Brownbp1/pharmmap fld #3
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…yet. Major changes include making the mutates serializable, removing most of the member data from the thread manager, adding final metrics, removing a bunch of extraneous crap that was deprecated by the expansion of the FragmentMutateInterface, and finally just some general cleanup.
…ed FLD to take a CheminfoProperty instead of a ScoreFunctionGeneric. I still construct the ScoreFunctionGeneric from the CheminfoProperty, though the constructor is hard-coded. If I want to alter other parts of ScoreFunctionGeneric from default, for example the calculation_type, I will need to expose those as options to FLD and pass them to the Worker struct.
…utateDecisionNode. There was a second one with the MutateRepeater, but for now I just commented out the repeater code, effectively making that cmdline flag useless. I have been debating making FragmentMutateInterface compound mutates anyway. But this is minor, can fix later. Otherwise seems to be working.
… another location.
…mentMutateInterface. Before it was just a string that was parsed in MapConformer as a CheminfoProperty, but we really should serialize it at the level of FragmentMutateInterface and pass it on down.
… to prepare molecules for input to FLD or Mutate.
…ure enhancement to Mutate to allow output of only final structure.
…e so that users have control over molecule standardization independent of the mutate used. Will also allow some more complex compound mutates. Some food for thought - consider allowing skipping of all Cleaning in a mutate if that mutate is just a step along a path for which we do not expect reasonable geometries and whatnot.
…Basically just expanding a the moveable indices during 3D conformer generation outside of RingSwap.
…evisited later, though. May be deeper issues related to the PossibleAtomTypes class that need addressed. Updated options.
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Looking to see if there is anything non-redundant in this branch to move over