Re: [Btk-developers] dead folders

[<EJ...@lb...>]

This sounds like a reasonable workaround.  As long as we all agree never to 
use APPS.

-E

----- Original Message -----
From: Timothy A Robertson <timr@u.washington.edu>
Date: Wednesday, July 24, 2002 5:24 pm
Subject: Re: [Btk-developers] dead folders

> cvs update -P btk
> 
> (-P = prune.)
> 
> CVS sucks.  This is the workaround for the dead directory problem.  
> As long as directories are empty, they won't be added when you do 
> an update.  Same thing works for checkout, too, btw.
> 
> Unfortunately, hacking the CVS archive is high-risk.  There's a non-
> zero chance that you'll trash the CVS tree, and then we'd have to 
> lose that context.  Of course, if no one cares about that, we could 
> always do the *easiest* thing, and freeze the tree, backup the 
> current source code, wipe the sourceforge archive, and re-import 
> the code.
> 
> -tim
> 
> On Wed, 24 Jul 2002, Chris Saunders wrote:
> 
> > 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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