Alyssa Travitz
cb569010a0
update docs for multiple protocol units ( #1793 )
2026-01-16 16:00:27 +00:00
Alyssa Travitz
ea1ae647db
expose KartografAtomMapper alongside other AtomMappers ( #1751 )
2025-12-16 15:38:45 -08:00
Alyssa Travitz
a3e1108ad8
add docs for gathering septop and abfe ( #1737 )
...
* add autodocs for gathering septop and abfe
* update docstrings
* add blurb to openfe gather docs
* add missing docstrings
* add warning
* add zstandard to docs mocks
* Apply suggestions from code review
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
* add cinnabar to doc mocks
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2025-12-08 08:41:26 -08:00
Irfan Alibay
66d14f61bc
ABFE protocol ( #1045 )
...
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
Hannah Baumann
7584efec66
SepTop Protocol ( #1057 )
...
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
1cb3ac79f1
debug rtd build memory error ( #1510 )
...
* try mambaforge build
* Revert "try mambaforge build"
This reverts commit 683e07f1ea
2025-09-15 13:32:22 -07:00
Alyssa Travitz
148af2694c
Update cli docs ( #1264 )
2025-04-30 13:46:11 -07:00
Alyssa Travitz
31bb2a777d
make gufe lowercase in docs ( #1190 )
...
* make gufe lowercase in docs
* Update docs/reference/index.rst
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
* Update docs/reference/api/index.rst
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
2025-03-14 09:55:24 -07:00
Josh Horton
4c9a1f0b6f
xfail openeye nagl tests, update CLI ref docs
2025-01-29 16:31:35 +00:00
Mike Henry
e6b3d61a7c
add notes from review and do 1 sentence = 1 line
2024-04-18 02:41:51 -07:00
Richard Gowers
d316c52139
Update index.rst
2024-04-18 09:44:30 +01:00
Mike Henry
b562b2c57f
added note about the GUFE package
2024-04-17 10:25:47 -07:00
Hannah Baumann
82125765a5
Merge branch 'main' into docs_protocol_cycles
2024-04-15 02:08:52 -07:00
richard gowers
aca53b1d89
docs: create quickrun execution page
2024-04-10 09:57:15 +01:00
hannahbaumann
6033481d16
small fix 2
2024-03-27 15:41:01 +01:00
hannahbaumann
752cfb253c
add details afe
2024-03-27 15:02:32 +01:00
IAlibay
fd91902469
Clean up unique settings entries
2024-03-08 17:53:45 +00:00
IAlibay
eb149bb00c
Moving settings around
2024-03-08 17:13:29 +00:00
IAlibay
f0db7a94b1
Add index entries for AFE specific duplicate settings
2024-03-08 13:52:18 +00:00
IAlibay
6779a463a4
Add top level settings entry for AFE solvation
2024-03-08 13:18:57 +00:00
IAlibay
295a03d747
Add settings entries for plain MD protocol
2024-03-08 12:05:54 +00:00
IAlibay
2dcc8f5680
Some more changes
2024-03-07 18:28:56 +00:00
IAlibay
d6b49fbe46
Checking that adding the settings to the one page works
2024-03-07 16:26:48 +00:00
richard gowers
4a2cf82694
docs: add openmm_md protocol page stub
...
split ligand_network page into two
first atom mappings and scorers
then entire page to ligand networks
2024-02-15 13:10:12 +00:00
richard gowers
99a94a6836
docs: remove Component from docs
...
this is a base class which isn't immediately usable
2024-02-15 13:10:12 +00:00
richard gowers
da6a1b5423
docs: remove Data Objects reference page
...
GufeTokenizable isn't relevant to openfe docs
2024-02-15 13:10:12 +00:00
richard gowers
1bd5e7c15b
remove old doc stubs for solvation
2024-02-06 17:55:07 +00:00
richard gowers
2a948cc0c4
remove doc stubs for removed settings
2024-02-06 11:50:24 +00:00
hannahbaumann
ef55cc9cda
add autopydantic entries for LambdaSettings
2024-01-12 13:43:26 +01:00
Richard Gowers
e60580c861
use Lomap package's bindings ( #478 )
...
* use Lomap package's bindings
* fix mypy complaints
* Code via suggestions because local branch is borked
Why can't I push this from my local?
* Update openfe/setup/atom_mapping/lomap_scorers.py
* try exporting __all__ (make RTD happy too)
* guess mypy didn't like that at __all__
* Oh, *that* would be how to fix the warning about mocks
* Update environment.yaml
* Update environment.yml
* Update conf.py
* remove lomap docs
* try adding lomap to docs build
* try adding lomap scorer docs back
* add generate_lomap_network to docs
* Update environment.yml
---------
Co-authored-by: David W.H. Swenson <david.swenson@omsf.io >
2023-11-03 11:20:37 +00:00
IAlibay
35b7735859
Add solvation_afe to doc index
2023-10-16 06:55:05 +01:00
IAlibay
51600637e3
noindex on settings
2023-10-11 05:16:13 +01:00
Irfan Alibay
77e67d9188
Merge branch 'main' into ahfe-refactor
2023-10-11 05:00:11 +01:00
IAlibay
73165431a3
try to fix the docs
2023-10-09 00:24:45 +01:00
Josh Mitchell
1549b181ec
More cookbooks
2023-09-05 18:34:35 +10:00
Josh Mitchell
96e119ff3d
Add loader links to flowchart
2023-08-29 14:22:40 +10:00
Josh Mitchell
588115fae1
Merge branch 'main' into more_api_refs
2023-08-29 14:20:35 +10:00
Josh Mitchell
5458def7de
Document GufeTokenizable
2023-08-28 18:59:25 +10:00
Josh Mitchell
b3921e8919
Switch subheading order in alchemical network ref page
2023-08-28 18:40:54 +10:00
Josh Mitchell
333c57c62d
Remove unimplemented TMCSR scorer from docs
2023-08-28 18:40:04 +10:00
Josh Mitchell
387da49f4b
Fix warnings and ensure everything is documented appropriately
2023-08-22 20:33:59 +10:00
Josh Mitchell
a53fc782b7
Reorganise API docs
2023-08-22 13:48:16 +10:00
Josh Mitchell
cbc4caac2f
Add executors anchor to reference
2023-08-21 20:40:44 +10:00
Josh Mitchell
05c074cf1b
More flowcharts
2023-08-17 12:17:12 +10:00
Josh Mitchell
7019be792a
Fix warnings
2023-08-10 13:28:01 +10:00
Josh Mitchell
59159f8434
Improve flowchart
2023-08-10 12:40:48 +10:00
Josh Mitchell
3d5e4a0ad1
Fix field ordering
2023-07-27 12:24:48 +10:00
Josh Mitchell
096b6e2e5a
Fix links in settings docs
2023-07-20 18:14:22 +10:00
Josh Mitchell
c0d747fdae
Limit reference TOC depth
2023-07-20 18:05:51 +10:00
Josh Mitchell
6c4943734d
Hide misleading field list from settings docs
2023-07-20 17:55:49 +10:00
