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
Attributes:
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.

Geometry utility classes

PredAtomTopologyIndex
Attributes:
BootstrapParticleFilter Implements a Bootstrap Particle Filter (BPF) to sample from the appropriate degrees of freedom.
GeometrySystemGenerator This is an internal utility class that generates OpenMM systems with only valence terms and special parameters to assist in geometry proposals.
GeometrySystemGeneratorFast Use updateParametersInContext to make energy evaluation fast.
PredHBond Example elaborating usage on: https://docs.eyesopen.com/toolkits/python/oechemtk/predicates.html#section-predicates-match
ProposalOrderTools This is an internal utility class for determining the order of atomic position proposals.