84 Commits

Author	SHA1	Message	Date
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	6dcf88467f	back to bold	2024-11-12 17:00:21 -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	e2c6c4e7d1	Update docs/guide/setup/index.rst ... 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 ... 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
Alyssa Travitz	5173b30f2b	edits to atom mappings and scores	2024-10-31 15:10:05 -07:00
Alyssa Travitz	1cca06856c	edits to chemical systems docs	2024-10-31 14:39:15 -07:00
Alyssa Travitz	22d9751f7b	setup index edits	2024-10-31 13:52:34 -07:00
Alyssa Travitz	4b90b00e1f	adding cross-page references	2024-10-31 13:30:36 -07:00
Richard Gowers	c6d1835634	Update chemical_systems_and_thermodynamic_cycles.rst	2024-04-16 17:02:08 +01:00
richard gowers	b50eb51211	docs: chemical system docs review comments	2024-04-16 14:04:32 +01:00
Richard Gowers	7a538ecf5f	Apply suggestions from code review ... Co-authored-by: Hannah Baumann <43765638+hannahbaumann@users.noreply.github.com>	2024-04-16 14:00:40 +01:00
richard gowers	53f8e297c5	docs: fixup reference to chemical systems docs	2024-04-15 12:26:10 +01:00
richard gowers	7c9d6de8a6	docs: add image of RBFE thermo cycle to chemical system docs	2024-04-15 12:26:01 +01:00
Richard Gowers	220d46333b	Merge branch 'main' into issue_759_chemical_system	2024-04-15 11:48:06 +01:00
Hannah Baumann	82125765a5	Merge branch 'main' into docs_protocol_cycles	2024-04-15 02:08:52 -07:00
richard gowers	c1d2a2b258	docs: more tweaks following review	2024-04-12 14:52:44 +01:00
Richard Gowers	ab6c254102	Apply suggestions from code review ... Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>	2024-04-12 14:49:04 +01:00
richard gowers	7e41f93582	docs: tweaks following review	2024-04-12 13:01:19 +01:00
Irfan Alibay	3e9b847c1c	Update docs/guide/setup/creating_ligand_networks.rst	2024-04-11 12:27:58 +01:00
Benjamin Ries	717778bc70	Update docs/guide/setup/creating_ligand_networks.rst ... Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>	2024-04-11 11:34:24 +02:00
Irfan Alibay	647d8a72cb	Merge branch 'main' into docs-ligandNetworks-rework	2024-04-11 07:59:38 +01:00
richard gowers	e778e4fa21	docs: fix links to cookbook nblink entities ... 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	a92604dc47	Actually copy over the right image	2024-04-10 17:12:18 +01:00
IAlibay	d2d41469d8	switch to Hannah's image for the AlchemicalNetwork	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
IAlibay	9cbaa137e5	uncommited stuff	2024-04-10 17:12:18 +01:00
IAlibay	7d3a39f2a9	fix create_alchemical_network cookbook link	2024-04-10 17:12:18 +01:00
IAlibay	c827a67adc	fix rbfe_cli_tutorial link	2024-04-10 17:12:18 +01:00
IAlibay	2fc8776598	relative links	2024-04-10 17:12:18 +01:00
IAlibay	60b57eaabd	update index	2024-04-10 17:12:18 +01:00
IAlibay	0c5cb0ced0	remove duplicate files and add reference label	2024-04-10 17:12:18 +01:00
IAlibay	e1f571627f	add reference label	2024-04-10 17:12:18 +01:00
IAlibay	1eedfb53fe	update note	2024-04-10 17:12:18 +01:00
IAlibay	d8c705f2eb	Add alchemical network creation userguide page	2024-04-10 17:12:18 +01:00
Irfan Alibay	e80a5cbc1f	Merge branch 'main' into docs-ligandNetworks-rework	2024-04-10 09:33:03 +01:00
Hannah Baumann	321de67bf4	Update docs/guide/setup/index.rst ... Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>	2024-04-08 09:47:03 +02:00
riesben	8729fe0004	including comments from #793	2024-04-06 09:13:40 +02:00
hannahbaumann	990e57870d	addressing review	2024-04-05 16:29:37 +02:00