more flexible distance "center"

[natedey]

I was thinking we could set the distance-based building to be even more flexible, and I see some use cases where the current code won't perform correctly. I think we should also allow the user to define a set of atoms (or a single atom) as the center of the sphere.

1. this would allow a user to define a specific seed atom as the geometric center. In the case of phosphoryl transfer reactions, we might want to define the center as just the phosphorous atom of the substrate, rather than the center of mass or Cartesian mean of the entire seed.
2. The user could define the geometric center as being a point between two residues. For example in TJ's hydrogenase case, we might want to define the center as being the average Cartesian coordinates of the S and N atoms that are undergoing the proton transfer, rather than the giant seed we defined in that project.

This is the kind of thing we can discuss in the software paper, without having to run any new QM-cluster model calculations. We could look at model composition of all the different permutations of distance-building options and see if anything actually changes. This is a hypothesis that has never been analyzed or tested in the community.

[natedey]

@tsuhagia has added a bunch of stuff, but we need confirmed tests from the group that it is working correctly. Thanks TJ!

-satom center_atoms, examples: A:301:C8,A:301:N9,A:302:C1,A:302:N1
python3 ~/git/RINRUS/bin/pdb_dist_rank.py -pdb 3bwm_h.pdb -satom A:301:C8,A:301:N9,A:302:C1,A:302:N1 -cut 5 -type mass -nohydro

[natedey]

need to test -satom flag (with PTP2 phosphorous) and add functionality to driver