From e0eb4b5302f288493376af0c01817e658a5a2d52 Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Tue, 11 Feb 2025 09:23:58 -0800 Subject: [PATCH 1/3] rename easy_r*fe to r*fe --- cookbook/bespoke_parameters_showcase.ipynb | 2 +- cookbook/create_alchemical_network.ipynb | 2 +- rbfe_tutorial/cli_tutorial.md | 24 +++++++------- rbfe_tutorial/python_tutorial.ipynb | 38 +++++++++++----------- 4 files changed, 33 insertions(+), 33 deletions(-) diff --git a/cookbook/bespoke_parameters_showcase.ipynb b/cookbook/bespoke_parameters_showcase.ipynb index 7b90cf0..86a28e8 100644 --- a/cookbook/bespoke_parameters_showcase.ipynb +++ b/cookbook/bespoke_parameters_showcase.ipynb @@ -89,7 +89,7 @@ " sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n", " sysB = openfe.ChemicalSystem(sysB_dict, name=f\"{mapping.componentB.name}_{leg}\")\n", "\n", - " prefix = \"easy_rbfe_\" # prefix is only to exactly reproduce CLI\n", + " prefix = \"rbfe_\" # prefix is only to exactly reproduce CLI\n", "\n", " transformation = openfe.Transformation(\n", " stateA=sysA,\n", diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb index edebab0..88caeb8 100644 --- a/cookbook/create_alchemical_network.ipynb +++ b/cookbook/create_alchemical_network.ipynb @@ -226,7 +226,7 @@ " mapping=mapping,\n", " protocol=protocol,\n", " # Using the same name as to_rbfe_alchemical_network()\n", - " name=f\"easy_rbfe_{system_a.name}_{system_b.name}\"\n", + " name=f\"rbfe_{system_a.name}_{system_b.name}\"\n", " )\n", " \n", " transformations.append(transformation)" diff --git a/rbfe_tutorial/cli_tutorial.md b/rbfe_tutorial/cli_tutorial.md index a579bf2..8454c3b 100644 --- a/rbfe_tutorial/cli_tutorial.md +++ b/rbfe_tutorial/cli_tutorial.md @@ -73,13 +73,13 @@ network_setup ├── ligand_network.graphml ├── network_setup.json └── transformations/ - ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json - ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json - ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json - ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json - ├── easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json - ├── easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json - ├── easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json + ├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json + ├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json + ├── rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json + ├── rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json + ├── rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json + ├── rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json + ├── rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json [continues] ``` @@ -98,7 +98,7 @@ The files that describe each individual simulation we will run are located withi `network_setup/transformations/`. Each JSON file represents a single alchemical leg to run and contains all the necessary information to run that leg. Filenames indicate ligand names as taken from the SDF; for example, the file -`easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json` is the leg +`rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json` is the leg associated with the transformation of the ligand `lig_ejm_31` into `lig_ejm_42` while in complex with the protein. @@ -273,7 +273,7 @@ openfe ```text results -├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex +├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex │   ├── shared_RelativeHybridTopologyProtocolUnit-3ea82011-75f0-4bb6-b415-e7d05bd012f6 │   │   ├── checkpoint.nc │   │   └── simulation.nc @@ -283,8 +283,8 @@ results │   └── shared_RelativeHybridTopologyProtocolUnit-7a6def34-2967-4452-8d47-483bc7219c06 │   ├── checkpoint.nc │   └── simulation.nc -├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json -├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex +├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json +├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex │   ├── shared_RelativeHybridTopologyProtocolUnit-ad113e55-5636-474e-9be3-ee77fe887e77 │   │   ├── checkpoint.nc │   │   └── simulation.nc @@ -294,7 +294,7 @@ results │   └── shared_RelativeHybridTopologyProtocolUnit-f848e671-fdd3-4b8d-8bd2-6eb5140e3ed3 │   ├── checkpoint.nc │   └── simulation.nc -├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json +├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json [continues] ``` diff --git a/rbfe_tutorial/python_tutorial.ipynb b/rbfe_tutorial/python_tutorial.ipynb index 97d1eea..d0abb6a 100644 --- a/rbfe_tutorial/python_tutorial.ipynb +++ b/rbfe_tutorial/python_tutorial.ipynb @@ -472,7 +472,7 @@ " sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n", " sysB = openfe.ChemicalSystem(sysB_dict, name=f\"{mapping.componentB.name}_{leg}\")\n", " \n", - " prefix = \"easy_rbfe_\" # prefix is only to exactly reproduce CLI\n", + " prefix = \"rbfe_\" # prefix is only to exactly reproduce CLI\n", " \n", " transformation = openfe.Transformation(\n", " stateA=sysA,\n", @@ -523,24 +523,24 @@ "name": "stdout", "output_type": "stream", "text": [ - "easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\n", - "easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\n", - "easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\n", - "easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\n", - "easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\n", - "easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\n", - "easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\n", - "easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\n", - "easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\n", - "easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\n", - "easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\n", - "easy_rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\n", - "easy_rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\n", - "easy_rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\n", - "easy_rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\n", - "easy_rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\n", - "easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\n", - "easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\n" + "rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\n", + "rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\n", + "rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\n", + "rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\n", + "rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\n", + "rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\n", + "rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\n", + "rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\n", + "rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\n", + "rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\n", + "rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\n", + "rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\n", + "rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\n", + "rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\n", + "rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\n", + "rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\n", + "rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\n", + "rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\n" ] } ], From 1b16067937257cec9c342538256f4f5bda9a4c6e Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 19 Feb 2025 09:38:29 -0800 Subject: [PATCH 2/3] bump openfe version to 1.3.0 --- showcase/openfe_showcase.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/showcase/openfe_showcase.ipynb b/showcase/openfe_showcase.ipynb index 977203e..94a865e 100644 --- a/showcase/openfe_showcase.ipynb +++ b/showcase/openfe_showcase.ipynb @@ -88,7 +88,7 @@ "if \"COLAB_RELEASE_TAG\" in os.environ:\n", " !pip install -q condacolab\n", " import condacolab\n", - " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.2.0/OpenFEforge-1.2.0-Linux-x86_64.sh\")" + " condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.3.0/OpenFEforge-1.3.0-Linux-x86_64.sh\")" ] }, { From 8a04a847632496c4d04df2837d091c55ee9c63ff Mon Sep 17 00:00:00 2001 From: Alyssa Travitz Date: Wed, 19 Feb 2025 16:27:12 -0800 Subject: [PATCH 3/3] adding easy_ back to just alchemical network for gufe dependency --- cookbook/create_alchemical_network.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cookbook/create_alchemical_network.ipynb b/cookbook/create_alchemical_network.ipynb index 88caeb8..edebab0 100644 --- a/cookbook/create_alchemical_network.ipynb +++ b/cookbook/create_alchemical_network.ipynb @@ -226,7 +226,7 @@ " mapping=mapping,\n", " protocol=protocol,\n", " # Using the same name as to_rbfe_alchemical_network()\n", - " name=f\"rbfe_{system_a.name}_{system_b.name}\"\n", + " name=f\"easy_rbfe_{system_a.name}_{system_b.name}\"\n", " )\n", " \n", " transformations.append(transformation)"