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[PAPRIKA] Host-Guest Free Energy Gradients #342

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[PAPRIKA] Host-Guest Free Energy Gradients #342

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24f3fc0
paprika - implement gradient protocol for host-guest binding
jeff231li Jan 16, 2021
e7849cf
fix docstring
jeff231li Jan 16, 2021
eef5b34
fix bug
jeff231li Jan 16, 2021
15df1b3
lint
jeff231li Jan 16, 2021
b435a12
fix time step default option
jeff231li Jan 16, 2021
b4ea18a
fix coordinate offset
jeff231li Feb 2, 2021
3fc217e
Merge branch 'master' into paprika-gradient-support
jeff231li Feb 2, 2021
4c8f029
fix openff-toolkit import namspace
jeff231li Feb 2, 2021
c7b45d2
update tests
jeff231li Feb 2, 2021
4577f9b
Merge remote-tracking branch 'origin/master' into paprika-gradient-su…
jeff231li Feb 17, 2021
03dc126
update paprika namespace
jeff231li Feb 17, 2021
65b7d94
fix namespace
jeff231li Feb 17, 2021
dc9e033
fix paprika namespace in tests
jeff231li Feb 18, 2021
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2 changes: 2 additions & 0 deletions openff/evaluator/datasets/taproom/taproom.py
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Original file line number Diff line number Diff line change
Expand Up @@ -398,6 +398,8 @@ def _build_metadata(
"n_pull_windows": n_pull_windows,
"release_windows_indices": [*range(len(attach_lambdas))],
"release_lambdas": release_lambdas,
"bound_window_index": [[*range(n_pull_windows)][0]],

@SimonBoothroyd SimonBoothroyd Feb 2, 2021

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Should bound_window_index and unbound_window_index be lists, or can they just be single values? I think if they can be single values this will simplify _paprika_build_end_states_protocol by a fair bit!

@jeff231li jeff231li Feb 3, 2021

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I set bound_window_index and unbound_window_index as lists because template_values from ProtocolReplicator requires a list as input. Are you referring to setting template_value and template_index instead?

openff-evaluator/openff/evaluator/workflow/schemas.py

Lines 136 to 138 in e55c86b

def apply(
self, protocols, template_values=None, template_index=-1, template_value=None
):

"unbound_window_index": [[*range(n_pull_windows)][-1]],
}
)

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