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grammatical fixes from review
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atravitz committed Oct 15, 2024
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6 changes: 3 additions & 3 deletions showcase/openfe_showcase.ipynb
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"from rdkit.Chem import AllChem\n",
"from rdkit.Chem import Draw\n",
"\n",
"# Extract the content of the sdf file and visualise it\n",
"# Extract the contents of the sdf file and visualise it\n",
"ligands_rdmol = [mol for mol in\n",
" Chem.SDMolSupplier('inputs/tyk2_ligands.sdf', removeHs=False)]\n",
"\n",
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"| Create ligand topologies | OpenFE interface - OpenFF tk |\n",
"| Create hybrid OpenMM topology | OpenFE interface - OpenMMTools (eventually - ex Perses) |\n",
"| Create Lambda Protocol | OpenFE interface - OpenMMTools (eventually - ex Perses) |\n",
"| Set up and run RBFE calculation | OpenFE interface - OpenMM + OpenMMTools |\n",
"| Analyze RBFE calculation | OpenFE interface - PyMBAR + OpenMMTools |"
"| Set up and run RBFE calculations | OpenFE interface - OpenMM + OpenMMTools |\n",
"| Analyze RBFE calculations | OpenFE interface - PyMBAR + OpenMMTools |"
]
},
{
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