Merge pull request #4017 from RosettaCommons/aleaverfay/matcher_bugfix_Jun2019
Aleaverfay/matcher bugfix jun2019
Belatedly fixing two bugs in the matcher brought to my attention by Indrek Kalvet.
1) When using ligand conformers, the "relevant atoms" (not the clearest of designations, tbh) needs to include not only the atoms that define the protein/ligand contact, but also the atoms that define the ligand's orientation -- the "orientation atoms" (oats). When these were not included in the list of relevant atoms by the MatcherTask, then two ligand conformers with very different locations for the protein-contacting atoms could be treated as equivalent. Once equivalent, then only the location of the oats is used to decide if the two conformers represent a match. This led to some pretty outrageous "matches" where the active site residues were ~8 A away from the Zn they were meant to be 2 A from.
2) When using the -dynamic_grid_refinement flag, it turned out that the process of estimating how many matches would be formed for a certain grid spacing was wicked slow. As a result, it was not really a time savings.
All of Indrek's test cases now look good.