mmtbx.dynamics package

Submodules

mmtbx.dynamics.cartesian_dynamics module

class mmtbx.dynamics.cartesian_dynamics.gradients_calculator_geometry_restraints(restraints_manager=None)

Bases: object

gradients(xray_structure, force_update_mask=False)
class mmtbx.dynamics.cartesian_dynamics.gradients_calculator_real_space_simple(restraints_manager=None, real_space_gradients_delta=0.25, unit_cell=None, target_map=None, sites_cart=None, wx=None, wc=None, update_gradient_threshold=0)

Bases: object

gradients(xray_structure, force_update_mask=False)
class mmtbx.dynamics.cartesian_dynamics.gradients_calculator_reciprocal_space(restraints_manager=None, fmodel=None, sites_cart=None, wx=None, wc=None, update_gradient_threshold=0)

Bases: object

gradients(xray_structure, force_update_mask=False)
class mmtbx.dynamics.cartesian_dynamics.interleaved_lbfgs_minimization(restraints_manager, sites_cart, max_iterations)

Bases: object

compute_functional_and_gradients()
mmtbx.dynamics.cartesian_dynamics.random_velocities(masses, target_temperature, zero_fraction=0, random_gauss=None, random_random=None, seed=None)
class mmtbx.dynamics.cartesian_dynamics.run(xray_structure, gradients_calculator, temperature=300, n_steps=200, time_step=0.0005, initial_velocities_zero_fraction=0, vxyz=None, n_print=20, n_collect=10, interleaved_minimization=False, reset_velocities=True, stop_cm_motion=False, log=None, stop_at_diff=None, random_seed=None, states_collector=None, verbose=-1)

Bases: object

accelerations()
center_of_mass_info()
print_dynamics_stat(text)
run_interleaved_minimization()
set_velocities()
stop_global_motion()
velocity_rescaling()
verlet_leapfrog_integration()

mmtbx.dynamics.constants module

mmtbx.dynamics.ensemble_cd module

class mmtbx.dynamics.ensemble_cd.cartesian_dynamics(structure, restraints_manager, temperature=300, protein_thermostat=False, n_steps=200, time_step=0.0005, initial_velocities_zero_fraction=0, vxyz=None, interleaved_minimization_params=None, n_print=20, fmodel=None, xray_target_weight=None, chem_target_weight=None, shift_update=0.0, xray_structure_last_updated=None, xray_gradient=None, reset_velocities=True, stop_cm_motion=False, update_f_calc=True, er_data=None, log=None, stop_at_diff=None, verbose=-1)

Bases: object

accelerations()
center_of_mass_info()
interleaved_minimization()
print_detailed_dynamics_stats()
set_velocities()
stop_global_motion()
store_temperatures()
velocity_rescaling()
verlet_leapfrog_integration()
xray_grads()
class mmtbx.dynamics.ensemble_cd.interleaved_lbfgs_minimization(conservative_pair_proxies, sites_cart, max_iterations)

Bases: object

compute_functional_and_gradients()
mmtbx.dynamics.ensemble_cd.random_velocities(masses, target_temperature, zero_fraction=0, random_gauss=None, random_random=None, seed=None)

mmtbx.dynamics.simulated_annealing module

mmtbx.dynamics.simulated_annealing.manager(params, target_weights, all_params, macro_cycle, h_params, fmodels, model, out=None, states_collector=None, callback=None)
mmtbx.dynamics.simulated_annealing.master_params()
class mmtbx.dynamics.simulated_annealing.run(params, restraints_manager, xray_structure=None, wx=None, wc=None, fmodel=None, target_map=None, real_space=False, log=None, states_collector=None, callback=None, verbose=True)

Bases: object

gradients_calculator()
show(curr_temp)

Module contents

class mmtbx.dynamics.kinetic_energy_and_temperature(velocities, masses)

Bases: object

mmtbx.dynamics.kinetic_energy_as_temperature(dof, e)
mmtbx.dynamics.temperature_as_kinetic_energy(dof, t)