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Make notebook transformations identical to CLI #61

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Merged
dwhswenson merged 3 commits into from
May 11, 2023
Merged

Make notebook transformations identical to CLI #61

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fdc83d0
Obvious additions after run-through
dwhswenson May 9, 2023
36426c2
Make notebook transformations identical to CLI
dwhswenson May 11, 2023
05d8f68
Merge branch 'main' of github.com:OpenFreeEnergy/ExampleNotebooks int…
dwhswenson May 11, 2023
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70 changes: 35 additions & 35 deletions rbfe_tutorial/python_tutorial.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -44,9 +44,7 @@
"source": [
"from rdkit import Chem\n",
"supp = Chem.SDMolSupplier(\"tyk2_ligands.sdf\", removeHs=False)\n",
"ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]\n",
"\n",
"name_to_ligand = {ligand.name: ligand for ligand in ligands}"
"ligands = [openfe.SmallMoleculeComponent.from_rdkit(mol) for mol in supp]"
]
},
{
Expand Down Expand Up @@ -173,7 +171,7 @@
},
{
"cell_type": "code",
"execution_count": 8,
"execution_count": 7,
"id": "2263838f",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -212,7 +210,7 @@
},
{
"cell_type": "code",
"execution_count": 9,
"execution_count": 8,
"id": "9d2fbc22",
"metadata": {},
"outputs": [],
Expand All @@ -223,7 +221,7 @@
},
{
"cell_type": "code",
"execution_count": 10,
"execution_count": 9,
"id": "3f1706ee",
"metadata": {},
"outputs": [],
Expand All @@ -233,7 +231,7 @@
},
{
"cell_type": "code",
"execution_count": 11,
"execution_count": 10,
"id": "710285ca",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -262,7 +260,7 @@
},
{
"cell_type": "code",
"execution_count": 12,
"execution_count": 11,
"id": "3f394a0d",
"metadata": {
"scrolled": true
Expand All @@ -282,7 +280,7 @@
},
{
"cell_type": "code",
"execution_count": 13,
"execution_count": 12,
"id": "fb839094",
"metadata": {},
"outputs": [
Expand All @@ -298,7 +296,7 @@
"298.15 <Unit('kelvin')>"
]
},
"execution_count": 13,
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -310,7 +308,7 @@
},
{
"cell_type": "code",
"execution_count": 14,
"execution_count": 13,
"id": "e83630f0",
"metadata": {},
"outputs": [],
Expand All @@ -331,7 +329,7 @@
},
{
"cell_type": "code",
"execution_count": 15,
"execution_count": 14,
"id": "7adf42d6",
"metadata": {},
"outputs": [],
Expand All @@ -352,7 +350,7 @@
},
{
"cell_type": "code",
"execution_count": 16,
"execution_count": 15,
"id": "44ba94ca",
"metadata": {},
"outputs": [],
Expand Down Expand Up @@ -388,7 +386,7 @@
},
{
"cell_type": "code",
"execution_count": 17,
"execution_count": 16,
"id": "66666a80",
"metadata": {},
"outputs": [],
Expand All @@ -410,12 +408,14 @@
" 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",
" \n",
" transformation = openfe.Transformation(\n",
" stateA=sysA,\n",
" stateB=sysB,\n",
" mapping={'ligand': mapping},\n",
" protocol=protocol, # use protocol created above\n",
" name=f\"{sysA.name}_{sysB.name}\"\n",
" name=f\"{prefix}{sysA.name}_{sysB.name}\"\n",
" )\n",
" transformations.append(transformation)\n",
"\n",
Expand All @@ -434,7 +434,7 @@
},
{
"cell_type": "code",
"execution_count": 18,
"execution_count": 17,
"id": "d6cebd9a",
"metadata": {},
"outputs": [],
Expand All @@ -451,32 +451,32 @@
},
{
"cell_type": "code",
"execution_count": 19,
"execution_count": 18,
"id": "b96b57a9",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"lig_ejm_31_complex_lig_ejm_42_complex.json\r\n",
"lig_ejm_31_complex_lig_ejm_46_complex.json\r\n",
"lig_ejm_31_complex_lig_ejm_47_complex.json\r\n",
"lig_ejm_31_complex_lig_ejm_48_complex.json\r\n",
"lig_ejm_31_complex_lig_ejm_50_complex.json\r\n",
"lig_ejm_31_solvent_lig_ejm_42_solvent.json\r\n",
"lig_ejm_31_solvent_lig_ejm_46_solvent.json\r\n",
"lig_ejm_31_solvent_lig_ejm_47_solvent.json\r\n",
"lig_ejm_31_solvent_lig_ejm_48_solvent.json\r\n",
"lig_ejm_31_solvent_lig_ejm_50_solvent.json\r\n",
"lig_ejm_42_complex_lig_ejm_43_complex.json\r\n",
"lig_ejm_42_solvent_lig_ejm_43_solvent.json\r\n",
"lig_ejm_46_complex_lig_jmc_23_complex.json\r\n",
"lig_ejm_46_complex_lig_jmc_27_complex.json\r\n",
"lig_ejm_46_complex_lig_jmc_28_complex.json\r\n",
"lig_ejm_46_solvent_lig_jmc_23_solvent.json\r\n",
"lig_ejm_46_solvent_lig_jmc_27_solvent.json\r\n",
"lig_ejm_46_solvent_lig_jmc_28_solvent.json\r\n"
"easy_rbfe_lig_ejm_31_complex_lig_ejm_42_complex.json\r\n",
"easy_rbfe_lig_ejm_31_complex_lig_ejm_46_complex.json\r\n",
"easy_rbfe_lig_ejm_31_complex_lig_ejm_47_complex.json\r\n",
"easy_rbfe_lig_ejm_31_complex_lig_ejm_48_complex.json\r\n",
"easy_rbfe_lig_ejm_31_complex_lig_ejm_50_complex.json\r\n",
"easy_rbfe_lig_ejm_31_solvent_lig_ejm_42_solvent.json\r\n",
"easy_rbfe_lig_ejm_31_solvent_lig_ejm_46_solvent.json\r\n",
"easy_rbfe_lig_ejm_31_solvent_lig_ejm_47_solvent.json\r\n",
"easy_rbfe_lig_ejm_31_solvent_lig_ejm_48_solvent.json\r\n",
"easy_rbfe_lig_ejm_31_solvent_lig_ejm_50_solvent.json\r\n",
"easy_rbfe_lig_ejm_42_complex_lig_ejm_43_complex.json\r\n",
"easy_rbfe_lig_ejm_42_solvent_lig_ejm_43_solvent.json\r\n",
"easy_rbfe_lig_ejm_46_complex_lig_jmc_23_complex.json\r\n",
"easy_rbfe_lig_ejm_46_complex_lig_jmc_27_complex.json\r\n",
"easy_rbfe_lig_ejm_46_complex_lig_jmc_28_complex.json\r\n",
"easy_rbfe_lig_ejm_46_solvent_lig_jmc_23_solvent.json\r\n",
"easy_rbfe_lig_ejm_46_solvent_lig_jmc_27_solvent.json\r\n",
"easy_rbfe_lig_ejm_46_solvent_lig_jmc_28_solvent.json\r\n"
]
}
],
Expand Down