13 Commits

Author	SHA1	Message	Date
Josh Horton	fe5de586ef	Merge branch 'main' into cli-partial-charges ... # Conflicts: # openfecli/commands/plan_rbfe_network.py # openfecli/commands/plan_rhfe_network.py # openfecli/parameters/__init__.py # openfecli/parameters/misc.py # openfecli/tests/commands/test_plan_rbfe_network.py # openfecli/tests/commands/test_plan_rhfe_network.py	2025-01-30 11:07:09 +00:00
Alyssa Travitz	00445dcf5c	add support for one repeat per json (#1076) ... * add n_protocol_repeats as cli parameter * add news item * update tests * add docstrings * adding n_repeats test * switch test to use full --n-protocol-repeats flag * updating help msg * updating news entry * Update openfecli/parameters/misc.py Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com> --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>	2025-01-29 14:23:15 -08:00
Josh Horton	c46e7c1e5a	add charges to cofactor sdf, fix docs, expose overwrite charges to plan CLI	2025-01-24 11:39:39 +00:00
Josh Horton	8602a39aa6	move ncores cli flag, fix tests, add tests for charge generation	2025-01-20 15:53:43 +00:00
Josh Horton	283d9e9ef0	add process pool, expose charge cli command	2025-01-16 15:57:43 +00:00
Richard Gowers	c96cb57163	Adds YAML input to CLI planning tools (#583) ... * [skip ci] draft of yaml format for CI * adds yaml reader for cli options input fixes #580 * change plan_rXfe_network_main functions to expect list of mappers * move settings yaml parsing to be parameter * add YAML_OPTIONS as parameter * add YAML_OPTIONS to plan_rbfe_network currently does nothing * cli: add interpretation of settings yaml * cli: enable settings yaml reading in plan_rbfe_network * cli: some extra documentation on load_yaml * cli: fix tests to account for normalisation * cli: add test for custom rbfe yaml usage * cli: update plan_rhfe to allow yaml options * cli: use v1/2 compatible Pydantic * cli: fixup pydantic v1/2 compat * remove draft yaml idea * cli: centralise parsing of yaml options and defaults * add pyyaml to deps --------- Co-authored-by: Irfan Alibay <IAlibay@users.noreply.github.com>	2023-11-17 10:56:09 +00:00
richard gowers	be3b512364	add COFACTORS to cli parameters	2023-06-22 13:00:32 +01:00
David W.H. Swenson	5fd25512b3	partial cleanup of moldir argument	2023-05-01 09:35:34 -05:00
riesben	9e713088da	rhfe and rbfe planner running first time	2023-04-04 08:58:22 +01:00
riesben	880bd37515	fireup cli tool :)	2023-04-04 08:58:22 +01:00
bries	4a470e2e47	adding proteinparam	2023-04-04 08:58:22 +01:00
David W.H. Swenson	c8a9cf1465	Combine visualization with CLI (#72) ... Co-authored-by: richard <richard@nextmovesoftware.com>	2022-03-01 15:07:10 +00:00
David W.H. Swenson	41068e0185	CLI for AtomMapping (#57) ... * Initial skeleton for the CLI Currently requires the OPS CLI to be installed as well; next steps: 1. Add parameter core classes to infrastructure 2. Fully separate infrastructure into its own package * switch to using plugcli * tests for CLI * helps if you add the tests... * pep8 and deps cleanup * add test_plugins * Start of CLI atommapping report * Add tests for parameters * Almost-working atommapping command * add hack to work-around lomap issue * fix test * pep8; docstrings; add header comments * Add tests for commands/atommapping * docstrings * add init to command to stop circular import error * remove init and it still works? Co-authored-by: richard <richard@nextmovesoftware.com>	2022-02-23 16:43:01 +00:00