))
# create a refiner to get all residues irrespective of how far down
they are in the hierarchy
refres=
DescendentsOfTypeParticleRefiner
(MolecularHierarchyDecorator.get_type_key(),
MolecularHierarchyDecorator.RESIDUE)
rtres = RefineOncePairScore(SphereDistancePairScore(), refres)
# a refiner to produce the proteins in each equivalence class
cpr= ChildrenParticleRefiner(traits)
erops= RefineOncePairScore(rtres, cpr)
# make a list of the particles defining the equivalence classes
classes= IMP.Particles()
classes.append(abp)
classes.append(cp)
r= ConnectivtyRestraint(erops, classes)
The changes necessary to do the above are quite easy.
On Dec 19, 2008, at 6:36 AM, Friedrich Foerster wrote:
hi daniel,
the Model hierarchy is not particularly awkward by itself. for me
the problem is more that dealing with a single hierarchy on the
representation level is hard.
i just constantly run into the problem that i want to press all my
restraints and representation into a single hierarchy - and i always
need to change it. so my hierarchy is basically just protein ->
fragment. whether a fragment is an atom, few residues, a domain, or
an entire protein varies from case to case. of course, i could add
another layer - but it'd be quite a bit of work to change it
everywhere and probably i'd need to change it again very soon.
for me a convenient framework for restraints would probably look
like that:
rest1 = upper_distance(particles_from_protein_A,
articles_from_protein_B)
rest2 = upper_distance(particles_from_protein_A,
articles_from_protein_C)
(protein_B and protein_C are both of the same protein type, e.g.,
lysozyme ). for tricky cases one could use several instances of
lower_scoring_one_of.
just a proposal....
cheers
frido
On Dec 19, 2008, at 2:02 PM, Daniel Russel wrote:
By the way, what exactly do you five cumbersome with the hierarchy
as it stands? Why do you find you are changing it a lot? Just
looking for ways to make things simpler.
--
Friedrich Foerster
Max-Planck Institut fuer Biochemie
Am Klopferspitz 18
D-82152 Martinsried
Tel: +49 89 8578 2651
Fax: +49 89 8578 2641
www.tomotronic.org
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