Re: [IMP-dev] Proposed bonded/nonbonded list interfaces

[Ben Webb <>]

Daniel Russel wrote:
> Since I needed caching of my bonds so I decided to refactor things to  
> have bonded and nonbonded lists. Here are my proposed interfaces for  
> people's perusal. I then have a DynamicExclusionVolumeRestraint and  
> DynamicBondRestraint which take pointers to these states and get their  
> particle pairs from them.

The interfaces look reasonable to me. But the list of bonded particles 
should be static, IMHO - it's a waste to rebuild it at every score 
evaluation - since it'll only change if you add/remove particles or 
bonds. But I guess that's an implementation detail.

> I don't know the best way to make things accessible from python (I  
> don't think the C++ iterators will work from python, but I haven't  
> tried).

I think we can punt on that. Anybody foolish enough to write a nonbonded 
term in Python is going to have to put up with incredibly slow 
performance anyway, so they may as well just do an NxN double loop.

> For reference, a BondDecorator is a decorator wrapping a particle  
> which contains information (length, stiffness, type) for a bond.

This is the only thing I have a problem with. What do these three 
parameters mean? I guess length and stiffness translate to the mean and 
standard deviation of a Gaussian restraint. But this isn't the best 
place to put this kind of thing - what if the user wanted to use a cubic 
spline instead? A bond generally just identifies a pair of atoms, and 
the restraint contains the length/stiffness/whatever information. This 
could in turn be populated from your force field (e.g. using atom types).

	Ben
--
                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle