Irfan Alibay
66d14f61bc
ABFE protocol ( #1045 )
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Add an Absolute Binding Free Energy Protocol to openfe.
Key features & limitations:
* Automatic Boresch restraint assignment.
* Does not handle net charge corrections yet.
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
Co-authored-by: hannahbaumann <hbaumann@uci.edu >
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
2025-10-21 11:45:37 +01:00
Alyssa Travitz
141960944b
deprecate openfe utils 3dviz in favor of gufe method ( #1592 )
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* deprecate openfe utils 3dviz in favor of gufe method
* add news item
* update news
* fix deprecation warning capture
* update guide
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2025-10-20 23:56:23 +00:00
Josh Horton
f681d5160b
add a note on the equilibration method ( #1581 )
2025-10-15 13:16:06 +00:00
Alyssa Travitz
4e603a1609
update docs theme ( #1545 )
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* adding new branding assets
* remove images
* update theme branch
* CantinaPurple accent
* lowercase convention
* updating text
* remove dark mode for now
* fix sidebars
* fix formatting
* capitalization
* don't break spaces
* bump ci
* favicon!
* whitespace :(
* pin to sphinx release
2025-10-02 10:13:25 -04:00
Hannah Baumann
ac06d1ca83
SepTop: Addressing issues raised in review ( #1532 )
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* SepTop docs improvements lambda schedule and restraint selection
* Remove set_openmm_threads_1 logic from test_septop_slow
* change femto acknowledgements
* update method docstring limitations
* Make sure we fail when we have virtual sites and reassign_velocities is False
* clean up usage of openmm imports
* clean up equil settings output indices so that it enforces all
* generate smc_off_B on the fly
* Update enforcement of all output indices
* Simulation overview unclear on if the same restraint is used between repeats
* Add test for output indices validation
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2025-09-29 10:39:51 +01:00
Hannah Baumann
7584efec66
SepTop Protocol ( #1057 )
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Adds an OpenMM-based SepTop Protocol.
---------
Co-authored-by: IAlibay <IAlibay@users.noreply.github.com >
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
Co-authored-by: Josh Horton <joshua.horton@openforcefield.org >
2025-09-23 09:52:11 +01:00
Alyssa Travitz
9f0800ffbb
update quickrun execution docs and add MPS link ( #1483 )
2025-08-21 08:52:37 -07:00
Irfan Alibay
abfb62c95f
Update userguide's ligand network wording for how scores are used. ( #1382 )
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* Update userguide's ligand network wording for how scores are used.
* Update creating_ligand_networks.rst
2025-06-25 16:19:52 +00:00
Alyssa Travitz
aaf6fddbd8
improve ligand network description ( #1172 )
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* hide todo from output
* trying to make ligand network description clearer
* adding api links
* updating language for clarity
* typo
2025-06-23 13:52:32 -07:00
Alyssa Travitz
e369a20b19
comment out TODO that was getting rendered ( #1375 )
2025-06-13 13:49:43 -07:00
Alyssa Travitz
148af2694c
Update cli docs ( #1264 )
2025-04-30 13:46:11 -07:00
Alyssa Travitz
939a7bdd29
moving under the hood to the user guide ( #1221 )
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* moving under the hood to the user guide
* adding pip to docs env dependencies
2025-04-03 12:19:12 -07:00
Alyssa Travitz
66ac2bdc64
migrate json loading to new gufe syntax ( #1177 )
...
* updates to cli from_json
* replacing dump instances with to_json
* Remove unnecessary imports of JSON_HANDLER
* addressing review
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
Co-authored-by: David L. Dotson <dotsdl@gmail.com >
2025-03-25 23:32:26 +00:00
IAlibay
9546bdbd07
Add some docs
2025-03-10 10:46:24 +00:00
Josh Horton
54a4d2b8da
Merge branch 'main' into charge_warning
2025-02-12 10:49:26 +00:00
Alyssa Travitz
f7b11d45b1
remove "easy_" prefix from cli output ( #1121 )
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* easy_rbfe -> rbfe
* remove addressed TODO
* adding news item
* easy_rhfe -> rhfe prefix
2025-02-11 14:43:21 -08:00
Alyssa Travitz
102c848168
Update docs/guide/introduction.rst
2025-02-11 08:21:11 -08:00
Josh Horton
0abc72d3ce
reorder tutorials and add links to cli tutorial
2025-02-11 13:41:11 +00:00
Josh Horton
0d8a3e3148
add a note on charge generation during network planning
2025-02-06 10:36:53 +00:00
Alyssa Travitz
4bb24610dd
Merge branch 'main' into cli-partial-charges
2025-01-30 07:21:06 -08:00
Josh Horton
ea1589a26b
fix docs
2025-01-29 17:26:58 +00:00
Josh Horton
80b632c159
Merge branch 'main' into cli-partial-charges
2025-01-29 17:16:42 +00:00
Josh Horton
a07608de8d
Merge branch 'main' into bootstrap_error
2025-01-29 17:15:33 +00:00
Josh Horton
4c9a1f0b6f
xfail openeye nagl tests, update CLI ref docs
2025-01-29 16:31:35 +00:00
Josh Horton
8552fff0a3
format list
2025-01-29 11:18:47 +00:00
Josh Horton
4caf47c173
Update docs/guide/execution/quickrun_execution.rst
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-01-29 11:11:06 +00:00
Josh Horton
c4d102f363
Update docs/guide/execution/quickrun_execution.rst
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-01-29 11:10:36 +00:00
Josh Horton
7e320e4630
Update docs/guide/execution/quickrun_execution.rst
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-01-29 11:10:29 +00:00
Josh Horton
b0405cf16b
add --n-protocol-repeats flag info
2025-01-24 13:49:41 +00:00
Josh Horton
d0920a0008
add info on parallel execution and gathering
2025-01-24 13:39:56 +00:00
Josh Horton
6b775a2c16
add news, update docs and fix typos
2025-01-16 10:17:50 +00:00
Alyssa Travitz
e9aaf1f5c7
revert ligand network section to be addressed later
2024-11-15 07:29:39 -08:00
Alyssa Travitz
3b66c5c985
adding See Also section back to alchemical network
2024-11-15 07:29:39 -08:00
Alyssa Travitz
4273a36607
Apply suggestions from code review
...
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
2024-11-14 17:19:25 -08:00
Alyssa Travitz
0c8f1304b9
making warning more visible
2024-11-14 12:53:04 -08:00
Alyssa Travitz
6dcf88467f
back to bold
2024-11-12 17:00:21 -08:00
Alyssa Travitz
96cb6f1d66
renaming to Results Gathering
2024-11-12 16:51:38 -08:00
Alyssa Travitz
10e13e71c8
making protocol description clearer
2024-11-12 16:50:36 -08:00
Alyssa Travitz
93eb486b7e
making language clearer
2024-11-12 15:09:14 -08:00
Alyssa Travitz
360e317a04
fixing typo
2024-11-12 11:43:41 -08:00
Alyssa Travitz
83d1093cab
fixing bash rendering
2024-11-12 11:43:41 -08:00
Alyssa Travitz
5a7737cd9e
Apply suggestions from code review
...
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com >
2024-11-12 11:41:24 -08:00
Alyssa Travitz
38958712fa
Apply suggestions from code review
...
Co-authored-by: Iván Pulido <2949729+ijpulidos@users.noreply.github.com >
Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com >
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2024-11-12 11:27:12 -08:00
Alyssa Travitz
0b2978d71f
adding links to introduction
2024-11-12 11:07:13 -08:00
Alyssa Travitz
e2c6c4e7d1
Update docs/guide/setup/index.rst
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2024-11-05 14:34:50 -08:00
Alyssa Travitz
e1926966d9
Update docs/guide/setup/defining_protocols.rst
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Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2024-11-05 14:33:29 -08:00
Alyssa Travitz
fae1a9dbb3
edits to alchemical network planners
2024-11-01 14:35:07 -07:00
Alyssa Travitz
52ff058f03
edits to ligand networks guide
2024-11-01 13:38:49 -07:00
Alyssa Travitz
4544d6064e
updating protocol user guide docs
2024-11-01 13:22:33 -07:00
Alyssa Travitz
4982c71307
formatting fixes to atom mappings
2024-11-01 12:45:20 -07:00
