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rename easy_rb(h)fe to rb(h)fe #190

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Merged
mikemhenry merged 3 commits into from
Feb 20, 2025
Merged

rename easy_rb(h)fe to rb(h)fe #190

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e0eb4b5
rename easy_r*fe to r*fe
atravitz Feb 11, 2025
1b16067
bump openfe version to 1.3.0
atravitz Feb 19, 2025
8a04a84
adding easy_ back to just alchemical network for gufe dependency
atravitz Feb 20, 2025
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2 changes: 1 addition & 1 deletion cookbook/bespoke_parameters_showcase.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
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2 changes: 1 addition & 1 deletion cookbook/create_alchemical_network.ipynb
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Expand Up @@ -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)"
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24 changes: 12 additions & 12 deletions rbfe_tutorial/cli_tutorial.md
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Expand Up @@ -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]
```

Expand All @@ -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.

Expand Down Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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]
```

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38 changes: 19 additions & 19 deletions rbfe_tutorial/python_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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"
]
}
],
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