Daniel Russel wrote: >> 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; > They eventually yes. At the moment they are not as people just get IMP > from svn and build in SVN.
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.
>> How are you "getting bonds" out of a PDB file? PDB files don't provide >> that information. > 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.
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