Merge pull request #513 from RosettaCommons/roccomoretti/re-startfrom
Update StartFrom ligand docking mover
* Fix a bug where (in practice) only the first position would ever be chosen if multiple positions were given in the XML tag.
* Unify the JSON file handling - you can now put multiple positions for the same protein in the same JSON file. Also, you can mix and match specification type, and it now recognizes default (no-tag) specifications.
* Add the ability to specify the start from positions with the heavyatom positions in a PDB file - useful if you want to place the ligand graphically with PyMol.
* Add option to place the ligand based on the neighbor atom (the constant point for conformer overlay) rather than the all-atom coordinate centroid.
* Generally clean up the code
New unit tests, but otherwise no tests expected.