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adding helpful links
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atravitz committed Oct 8, 2024
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"source": [
"### Creating OpenFE SmallMoleculeComponents\n",
"\n",
"In order to keep track of the various inputs being passed through the OpenFE\n",
"To keep track of the various inputs being passed through the OpenFE\n",
"toolkit, OpenFE implements a set of Components which define the proteins,\n",
"small molecules and solvent components which a system may contain. Here we\n",
"use the [SmallMoleculeComponent](https://github.com/OpenFreeEnergy/gufe/blob/main/gufe/smallmoleculecomponent.py)\n",
"small molecules, and solvent components which a system may contain. Here we\n",
"use the [SmallMoleculeComponent](https://github.com/OpenFreeEnergy/gufe/blob/main/gufe/components/smallmoleculecomponent.py)\n",
"which takes in either [RDKit molecules](https://www.rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html)\n",
"or [OpenFF molecules](https://open-forcefield-toolkit.readthedocs.io/en/0.9.2/api/generated/openff.toolkit.topology.Molecule.html).\n",
"\n",
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"id": "3128085c-db8a-4a70-89ef-0fde956fdb40",
"metadata": {},
"source": [
"In the hybrid topology RBFE protocol, an atom mapping defines which atoms are mutated during the alchemical transformation.\n",
"In the [hybrid topology RBFE protocol](https://docs.openfree.energy/en/latest/guide/protocols/relativehybridtopology.html) , an atom mapping defines which atoms are mutated during the alchemical transformation.\n",
"The user can choose between two different atom mappers:\n",
"1. `LomapAtomMapper`\n",
" * based on the maximum common substructure (MCS)\n",
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