.. _rjmc: Molecular geometry generation via RJMC ************************************** Reversible jump Monte Carlo (RJMC) engine for sampling molecular geometries in which atoms are created/destroyed. Atom mapping ------------ .. currentmodule:: perses.rjmc.atom_mapping .. autosummary:: :nosignatures: :toctree: api/generated/ AtomMapping AtomMapper Topology proposal engines ------------------------- .. currentmodule:: perses.rjmc.topology_proposal .. autosummary:: :nosignatures: :toctree: api/generated/ TopologyProposal ProposalEngine .. SmallMoleculeAtomMapper .. PremappedSmallMoleculeSetProposalEngine SmallMoleculeSetProposalEngine PolymerProposalEngine PointMutationEngine PeptideLibraryEngine .. JRG: This class does not exist anymore? .. ButaneProposalEngine .. NaphthaleneProposalEngine .. PropaneProposalEngine .. NullProposalEngine OpenMM System generation utilities ---------------------------------- .. currentmodule:: perses.rjmc.topology_proposal .. autosummary:: :nosignatures: :toctree: api/generated/ .. .. This has moved to openforcefields? .. SystemGenerator Geometry proposal engines ------------------------- .. currentmodule:: perses.rjmc.geometry .. autosummary:: :nosignatures: :toctree: api/generated/ GeometryEngine FFAllAngleGeometryEngine .. JRG: This class does not exist anymore? .. OmegaGeometryEngine Geometry utility classes ------------------------ .. currentmodule:: perses.rjmc.geometry .. autosummary:: :nosignatures: :toctree: api/generated/ GeometrySystemGenerator .. JRG: These classes does not exist anymore? .. BootstrapParticleFilter .. GeometrySystemGeneratorFast .. PredAtomTopologyIndex .. PredHBond .. .. This one is also dead code in some modules! .. ProposalOrderTools