Molecular geometry generation via RJMC
Reversible jump Monte Carlo (RJMC) engine for sampling molecular geometries in which atoms are created/destroyed.
Topology proposal engines
TopologyProposal |
This is a container class with convenience methods to access various objects needed for a topology proposal |
ProposalEngine |
This defines a type which, given the requisite metadata, can produce Proposals (namedtuple) of new topologies. |
SmallMoleculeAtomMapper |
This is a utility class for generating and retrieving sets of atom maps between molecules using OpenEye. |
PremappedSmallMoleculeSetProposalEngine |
This proposal engine uses the SmallMoleculeAtomMapper to have all atoms premapped and the proposal distribution pre-formed and checked. |
SmallMoleculeSetProposalEngine |
This class proposes new small molecules from a prespecified set. |
PolymerProposalEngine |
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PointMutationEngine |
Arguments |
PeptideLibraryEngine |
Arguments |
NullProposalEngine |
Base class for NaphthaleneProposalEngine and ButantProposalEngine Not intended for use on its own |
NaphthaleneProposalEngine |
Custom ProposalEngine to use with NaphthaleneTestSystem defines two “states” of naphthalene, identified ‘naphthalene-A’ and ‘naphthalene-B’, which are tracked by adding a custom _state_key attribute to the topology |
ButaneProposalEngine |
Custom ProposalEngine to use with ButaneTestSystem defines two “states” of butane, identified ‘butane-A’ and ‘butane-B’, which are tracked by adding a custom _state_key attribute to the topology |
PropaneProposalEngine |
Custom ProposalEngine to use with PropaneTestSystem defines two “states” of butane, identified ‘propane-A’ and ‘propane-B’, which are tracked by adding a custom _state_key attribute to the topology |
OpenMM System generation utilities
SystemGenerator |
This is a utility class to generate OpenMM Systems from topology objects. |
Geometry proposal engines
GeometryEngine |
This is the base class for the geometry engine. |
FFAllAngleGeometryEngine |
This is an implementation of GeometryEngine which uses all valence terms and OpenMM |
OmegaGeometryEngine |
This class proposes new small molecule geometries based on a set of precomputed omega geometries. |