perses.rjmc.geometry.GeometrySystemGenerator¶
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class
perses.rjmc.geometry.GeometrySystemGenerator(reference_system, growth_indices, parameter_name, add_extra_torsions=True, add_extra_angles=True, reference_topology=None, use_sterics=False, force_names=None, force_parameters=None, verbose=True)[source]¶ This is an internal utility class that generates OpenMM systems with only valence terms and special parameters to assist in geometry proposals.
Methods
get_modified_system()Create a modified system with parameter_name parameter. set_growth_parameter_index(…[, context])Set the growth parameter index -
__init__(reference_system, growth_indices, parameter_name, add_extra_torsions=True, add_extra_angles=True, reference_topology=None, use_sterics=False, force_names=None, force_parameters=None, verbose=True)[source]¶ Parameters: - reference_system : simtk.openmm.System object
The system containing the relevant forces and particles
- growth_indices : list of atom
The order in which the atom indices will be proposed
- parameter_name : str
The name of the global context parameter
- add_extra_torsions : bool, optional
Whether to add additional torsions to keep rings flat. Default true.
- force_names : list of str
A list of the names of forces that will be included in this system
- force_parameters : dict
Options for the forces (e.g., NonbondedMethod : ‘CutffNonPeriodic’)
- verbose : bool, optional, default=False
If True, will print verbose output.
Methods
__init__(reference_system, growth_indices, …)Parameters: get_modified_system()Create a modified system with parameter_name parameter. set_growth_parameter_index(…[, context])Set the growth parameter index -
get_modified_system()[source]¶ Create a modified system with parameter_name parameter. When 0, only core atoms are interacting; for each integer above 0, an additional atom is made interacting, with order determined by growth_index.
Returns: - growth_system : simtk.openmm.System object
System with the appropriate modifications, with growth parameter set to maximum.
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