[Btk-developers] dead folders

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

you can blame we for those extra folders. I understand that eliminating
any folder from a CVS tree is non-trivial. I'm sure everyone agrees they
should go, but how?

On Wed, 24 Jul 2002 EJ...@lb... wrote:

> Oh, in that case who cares about support for self-energies.  If the user wants it,
> he/she can define it using some other rules like I mentioned previously with
> residue numbers.  If they're really concerned about it, they can download the
> param files from some website, they have files for almost anything you could
> possibly imagine.
>
> On an unrelated note:
> can we get rid of the APPS subdirectory?  Apple OS X is case preserving, but
> case insensitive.  This means when you check things out of CVS it cant tell the
> difference between apps and APPS, and everything gets chucked into APPS.
> Doesn't look like there's anything in there anyway.
>
> -E
>
> ----- Original Message -----
> From: Chris Saunders <ctsa@u.washington.edu>
> Date: Wednesday, July 24, 2002 4:10 pm
> Subject: Re: [Btk-developers] generic molecule self-energy
>
> > 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.
> > >
> >
> >
> >
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