rework handle_trajectories to use replicas #539
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
functions now expect a replica id, can trivially convert from state id to replica id trajectory_from_multistate can now either do constant-state or constant-replica trajectories
Codecov ReportPatch coverage:
Additional details and impacted files@@ Coverage Diff @@
## main #539 +/- ##
==========================================
- Coverage 92.07% 90.98% -1.09%
==========================================
Files 113 114 +1
Lines 6938 6876 -62
==========================================
- Hits 6388 6256 -132
- Misses 550 620 +70
☔ View full report in Codecov by Sentry. |
IAlibay
requested changes
Aug 29, 2023
openfe/utils/handle_trajectories.py
Outdated
| @@ -42,7 +42,7 @@ def _state_positions_at_frame(dataset: nc.Dataset, state_num: int, | |||
| ---------- | |||
| dataset : netCDF4.Dataset | |||
| Dataset containing the MultiState information. | |||
| state_num : int | |||
| replica_id : int | |||
| State index to extract positions for. | |||
There was a problem hiding this comment.
Shoudl this be changed to replica index?
openfe/utils/handle_trajectories.py
Outdated
| @@ -33,7 +32,8 @@ def _effective_replica(dataset: nc.Dataset, state_num: int, | |||
| return np.where(state_distribution == state_num)[0][0] | |||
|
|
|||
|
|
|||
| def _state_positions_at_frame(dataset: nc.Dataset, state_num: int, | |||
| def _state_positions_at_frame(dataset: nc.Dataset, | |||
IAlibay
approved these changes
Aug 29, 2023
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
functions now expect a replica id, can trivially convert from state id to replica id
trajectory_from_multistate can now either do constant-state or constant-replica trajectories
Developers certificate of origin