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 |
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This defines a type which, given the requisite metadata, can produce Proposals (namedtuple) of new topologies. |
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This class proposes new small molecules from a prespecified set. |
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Base class for ProposalEngine implementations that modify polymer components of systems. |
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ProposalEngine for generating point mutation variants of a wild-type polymer |
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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. |
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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. |
