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82 lines
1.7 KiB
ReStructuredText
82 lines
1.7 KiB
ReStructuredText
.. _Atom Mappers:
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Atom Mappings
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=============
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Tools for mapping atoms in one molecule to those in another. Used to generate efficient ligand networks.
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.. module:: openfe.setup.atom_mapping
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.. rubric:: Abstract Base Class
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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LigandAtomMapper
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.. rubric:: Implementations
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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KartografAtomMapper
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LomapAtomMapper
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PersesAtomMapper
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.. rubric:: Data Types
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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LigandAtomMapping
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.. _Atom Map Scorers:
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Atom Map Scorers
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----------------
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Scoring functions for a mapping between ligands. These are used as objective functions for :any:`Ligand Network Planners`.
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Lomap Scorers
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~~~~~~~~~~~~~
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Scorers implemented by the `LOMAP <https://github.com/OpenFreeEnergy/Lomap>`_ package.
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.. apparently we need the atom_mapping because internally autofunction is
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trying ``import openfe.setup.lomap_scorers``, which doesn't work (whereas
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``from openfe.setup import lomap_scorers`` does)
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.. module:: openfe.setup.atom_mapping.lomap_scorers
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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default_lomap_score
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ecr_score
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mcsr_score
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mncar_score
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atomic_number_score
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hybridization_score
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sulfonamides_score
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heterocycles_score
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transmuting_methyl_into_ring_score
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transmuting_ring_sizes_score
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Perses Scorers
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~~~~~~~~~~~~~~
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Scorers implemented by the `Perses <https://github.com/choderalab/perses>`_ package.
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.. module:: openfe.setup.atom_mapping.perses_scorers
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.. autosummary::
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:nosignatures:
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:toctree: generated/
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default_perses_scorer
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