hi,
quick question:
Given two proteins, represented as rigid bodies. Constructing a PairsRestraint on the two rigid bodies, what should be the result on the get_interacting_particles() ? for some reason I am getting 0, also after evaluating the restraint. I would have expected to get one list with two entries ( the two rigid bodies). what am i doing wrong ?
thank you, Keren.
Sounds like a bug. It should return the pair. I'll look in the morning. In general, getinteractingparticles is very poorly tested.
On Sep 6, 2009, at 11:13 PM, Keren Lasker kerenl@salilab.org wrote:
> hi, > > quick question: > > Given two proteins, represented as rigid bodies. > Constructing a PairsRestraint on the two rigid bodies, what should > be the result on the get_interacting_particles() ? > for some reason I am getting 0, also after evaluating the restraint. > I would have expected to get one list with two entries ( the two > rigid bodies). > what am i doing wrong ? > > thank you, > Keren. > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
Which reminds me: many of the interactions are via score states, so we might need an equivalent for them.
On Sep 6, 2009, at 11:13 PM, Keren Lasker kerenl@salilab.org wrote:
> hi, > > quick question: > > Given two proteins, represented as rigid bodies. > Constructing a PairsRestraint on the two rigid bodies, what should > be the result on the get_interacting_particles() ? > for some reason I am getting 0, also after evaluating the restraint. > I would have expected to get one list with two entries ( the two > rigid bodies). > what am i doing wrong ? > > thank you, > Keren. > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
not completely sure i got this comment .... - you mean that ScoreState should have get_interacting_particles function ? that makes sense for many analysis procedures. On Sep 6, 2009, at 11:58 PM, Daniel Russel wrote:
> Which reminds me: many of the interactions are via score states, so > we might need an equivalent for them. > > > > On Sep 6, 2009, at 11:13 PM, Keren Lasker kerenl@salilab.org wrote: > >> hi, >> >> quick question: >> >> Given two proteins, represented as rigid bodies. >> Constructing a PairsRestraint on the two rigid bodies, what should >> be the result on the get_interacting_particles() ? >> for some reason I am getting 0, also after evaluating the restraint. >> I would have expected to get one list with two entries ( the two >> rigid bodies). >> what am i doing wrong ? >> >> thank you, >> Keren. >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
On Sep 7, 2009, at 12:04 AM, Keren Lasker wrote:
> not completely sure i got this comment .... - you mean that > ScoreState should have get_interacting_particles function ? Yes. And that it is needed to get the full interaction graph.
> that makes sense for many analysis procedures.
> On Sep 6, 2009, at 11:58 PM, Daniel Russel wrote: > >> Which reminds me: many of the interactions are via score states, so >> we might need an equivalent for them. >> >> >> >> On Sep 6, 2009, at 11:13 PM, Keren Lasker kerenl@salilab.org wrote: >> >>> hi, >>> >>> quick question: >>> >>> Given two proteins, represented as rigid bodies. >>> Constructing a PairsRestraint on the two rigid bodies, what should >>> be the result on the get_interacting_particles() ? >>> for some reason I am getting 0, also after evaluating the restraint. >>> I would have expected to get one list with two entries ( the two >>> rigid bodies). >>> what am i doing wrong ? >>> >>> thank you, >>> Keren. >>> _______________________________________________ >>> IMP-dev mailing list >>> IMP-dev@salilab.org >>> https://salilab.org/mailman/listinfo/imp-dev >> _______________________________________________ >> IMP-dev mailing list >> IMP-dev@salilab.org >> https://salilab.org/mailman/listinfo/imp-dev > > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
I can't reproduce the error.
>>> import IMP.core >>> m=IMP.Model() >>> p0= IMP.core.XYZ.setup_particle(IMP.Particle(m)) >>> p1= IMP.core.XYZ.setup_particle(IMP.Particle(m)) >>> dps= IMP.core.DistancePairScore(IMP.core.Linear(0,1)) >>> lpc= IMP.core.ListPairContainer() >>> lpc.add_particle_pair(IMP.ParticlePair(p0.get_particle(), p1.get_particle())) 0 >>> pr= IMP.core.PairsRestraint(dps, lpc) >>> ip= pr.get_interacting_particles() >>> len(ip) 1 >>> len(ip[0]) 2
On Sep 6, 2009, at 11:13 PM, Keren Lasker wrote:
> hi, > > quick question: > > Given two proteins, represented as rigid bodies. > Constructing a PairsRestraint on the two rigid bodies, what should > be the result on the get_interacting_particles() ? > for some reason I am getting 0, also after evaluating the restraint. > I would have expected to get one list with two entries ( the two > rigid bodies). > what am i doing wrong ? > > thank you, > Keren. > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
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Daniel Russel -
Keren Lasker