dock pdb into density app (#5053)
This is one of the apps I've made as part of my thesis project.
it's purpose is to dock a pdb file, or ensemble of pdb files, into density and report back the ones that best fit the density
currently i've called it dgdp for density guided domain placement, but that's sort of a strange name. maybe I'll just take over frank's pilot apps name (dock_pdb_into_density)
It unfortunately overlaps with the DockIntoDensityMover a lot, but its differences are:
it can be parallelized much more
(which is necessary when docking large poses into density, otherwise one pdb can take 1+ days).
there are important differences in the ways clustering is performed
things are clustered not at the "point level" but rather over all points
different mapresolutions are used during different stages to obtain more accurate density scoring.
there is native checking implemented for multiple natives (ie multiple copies of the same chain in the complex)
it also comes with a python script that manages the job distribution on a Slurm cluster (although I will add an option to run it locally)
add documentation
test script
add some integration tests
review the code and see what crazy things I was doing 4 years ago
can confirm it's crazy
change fragment docker name to dockfragmentmover