Alyssa Travitz
be13099aee
fix formatting
2025-04-04 16:27:24 -07:00
Alyssa Travitz
d7f89cd6e2
making it look better in sphinx
2025-04-04 10:41:09 -07:00
Alyssa Travitz
f58e5372ec
fix cli list formatting
2025-04-04 10:22:50 -07:00
Alyssa Travitz
5b2b6334c3
Add lomap network generator ( #1082 )
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* add lomap_network_generator
* add news item
* switching to lomap as custom yaml test
* renaming var for clarity
* switch to cdk8 data
2025-01-31 12:23:35 -08:00
Josh Horton
fe5de586ef
Merge branch 'main' into cli-partial-charges
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# 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 )
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* 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
4c9a1f0b6f
xfail openeye nagl tests, update CLI ref docs
2025-01-29 16:31:35 +00:00
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
43efb185b4
Update openfecli/parameters/plan_network_options.py
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-01-20 13:48:48 +00:00
Josh Horton
e192f95a3c
Update openfecli/parameters/plan_network_options.py
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-01-20 13:48:39 +00:00
Josh Horton
c5e59004b9
Update openfecli/parameters/plan_network_options.py
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-01-20 13:48:33 +00:00
Josh Horton
aa53762e68
Update openfecli/parameters/plan_network_options.py
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Co-authored-by: Alyssa Travitz <31974495+atravitz@users.noreply.github.com >
2025-01-20 13:48:27 +00:00
Josh Horton
283d9e9ef0
add process pool, expose charge cli command
2025-01-16 15:57:43 +00:00
Josh Horton
c5f0371a38
Merge branch 'main' into cli-partial-charges
2025-01-16 10:21:18 +00:00
Alyssa Travitz
915d11022c
Support outdir created at runtime ( #1072 )
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* adding test
* create directories
* fixing a word
* update news
* update news
2025-01-14 16:50:37 +00:00
IAlibay
a5075eb350
update that one thing
2025-01-07 20:25:04 +00:00
IAlibay
b716571cbc
Testing out what partial charges could look over the CLI
2025-01-07 19:03:03 +00:00
Alyssa Travitz
bb90b0715c
Simplify settings help message ( #1052 )
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* reducing verbosity
* simplifying supported option specs
* clarifying settings wording
* add generate_radial_network as option
2024-12-20 08:37:01 -08:00
Alyssa Travitz
8374172479
add warning for unsupported settings yaml parameters ( #1051 )
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* adding warning and test
* be more precise about allowed fields handling
* using more explicit set notation
* add rever file
2024-12-13 12:49:09 -07:00
Alyssa Travitz
c2e4ee9bda
986 input validation for directory names ( #1024 )
2024-12-06 16:40:31 -08:00
Richard Gowers
1dd5d7eab6
update LomapAtomMapper default settings to established best practices ( #730 )
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* update LomapAtomMapper default settings to established best practices
* fixup tests for relative_alchemical_network_planner following lomap default change
make these tests use the legacy default settings for Lomap, they're just smoke testing and the actual mappings don't matter
* fixup regression tests for command line plan-rbfe
these are different now that the lomap defaults have been changed for 1.0
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
2024-03-26 19:49:35 -07:00
richard gowers
939f1abc93
docs: fix indentation on example yaml section
2024-02-22 13:43:05 +00:00
Richard Gowers
65ad6eaee5
docs: start better documenting CLI yaml possibilities
2024-02-22 13:05:57 +00:00
Benjamin Ries
7d40a633e4
Kartograf integration ( #249 )
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* preparing openFE for wally integration
* name n refactor
* improving import managment.
* fixing network changes..
* reverting network extraction
* reverting network extraction
* refactor
* adding license
* refactor name
* removing the layer too much.
* Update environment.yml
* Update kartograf_mapper.py
* Update openfe/setup/__init__.py
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
* Update environment.yaml
* Update environment.yml
* Update environment.yaml
* pin kartograf to v1.0.0 and above
* fixup merge mistake in generate_radial_network
* Update environment.yaml
* add kartograf integration to yaml cli
---------
Co-authored-by: Mike Henry <11765982+mikemhenry@users.noreply.github.com >
Co-authored-by: Richard Gowers <richardjgowers@gmail.com >
2023-11-17 18:04:33 +01:00
Richard Gowers
c96cb57163
Adds YAML input to CLI planning tools ( #583 )
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* [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
0c9703f086
use -C for cofactors input
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allow multiple cofactor files
2023-06-22 13:00:32 +01:00
richard gowers
be3b512364
add COFACTORS to cli parameters
2023-06-22 13:00:32 +01:00
David W.H. Swenson
98f7aee1f1
Merge branch 'main' into cli-moldir-cleanup
2023-05-03 14:51:14 -05:00
David W.H. Swenson
2ede42a09a
add test for multimol SDF
2023-05-02 19:29:54 -05:00
David W.H. Swenson
76ab2af747
finish molecules parameter
2023-05-02 19:03:35 -05:00
David W.H. Swenson
5fd25512b3
partial cleanup of moldir argument
2023-05-01 09:35:34 -05:00
David W.H. Swenson
1743cfe8a9
Remove openfe import to make help
2023-04-29 08:15:21 +01:00
richard gowers
8c3e32b220
cli: allow mol-dir command to unpack multi mol sdf files
2023-04-04 08:58:22 +01:00
richard gowers
76ea903f17
cli: use -M for mol-dir parameter
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avoids conflict with -m option
2023-04-04 08:58:22 +01:00
richard gowers
72e4a7b36c
cli: nest rdkit import inside functions
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improves cli import speed (responsiveness for help queries)
2023-04-04 08:58:22 +01:00
riesben
cc4f53b006
adding a little nicer desc
2023-04-04 08:58:22 +01:00
riesben
0a211f7f07
updates on cli from @swensons feedback.
2023-04-04 08:58:22 +01:00
bries
a80bd8ce15
cli Doctsrings
2023-04-04 08:58:22 +01:00
bries
56b3143a3f
git fixing cli tests
2023-04-04 08:58:22 +01:00
bries
67e43327ee
adding cli test, only need to fix one last
2023-04-04 08:58:22 +01:00
bries
8fe515596e
correcting params
2023-04-04 08:58:22 +01:00
riesben
9e713088da
rhfe and rbfe planner running first time
2023-04-04 08:58:22 +01:00
riesben
c8fd779cd5
minor changes, temporary forbid element changes - to be removed
2023-04-04 08:58:22 +01:00
riesben
880bd37515
fireup cli tool :)
2023-04-04 08:58:22 +01:00
riesben
3d290673d1
fireup cli tool :)
2023-04-04 08:58:22 +01:00
bries
4a470e2e47
adding proteinparam
2023-04-04 08:58:22 +01:00
bries
e33b8dfc06
improving the cmd tool
2023-04-04 08:58:22 +01:00
richard
d67350ea37
openfecli fixups following refactor
2023-02-06 10:00:43 +00:00
David W.H. Swenson
f06078268a
Error if JSON output file already exists
2022-10-24 14:10:46 -05:00
