|
From: Chris S. <ctsa@u.washington.edu> - 2002-07-25 00:07:08
|
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. > > > > > > > > > > > ------------------------------------------------------- > > This sf.net email is sponsored by: Jabber - The world's fastest > > growing > > real-time communications platform! Don't just IM. Build it in! > > http://www.jabber.com/osdn/xim > > _______________________________________________ > > Btk-developers mailing list > > Btk...@li... > > https://lists.sourceforge.net/lists/listinfo/btk-developers > > > > > > ------------------------------------------------------- > This sf.net email is sponsored by: Jabber - The world's fastest growing > real-time communications platform! Don't just IM. Build it in! > http://www.jabber.com/osdn/xim > _______________________________________________ > Btk-developers mailing list > Btk...@li... > https://lists.sourceforge.net/lists/listinfo/btk-developers > |