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
ProposalEngine
SmallMoleculeSetProposalEngine
PolymerProposalEngine
PointMutationEngine
PeptideLibraryEngine
NullProposalEngine
NaphthaleneProposalEngine
ButaneProposalEngine
PropaneProposalEngine

OpenMM System generation utilities

SystemGenerator

Geometry proposal engines

GeometryEngine
FFAllAngleGeometryEngine
OmegaGeometryEngine

Geometry utility classes

PredAtomTopologyIndex
BootstrapParticleFilter
GeometrySystemGenerator
GeometrySystemGeneratorFast
PredHBond
ProposalOrderTools