Lots of people have been bumping into the fact that it is kind of annoying to handle the following sort of work flow: - read a pdb - create a coarse grained rigid model - move the coarse grained rigid model around (ignoring the atoms as much as possible, for efficiency) - write an appropriately transformed version of the pdb
The problems are: - doing this reliably requires you saving the initial transformation of the rigid body and then transforming the components of the initial pdb by the difference between the initial and final. There are lots of plausible seeming ways of doing the job that don't work reliably. - less troublesome, creating all the particles for a large pdb can take a bit of time
I'm not sure of a way of providing a simple interface to this that is easy to implement reliably. And so I thought it might be worth having a brainstorming session/discussion on the topic to see if we can come up with a nice, canned solution. Interested?
Some possible bits of solutions are: - IMP::atom::create_rigid_body can store the initial transform internally and provide a method to get how much the molecule moved - the hierarchy clone method could keep a link back to the hierarchy it was created from to help you in going back (if you want to keep the whole hierarchy in memory) - we could provide a single method that transforms a pdb file without creating particles from it