Molecular geometry generation via RJMC

Reversible jump Monte Carlo (RJMC) engine for sampling molecular geometries in which atoms are created/destroyed.

Topology proposal engines


This is a container class with convenience methods to access various objects needed for a topology proposal


This defines a type which, given the requisite metadata, can produce Proposals (namedtuple) of new topologies.


This class proposes new small molecules from a prespecified set.


Base class for ProposalEngine implementations that modify polymer components of systems.


ProposalEngine for generating point mutation variants of a wild-type polymer


Note: The PeptideLibraryEngine currently doesn’t work because PolymerProposalEngine has been modified to handle only one mutation at a time (in accordance with the geometry engine). Arguments ——– system_generator : SystemGenerator library : list of strings each string is a 1-letter-code list of amino acid sequence chain_id : str id of the chain to mutate (using the first chain with the id, if there are multiple) proposal_metadata : dict – OPTIONAL Contains information necessary to initialize proposal engine.

OpenMM System generation utilities

Geometry proposal engines


This is the base class for the geometry engine.


This is an implementation of GeometryEngine which uses all valence terms and OpenMM

Geometry utility classes


Internal utility class to generate OpenMM systems with only valence terms and special parameters for newly placed atoms to assist in geometry proposals.