Openff handlers #1
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allow multiple protein_ffs (again)
incorporate openff interchange valence handlers
fix try except for off reversible bond handler
add ff to smirnoff_interchange
add precomputed lennard jones handler for openff mol
specify type of lennard jones precomputed handler as off
add `load_precomputed_off_default` to `Forcefield` as class method
allow passing of openff Molecule to rbfe. must yet modify single_topology
add space filling params, smirks, props, counts params for OFF bonded handlers
allow passing openff molecule object to `BaseTopology`; subclassing is hard so used some if else statements :/
pass off Molecule to single topology and parameterizers/handlers
bad `value` import
bad import value in handlers/nonbonded
rearrange `pass_mol_as_rdkit`
import `pass_mol_as_rdkit`
util import of `pass_mol_as_rdkit`
single top import of `pass_mol_as_rdkit`
pass self mol attribute in AtomMixin
use self.mol again for SingleTopology in init method
load off forcefield differently for nonbonded handler
add off Forcefield to bonded handler
forgot self attr in `static_parameterize` in OFF bonded handlers
rework getter for off handler in static_parameterize
fix `generate_off_idxs_params` with potential params
handle good arrays with None
fix returnable outside loop
add none params to precomputed lj handler
add partial/parameterize functionality to off lj handler
…oteneer#1281) * Adds failing test * Fixes TIBDExchange by using the correct weights * Adds check for the likelihood of moving the selected water * Updates the targeted exchange reference data
add parameterization mol for `DualTopology`
allow openff mol to minimizer
add param_mol to `setup_optimized_host`
allow saving of only endstate frames as default.
adding divisor by idivf to torsion and improper torsion because idk why this is a thing.
add test for `BaseTopology` energy validation with both rdkit and openff mol routines
add single topology validation check on hif2a ligands; fails due to inconsistent treatment of dummy atoms/groups...
allow kwargs to `run_sims_hrex`
allow to not save hrex trajs at all because memory and disk space.
changed my mind about nesting hrex saves; don't place them here.
remove kwargs, and save baseline mol (either rdkit or openff mol) in rbfe calc
allow saving or not saving of trajs
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integrate openff.Molecule parameterization route for rbfes.