Daniel Russel wrote:
They eventually yes. At the moment they are not as people just get IMP from svn and build in SVN.We're talking about two different things here. You want to distribute your PDB reader with IMP. I don't want to include the code in IMP SVN. The two issues are orthogonal;
I think you misunderstood my post - I was talking about SVN externals: http://svnbook.red-bean.com/en/1.4/svn.advanced.externals.html
That should work fine with the current "get IMP from SVN" approach.
It doesn't make sense to talk about a molecule without it bonds, so a molecule loader better handle it on one level or another. BALL handles standard bonds as a cleanup pass after reading which is a good solution too, but makes it a bit funny for connect records as these bonds are created on reading while other, more standard bonds need to wait for the cleanup.How are you "getting bonds" out of a PDB file? PDB files don't provide that information.
Well, sure, but to do that you need to know the topology - i.e. which atoms are connected in which residues, and at what distances and angles. That's what a topology file (half of an MM force field) does. It's not good to hardcode this because, for example, you may want to fill in missing atoms in a heme residue.
Ben
--
http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
- Sir Arthur Conan Doyle