perses.rjmc.geometry.BootstrapParticleFilter¶
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class
perses.rjmc.geometry.BootstrapParticleFilter(growth_context, atom_torsions, initial_positions, beta, n_particles=18, resample_frequency=10)[source]¶ Implements a Bootstrap Particle Filter (BPF) to sample from the appropriate degrees of freedom. Designed for use with the dimension-matching scheme of Perses.
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__init__(growth_context, atom_torsions, initial_positions, beta, n_particles=18, resample_frequency=10)[source]¶ Parameters: - growth_context : simtk.openmm.Context object
Context containing appropriate “growth system”
- atom_torsions : dict
parmed.Atom : parmed.Dihedral dict that specifies what torsion to use to propose each atom
- initial_positions : np.ndarray [n,3]
The positions of existing atoms.
- beta : simtk.unit.Quantity
The inverse temperature, with units
- n_particles : int, optional
The number of particles in the BPF (note that this is NOT the number of atoms). Default 18.
- resample_frequency : int, optional
How often to resample particles. default 10
Methods
__init__(growth_context, atom_torsions, …)Parameters: -
