From d9e75ee1a929e917895e176d7d233623a7ebd861 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 17 Jan 2025 09:31:30 -0800 Subject: [PATCH 1/6] adding TODO --- openfecli/parameters/plan_network_options.py | 1 + 1 file changed, 1 insertion(+) diff --git a/openfecli/parameters/plan_network_options.py b/openfecli/parameters/plan_network_options.py index bdca9318c..ab0e8d091 100644 --- a/openfecli/parameters/plan_network_options.py +++ b/openfecli/parameters/plan_network_options.py @@ -159,6 +159,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption 'mst': generate_minimal_spanning_network, 'generate_minimal_redundant_network': generate_minimal_redundant_network, 'generate_maximal_network': generate_maximal_network, + # TODO: add lomap network generator } try: From dbceeb03c8a7f461dd4884d5ec8609b4f3317ab2 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 17 Jan 2025 11:16:14 -0800 Subject: [PATCH 2/6] add lomap_network_generator --- openfecli/parameters/plan_network_options.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/openfecli/parameters/plan_network_options.py b/openfecli/parameters/plan_network_options.py index ab0e8d091..11b4ee652 100644 --- a/openfecli/parameters/plan_network_options.py +++ b/openfecli/parameters/plan_network_options.py @@ -106,6 +106,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption generate_minimal_spanning_network, generate_maximal_network, generate_minimal_redundant_network, + generate_lomap_network, ) from openfe.setup import ( LomapAtomMapper, @@ -159,7 +160,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption 'mst': generate_minimal_spanning_network, 'generate_minimal_redundant_network': generate_minimal_redundant_network, 'generate_maximal_network': generate_maximal_network, - # TODO: add lomap network generator + 'generate_lomap_network': generate_lomap_network, } try: From 29e0652a2deb19ff51ca72cec25da352409912f3 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 17 Jan 2025 11:21:30 -0800 Subject: [PATCH 3/6] add news item --- news/add_lomap_network_generator_to_cli.rst | 23 +++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 news/add_lomap_network_generator_to_cli.rst diff --git a/news/add_lomap_network_generator_to_cli.rst b/news/add_lomap_network_generator_to_cli.rst new file mode 100644 index 000000000..9cf0564fc --- /dev/null +++ b/news/add_lomap_network_generator_to_cli.rst @@ -0,0 +1,23 @@ +**Added:** + +* Added CLI support for ``generate_lomap_network``. This option can be specified as a `YAML-defined setting `_ + +**Changed:** + +* + +**Deprecated:** + +* + +**Removed:** + +* + +**Fixed:** + +* + +**Security:** + +* From 88edd93a0e186f97f13a446a9909afbaaaa8dbb4 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Thu, 30 Jan 2025 16:00:17 -0800 Subject: [PATCH 4/6] switching to lomap as custom yaml test --- openfecli/tests/commands/test_plan_rbfe_network.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/openfecli/tests/commands/test_plan_rbfe_network.py b/openfecli/tests/commands/test_plan_rbfe_network.py index 25b703811..5f8ea1eae 100644 --- a/openfecli/tests/commands/test_plan_rbfe_network.py +++ b/openfecli/tests/commands/test_plan_rbfe_network.py @@ -210,9 +210,9 @@ def test_plan_rbfe_network_charge_changes(cdk8_files): def custom_yaml_settings(): return """\ network: - method: generate_minimal_redundant_network + method: generate_lomap_network settings: - mst_num: 2 + max_path_length: 6 mapper: method: LomapAtomMapper @@ -221,8 +221,7 @@ def custom_yaml_settings(): element_change: True """ - -def test_custom_yaml_plan_rbfe_smoke_test(custom_yaml_settings, eg5_files, tmpdir): +def test_lomap_yaml_plan_rbfe_smoke_test(custom_yaml_settings, eg5_files, tmpdir): protein, ligand, cofactor = eg5_files settings_path = tmpdir / "settings.yaml" with open(settings_path, "w") as f: From fa8447d50a96fc7118c76982221b980eaacda189 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 31 Jan 2025 08:25:33 -0800 Subject: [PATCH 5/6] renaming var for clarity --- openfecli/parameters/plan_network_options.py | 1 + openfecli/tests/commands/test_plan_rbfe_network.py | 6 +++--- 2 files changed, 4 insertions(+), 3 deletions(-) diff --git a/openfecli/parameters/plan_network_options.py b/openfecli/parameters/plan_network_options.py index 11b4ee652..cc5b623b4 100644 --- a/openfecli/parameters/plan_network_options.py +++ b/openfecli/parameters/plan_network_options.py @@ -194,6 +194,7 @@ def load_yaml_planner_options(path: Optional[str], context) -> PlanNetworkOption - `generate_minimal_spanning_tree` - `generate_minimal_redundant_network` - `generate_radial_network` + - `generate_lomap_network` The `settings:` allows for passing in any keyword arguments of the method's corresponding Python API. diff --git a/openfecli/tests/commands/test_plan_rbfe_network.py b/openfecli/tests/commands/test_plan_rbfe_network.py index 5f8ea1eae..144022791 100644 --- a/openfecli/tests/commands/test_plan_rbfe_network.py +++ b/openfecli/tests/commands/test_plan_rbfe_network.py @@ -207,7 +207,7 @@ def test_plan_rbfe_network_charge_changes(cdk8_files): @pytest.fixture -def custom_yaml_settings(): +def lomap_yaml_settings(): return """\ network: method: generate_lomap_network @@ -221,11 +221,11 @@ def custom_yaml_settings(): element_change: True """ -def test_lomap_yaml_plan_rbfe_smoke_test(custom_yaml_settings, eg5_files, tmpdir): +def test_lomap_yaml_plan_rbfe_smoke_test(lomap_yaml_settings, eg5_files, tmpdir): protein, ligand, cofactor = eg5_files settings_path = tmpdir / "settings.yaml" with open(settings_path, "w") as f: - f.write(custom_yaml_settings) + f.write(lomap_yaml_settings) assert settings_path.exists() From 9203f60b82e7a8d46d7c960643097f9fb9a9a08e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Fri, 31 Jan 2025 10:10:27 -0800 Subject: [PATCH 6/6] switch to cdk8 data --- openfecli/tests/commands/test_plan_rbfe_network.py | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/openfecli/tests/commands/test_plan_rbfe_network.py b/openfecli/tests/commands/test_plan_rbfe_network.py index 048e41497..b8cdd569e 100644 --- a/openfecli/tests/commands/test_plan_rbfe_network.py +++ b/openfecli/tests/commands/test_plan_rbfe_network.py @@ -350,15 +350,15 @@ def lomap_yaml_settings(): settings: time: 45 element_change: True - + partial_charge: method: nagl settings: nagl_model: openff-gnn-am1bcc-0.1.0-rc.3.pt """ -def test_lomap_yaml_plan_rbfe_smoke_test(lomap_yaml_settings, eg5_files, tmpdir): - protein, ligand, cofactor = eg5_files +def test_lomap_yaml_plan_rbfe_smoke_test(lomap_yaml_settings, cdk8_files, tmpdir): + protein, ligand = cdk8_files settings_path = tmpdir / "settings.yaml" with open(settings_path, "w") as f: f.write(lomap_yaml_settings) @@ -368,8 +368,7 @@ def test_lomap_yaml_plan_rbfe_smoke_test(lomap_yaml_settings, eg5_files, tmpdir) args = [ '-p', protein, '-M', ligand, - '-C', cofactor, - '-s', settings_path, + '-s', settings_path ] runner = CliRunner()