Irfan Alibay
d46db57e32
expose the septop and abfe analysis tutorials ( #1664 )
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-11-07 07:25:27 -08:00
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.
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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
d87dd8ffc0
fix nb link ( #1574 )
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* fix nb link
* bump examplenotebooks version
2025-10-13 18:56:26 +01:00
Hannah Baumann
7584efec66
SepTop Protocol ( #1057 )
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Adds an OpenMM-based SepTop Protocol.
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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
395ed35837
update notebook names ( #1279 )
2025-05-20 13:04:46 -07:00
Alyssa Travitz
0e21b35b00
Clean up tutorial index ( #1233 )
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* switch to concise bulleted list for clarity
* updating description
2025-04-23 15:52:46 -07:00
Alyssa Travitz
446ef8cb74
reordering tutorials ( #1141 )
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Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
2025-02-19 22:30:11 +00:00
Alyssa Travitz
cf20731ae4
Update docs/tutorials/index.rst
2025-02-11 08:21:20 -08:00
Josh Horton
0abc72d3ce
reorder tutorials and add links to cli tutorial
2025-02-11 13:41:11 +00:00
Josh Horton
503aa71d39
add tutorial description to the index
2025-02-07 09:56:32 +00:00
Josh Horton
356d934bf6
add links to tutorials
2025-02-07 09:51:38 +00:00
Mike Henry
e8492ea43c
debug script for people to test openmm ( #733 )
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* debug script for people to test openmm
* Added news entry
* added checking which platforms can do mixed p
* fix typo in debug script
* added how to run script
* point to new showcase
* give full path to assests to avoid copying notebooking into build env
* rerun ci
* fix mypy env
* looks like we still need to pin mypy but can relax python
---------
Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com >
2024-05-06 12:57:29 -07:00
Hannah Baumann
82125765a5
Merge branch 'main' into docs_protocol_cycles
2024-04-15 02:08:52 -07:00
richard gowers
e778e4fa21
docs: fix links to cookbook nblink entities
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this adds a reference anchor in the nbsphinx prolog for each nblink included cookbook
include rfe_alchemical_planners in cookbook list
2024-04-10 17:12:18 +01:00
IAlibay
6d0e1c0286
Change cookbook and tutorial links to refs
2024-04-10 17:12:18 +01:00
Hannah Baumann
d487f5fa6c
Merge branch 'main' into docs_protocol_cycles
2024-03-28 05:50:21 -07:00
Richard Gowers
936f4647ce
Update index.rst
2024-03-28 11:50:44 +00:00
Richard Gowers
b75f4cfc13
Update index.rst
2024-03-28 11:40:39 +00:00
hannahbaumann
6e86ea1460
change links relative
2024-03-28 12:36:23 +01:00
hannahbaumann
dee8177fbf
first pass relative protocol
2024-03-28 12:13:01 +01:00
IAlibay
3801cb1d89
clean up index
2024-03-27 16:57:45 +00:00
Irfan Alibay
a109099e68
Merge branch 'main' into add-tutorials
2024-03-27 16:46:10 +00:00
IAlibay
1e71f7426e
fix nblink
2024-03-27 16:13:47 +00:00
IAlibay
041aab3aa2
Add in the assets for the MD tutorial
2024-03-27 16:03:23 +00:00
IAlibay
f5e5ebe7ce
Add cinnabar entry
2024-03-27 13:52:03 +00:00
IAlibay
88d0b3895a
clean up index
2024-03-27 13:13:46 +00:00
IAlibay
b45b18f796
Merge remote-tracking branch 'origin/add_tutorial_md' into add-tutorials
2024-03-27 13:04:15 +00:00
IAlibay
d41e1cc6b3
clean up assets
2024-03-27 12:52:07 +00:00
IAlibay
fe6985d214
Add to toctree
2024-03-27 12:44:41 +00:00
IAlibay
a89bffe83b
Try to fix json
2024-03-27 12:39:39 +00:00
IAlibay
d5a5e101a4
Add nblink for ahfe tutorial
2024-03-27 12:00:18 +00:00
hannahbaumann
2ce3ce6e30
Small fixes
2024-03-01 08:49:35 -08:00
hannahbaumann
44df398c62
Remove extra field
2024-02-16 16:58:40 +01:00
hannahbaumann
b1e27ab40f
make underline header longer
2024-02-16 16:33:49 +01:00
hannahbaumann
8ba3b25863
Change inputs loc
2024-02-16 16:15:14 +01:00
hannahbaumann
0d39ec4d89
Add an MD totorial
2024-02-16 16:12:26 +01:00
Josh A. Mitchell
e2013b83f3
Merge branch 'main' into sideload_examples
2023-09-05 20:03:06 -04:00
Josh Mitchell
1549b181ec
More cookbooks
2023-09-05 18:34:35 +10:00
Josh Mitchell
f8ec78a7fd
Include inputs as well as assets in showcase nblink
2023-09-04 15:31:49 +10:00
Josh Mitchell
a1cf219935
Remove generated assets directory from git
2023-09-04 15:30:52 +10:00
richard gowers
754ce7ba04
docs: fixup typo in tutorial links
2023-08-31 14:47:19 +01:00
Josh Mitchell
d04cd0851c
Hide tutorial toctree
2023-08-30 17:54:29 +10:00
Josh Mitchell
370c4f6c42
Get existing tutorials rendering in Sphinx
2023-08-29 19:15:23 +10:00
David W.H. Swenson
6ece5d713a
Update links to docs
2023-05-12 14:17:47 -04:00
David W.H. Swenson
7e7db849cf
Fix links in docs
2023-05-12 05:57:05 -04:00
IAlibay
2d822300d7
update tutorials page
2023-05-08 11:40:11 +01:00
David W.H. Swenson
152fdf1f79
restructure following discussion today
2023-04-07 13:13:23 -05:00
