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minor typo fixes and formatting
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atravitz committed Oct 8, 2024
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"\n",
"Welcome to the Open Free Energy toolkit!\n",
"\n",
"The OpenFE toolkit provides open-source frameworks for calculating alchemical free energies. This notebook showcases the methods that are available in OpenFE and their usuage.\n",
"The OpenFE toolkit provides open-source frameworks for calculating alchemical free energies. This notebook showcases the methods that are available in OpenFE and their usage.\n",
"\n",
"Throughout this showcase, we will introduce different interchangeable components that users can choose from during the setup of free energy calculations. OpenFE allows you to mix and match different components, such as:\n",
"\n",
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"from rdkit.Chem import AllChem\n",
"from rdkit.Chem import Draw\n",
"\n",
"# Extract the contents of the sdf file and visualise it\n",
"# Extract the content 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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"id": "3a8d5433"
},
"source": [
"OpenFE SmallMoleculeComponents have some useful built in attributes and methods.\n",
"OpenFE `SmallMoleculeComponent`s have some useful built-in attributes and methods.\n",
"\n",
"For example the molecule's name (as defined by the SDF file) can be accessed:"
"For example, the molecule's name (as defined by the SDF file) can be accessed:"
]
},
{
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"id": "b24a3ffa"
},
"source": [
"As previously stated `SmallMoleculeComponent`s also use the OpenFF backend to allow conversion between different object types. For example, it's possible to obtain an OpenFF Molecule:"
"As previously stated, `SmallMoleculeComponent`s also use the OpenFF backend to allow conversion between different object types. For example, it's possible to obtain an OpenFF Molecule:"
]
},
{
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"\n",
"Here we work through its usage for the `lig_ejm_31` -> `lig_ejm_47` binding free energy\n",
"test case. As this involves both a relative binding free energy in solvent\n",
"and complex phases, the `RelativeHybridTopologyProtocol` Protocol will\n",
"and complex phases, the `RelativeHybridTopologyProtocol` protocol will\n",
"be used to build two separate `ProtocolDAG` (directed-acyclic-graph) classes, one for each phase.\n",
"These `DAG`s (which contain the necessary individual simulations), are then executed to yield\n",
"the desired free energy results.\n",
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