Re: [Btk-developers] generic molecule self-energy

[Chris S. <ctsa@u.washington.edu>]

I think I see some confusion. Generic molecule exists to define the
operations that you can do without having to know or bother with the
molecule's topology. You can read any old thing in from a pdb, rotate it,
write it back out etc.. When you say the generic molecule energies can be
calculated "with a topology file", you aren't refering to the generic
molecule class concept anymore, but the buildable molecule concept.


> > This might be tricky to implement.  Unless, by "undefined" you mean
> > "energy function will spit out a value, but value will be
> > meaningless."
> >  Then it's not so hard.
>
> I think it's actually doable given a topology file, although either the Molecule
> itself would have to carry extra topo info, or the e functions would need a topo
> table passed in.  The latter case is nice because it leaves things up to the user -
> for example I might want to scale down interactions between backbone atoms of
> adjacent residues which should work without any info about topology.
>