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IAlibayIAlibay
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Merge branch 'main' into update-md-tutorial
2 parents fefa8d5 + d0043f2 commit a53aa7c

8 files changed

+308
-35
lines changed

‎.pre-commit-config.yaml

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@@ -6,10 +6,10 @@ ci:
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files: (^notebooks)
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repos:
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- repo: https://github.com/psf/black
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rev: 24.10.0
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rev: 25.1.0
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hooks:
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- id: black
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- repo: https://github.com/psf/black
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rev: 24.10.0
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rev: 25.1.0
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hooks:
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- id: black-jupyter

‎cookbook/assets/calc_dg.tsv

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ligand DG(MLE) (kcal/mol) uncertainty (kcal/mol)
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lig_ejm_31 -0.09 0.05
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lig_ejm_42 0.7 0.1
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lig_ejm_46 -0.98 0.05
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lig_ejm_47 -0.1 0.1
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lig_ejm_48 0.53 0.09
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lig_ejm_50 0.91 0.06
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lig_ejm_43 2.0 0.2
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lig_jmc_23 -0.68 0.09
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lig_jmc_27 -1.1 0.1
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lig_jmc_28 -1.25 0.08

‎cookbook/assets/experimental.tsv

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ligand estimate (kcal/mol) uncertainty (kcal/mol)
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lig_ejm_42 -9.81 0.18
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lig_ejm_43 -8.29 0.18
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lig_ejm_45 -9.59 0.18
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lig_ejm_46 -11.35 0.17
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lig_ejm_47 -9.73 0.18
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lig_ejm_48 -9.03 0.18
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lig_ejm_50 -9.01 0.18
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lig_ejm_54 -10.57 0.18
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lig_ejm_55 -9.24 0.18
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lig_jmc_23 -11.74 0.18
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lig_jmc_27 -11.31 0.17
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lig_jmc_28 -11.01 0.18

‎cookbook/bespoke_parameters_showcase.ipynb

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@@ -89,7 +89,7 @@
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" sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n",
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" sysB = openfe.ChemicalSystem(sysB_dict, name=f\"{mapping.componentB.name}_{leg}\")\n",
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"\n",
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" prefix = \"easy_rbfe_\" # prefix is only to exactly reproduce CLI\n",
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" prefix = \"rbfe_\" # prefix is only to exactly reproduce CLI\n",
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"\n",
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" transformation = openfe.Transformation(\n",
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" stateA=sysA,\n",

‎cookbook/cinnabar_absolute.ipynb

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‎rbfe_tutorial/cli_tutorial.md

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@@ -73,13 +73,13 @@ network_setup
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├── ligand_network.graphml
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├── network_setup.json
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└── transformations/
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json
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├── easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json
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├── easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json
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├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
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├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
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├── rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json
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├── rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json
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├── rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json
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├── rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json
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├── rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json
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[continues]
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```
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@@ -98,7 +98,7 @@ The files that describe each individual simulation we will run are located withi
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`network_setup/transformations/`. Each JSON file represents a single alchemical
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leg to run and contains all the necessary information to run that leg.
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Filenames indicate ligand names as taken from the SDF; for example, the file
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`easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json` is the leg
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`rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json` is the leg
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associated with the transformation of the ligand `lig_ejm_31` into `lig_ejm_42`
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while in complex with the protein.
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@@ -273,7 +273,7 @@ openfe
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```text
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results
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex
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├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex
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│   ├── shared_RelativeHybridTopologyProtocolUnit-3ea82011-75f0-4bb6-b415-e7d05bd012f6
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│   │   ├── checkpoint.nc
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│   │   └── simulation.nc
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│   └── shared_RelativeHybridTopologyProtocolUnit-7a6def34-2967-4452-8d47-483bc7219c06
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│   ├── checkpoint.nc
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│   └── simulation.nc
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex
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├── rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json
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├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex
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│   ├── shared_RelativeHybridTopologyProtocolUnit-ad113e55-5636-474e-9be3-ee77fe887e77
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│   │   ├── checkpoint.nc
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│   │   └── simulation.nc
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│   └── shared_RelativeHybridTopologyProtocolUnit-f848e671-fdd3-4b8d-8bd2-6eb5140e3ed3
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│   ├── checkpoint.nc
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│   └── simulation.nc
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├── easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
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├── rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json
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[continues]
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```
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‎rbfe_tutorial/python_tutorial.ipynb

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@@ -472,7 +472,7 @@
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" sysA = openfe.ChemicalSystem(sysA_dict, name=f\"{mapping.componentA.name}_{leg}\")\n",
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" sysB = openfe.ChemicalSystem(sysB_dict, name=f\"{mapping.componentB.name}_{leg}\")\n",
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" \n",
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" prefix = \"easy_rbfe_\" # prefix is only to exactly reproduce CLI\n",
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" prefix = \"rbfe_\" # prefix is only to exactly reproduce CLI\n",
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" \n",
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" transformation = openfe.Transformation(\n",
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" stateA=sysA,\n",
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\n",
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"easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\n",
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"easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\n",
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"easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\n",
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"easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\n",
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"easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\n",
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"easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\n",
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"easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\n",
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"easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\n",
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"easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\n",
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"easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\n",
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"easy_rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\n",
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"easy_rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\n",
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"easy_rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\n",
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"easy_rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\n",
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"easy_rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\n",
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"easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\n",
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"easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\n"
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"rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\n",
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"rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\n",
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"rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\n",
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"rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\n",
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"rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\n",
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"rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\n",
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"rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\n",
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"rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\n",
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"rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\n",
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"rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\n",
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"rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\n",
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"rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\n",
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"rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\n",
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"rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\n",
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"rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\n",
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"rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\n",
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"rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\n",
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"rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\n"
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]
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}
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],

‎showcase/openfe_showcase.ipynb

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"if \"COLAB_RELEASE_TAG\" in os.environ:\n",
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" !pip install -q condacolab\n",
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" import condacolab\n",
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.2.0/OpenFEforge-1.2.0-Linux-x86_64.sh\")"
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" condacolab.install_from_url(\"https://github.com/OpenFreeEnergy/openfe/releases/download/v1.3.1/OpenFEforge-1.3.1-Linux-x86_64.sh\")"
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]
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},
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{

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