Builders for classical md workflows #1088
Open
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
orionarcher
force-pushed
the
md_core_and_builders
branch
from
7dd7a46
to
bc2265b
Compare
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #1088 +/- ##
==========================================
- Coverage 90.03% 89.93% -0.10%
==========================================
Files 147 154 +7
Lines 13460 13883 +423
==========================================
+ Hits 12119 12486 +367
- Misses 1341 1397 +56 ☔ View full report in Codecov by Sentry. |
2 tasks
orionarcher
force-pushed
the
md_core_and_builders
branch
from
bc2265b
to
8a5cf93
Compare
orionarcher
force-pushed
the
md_core_and_builders
branch
from
8a5cf93
to
73a02e1
Compare
orionarcher
force-pushed
the
md_core_and_builders
branch
from
73a02e1
to
9f37353
Compare
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Outdated suggestions cannot be applied.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.
This PR implements ElectrolyteBuilder and SolventBenchmarkBuilder classes for analysis of trajectories generated by atomate2.openmm.
The core Builder classes are supported by a variety of utility functions that interact with MDAnalysis, SolvationAnalysis, and TransportAnalysis. In addition to the usual get_items, process_items, update_targets workflow, users can also manually create an MDAnalysis.Universe directly from the taskdoc with ElectrolyteBuilder.instantiate_universe. This makes manual analysis of a small number of systems much easier.
Everything is reasonably well tested and once CI passes this will be ready for review.
NOTE: this is essentially a vastly cleaned up version of PR #1010. I linearized the commit history so that this PR is an update of PR #1087, which can be reviewed separately and merged independently of this PR.