hi,
Currently we have a generic XYZR decorator. For mass we have atom::Mass, but when dealing with beads, it does not really make sense to use it. Do you think it makes sense to create a generic XYZRW decorator in core ? the default W key can be atom::Mass::get_mass_key()
??
Keren.
Why doesn't it make sense to use mass with beads? Its is what I have been doing.
On Jan 22, 2010, at 9:14 PM, Keren Lasker wrote:
> hi, > > Currently we have a generic XYZR decorator. > For mass we have atom::Mass, but when dealing with beads, it does not really make sense to use it. > Do you think it makes sense to create a generic XYZRW decorator in core ? the default W key can be atom::Mass::get_mass_key() > > ?? > > Keren. > _______________________________________________ > IMP-dev mailing list > IMP-dev@salilab.org > https://salilab.org/mailman/listinfo/imp-dev
just because it in not necessarily the exact molecular mass, and it you use it you need to handle two decorators one for XYZR and one for mass, it is easier to have a joint decorator - no ? On Jan 23, 2010, at 9:07 AM, Daniel Russel wrote:
> Why doesn't it make sense to use mass with beads? Its is what I have > been doing. > > On Jan 22, 2010, at 9:14 PM, Keren Lasker wrote: > >> hi, >> >> Currently we have a generic XYZR decorator. >> For mass we have atom::Mass, but when dealing with beads, it does >> not really make sense to use it. >> Do you think it makes sense to create a generic XYZRW decorator in >> core ? the default W key can be atom::Mass::get_mass_key() >> >> ?? >> >> 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 Jan 22, 2010, at 11:13 PM, Keren Lasker wrote:
> just because it in not necessarily the exact molecular mass, Ahh, you mean weight as in "an arbitrary weight assigned to things" which has nothing at all to do with mass? :-) What other functionality would be associated with it other than getting or setting an arbitrary floating point attribute? I suspect any more functionality will vary between applications of the weight. So it may make sense to have it close to the use point eg have a WeightDecorator in em which is used by the FitRestraint (and defaults to Mass as the key). Not sure.
> and it you use it you need to handle two decorators one for XYZR and one for mass, it is easier to have a joint decorator - no ? It's not that much easier :-) Either writing Weight(p).get_weight() or have a weight decorator. But if there is general functionality (outside of the guts of em code) that depends on the weights and the radius and the coordinates, then it could make sense. What do you have in mind for it to do?
> On Jan 23, 2010, at 9:07 AM, Daniel Russel wrote: > >> Why doesn't it make sense to use mass with beads? Its is what I have been doing. >> >> On Jan 22, 2010, at 9:14 PM, Keren Lasker wrote: >> >>> hi, >>> >>> Currently we have a generic XYZR decorator. >>> For mass we have atom::Mass, but when dealing with beads, it does not really make sense to use it. >>> Do you think it makes sense to create a generic XYZRW decorator in core ? the default W key can be atom::Mass::get_mass_key() >>> >>> ?? >>> >>> 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
On Jan 22, 2010, at 11:26 PM, Daniel Russel wrote: > On Jan 22, 2010, at 11:13 PM, Keren Lasker wrote: > >> just because it in not necessarily the exact molecular mass, > Ahh, you mean weight as in "an arbitrary weight assigned to things" which has nothing at all to do with mass? :-) What other functionality would be associated with it other than getting or setting an arbitrary floating point attribute? I suspect any more functionality will vary between applications of the weight. So it may make sense to have it close to the use point eg have a WeightDecorator in em which is used by the FitRestraint (and defaults to Mass as the key). Not sure. Another set of places it could conceivably be used is to provide weights when computing centroids and such in core. But, in that context, only a weighted point (not a weighted ball) makes sense.
On a tangentially related note, physical rigid bodies (with inertia) should use the mass decorator (in core), which can't currently be done as the decorator is in atom.
>> and it you use it you need to handle two decorators one for XYZR and one for mass, it is easier to have a joint decorator - no ? > It's not that much easier :-) Either writing Weight(p).get_weight() or have a weight decorator. Forgot to pass the key, so it would have to be Weight(p, weight_key).get_weight(), which is little more verbose :-)
> >> On Jan 23, 2010, at 9:07 AM, Daniel Russel wrote: >> >>> Why doesn't it make sense to use mass with beads? Its is what I have been doing. >>> >>> On Jan 22, 2010, at 9:14 PM, Keren Lasker wrote: >>> >>>> hi, >>>> >>>> Currently we have a generic XYZR decorator. >>>> For mass we have atom::Mass, but when dealing with beads, it does not really make sense to use it. >>>> Do you think it makes sense to create a generic XYZRW decorator in core ? the default W key can be atom::Mass::get_mass_key() >>>> >>>> ?? >>>> >>>> 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 >
On 1/22/10 9:14 PM, Keren Lasker wrote: > Currently we have a generic XYZR decorator. > For mass we have atom::Mass, but when dealing with beads, it does not > really make sense to use it. > Do you think it makes sense to create a generic XYZRW decorator in core > ? the default W key can be atom::Mass::get_mass_key()
I think it would only make sense to create an XYZRW decorator if you had a specific class of Particle where it doesn't make sense for it to have a weight without coordinates, or vice versa. But it seems to me that you may want to weight Particles that don't have coordinates. Thus, simply adding an attribute for such Particles seems sufficient to me rather than a decorator.
Of course, it may make sense for your specific application to create a non-generic "Bead" decorator, and I see no problem with that.
Ben
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Ben Webb -
Daniel Russel -
Keren Lasker