
Friedrich Foerster wrote: > i spread imp throughout the world. even in exotic bavaria imp is > functional now. > here, i am trying ever more challenging things: i am using restraints > from different sources and want to weight these terms differently. for > that purpose, i want to employ a common strategy in x-ray: the different > restraints are weighted according to the inverse magnitude of the > corresponding derivatives. > Do you know a way how to get the derivatives of a particle with respect > to a specific restraint set in IMP. Particle.get_derivative uses the > full scoring function as i understand it...
It's not something that's immediately possible, as I see it, in IMP currently. But I suppose you could go through every *other* restraint and call set_is_active(false). Otherwise, if what you want to do is precisely that - weight the restraints by the derivatives - then perhaps we could add extra functionality to the DerivativeAccumulator to allow for that.
Ben

On Jun 25, 2008, at 5:02 PM, Ben Webb wrote:
> Friedrich Foerster wrote: >> i spread imp throughout the world. even in exotic bavaria imp is >> functional now. >> here, i am trying ever more challenging things: i am using restraints >> from different sources and want to weight these terms differently. >> for >> that purpose, i want to employ a common strategy in x-ray: the >> different >> restraints are weighted according to the inverse magnitude of the >> corresponding derivatives. >> Do you know a way how to get the derivatives of a particle with >> respect >> to a specific restraint set in IMP. Particle.get_derivative uses the >> full scoring function as i understand it... > > It's not something that's immediately possible, as I see it, in IMP > currently. But I suppose you could go through every *other* restraint > and call set_is_active(false). Otherwise, if what you want to do is > precisely that - weight the restraints by the derivatives - then > perhaps > we could add extra functionality to the DerivativeAccumulator to allow > for that. To expand a little, it wouldn't be too hard to have the DA compute some metric on the derivatives it has been used to accumulate and then have a restraint set which looks at this value and uses it to compute its weight. The DA doesn't have any way of differentiating between different attributes though, in case that matters.

thanks. i will employ ben's solution for the time being. if it my method is successful and of use for others i will bug you to find a more elegant and faster solution.
best
frido
On Jun 26, 2008, at 4:30 PM, Daniel Russel wrote:
> > On Jun 25, 2008, at 5:02 PM, Ben Webb wrote: > >> Friedrich Foerster wrote: >>> i spread imp throughout the world. even in exotic bavaria imp is >>> functional now. >>> here, i am trying ever more challenging things: i am using >>> restraints >>> from different sources and want to weight these terms differently. >>> for >>> that purpose, i want to employ a common strategy in x-ray: the >>> different >>> restraints are weighted according to the inverse magnitude of the >>> corresponding derivatives. >>> Do you know a way how to get the derivatives of a particle with >>> respect >>> to a specific restraint set in IMP. Particle.get_derivative uses the >>> full scoring function as i understand it... >> >> It's not something that's immediately possible, as I see it, in IMP >> currently. But I suppose you could go through every *other* restraint >> and call set_is_active(false). Otherwise, if what you want to do is >> precisely that - weight the restraints by the derivatives - then >> perhaps >> we could add extra functionality to the DerivativeAccumulator to >> allow >> for that. > To expand a little, it wouldn't be too hard to have the DA compute > some metric on the derivatives it has been used to accumulate and > then have a restraint set which looks at this value and uses it to > compute its weight. The DA doesn't have any way of differentiating > between different attributes though, in case that matters.
participants (3)
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Ben Webb
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Daniel Russel
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Friedrich Foerster