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IMP
2.1.1
The Integrative Modeling Platform
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IMP
2.1.1
The Integrative Modeling Platform
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Simple Brownian dynamics optimizer. More...
#include <IMP/atom/BrownianDynamics.h>
Inheritance diagram for IMP::atom::BrownianDynamics:Public Member Functions | |
| BrownianDynamics (kernel::Model *m, std::string name="BrownianDynamics%1%", double wave_factor=1.0) | |
| Create the optimizer. More... | |
| virtual std::string | get_type_name () const |
| virtual ::IMP::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. | |
| void | set_maximum_move (double ms) |
| void | set_use_stochastic_runge_kutta (bool tf) |
| Public Member Functions inherited from IMP::atom::Simulator | |
| Simulator (kernel::Model *m, std::string name="Simulator %1%", double wave_factor=1.0) | |
| double | get_current_time () const |
| double | get_kt () const |
| kernel::ParticleIndexes | get_simulation_particle_indexes () const |
| kernel::ParticlesTemp | get_simulation_particles () const |
| double | get_temperature () const |
| void | set_current_time (double ct) |
| void | set_temperature (double d) |
| double | simulate (double time_in_fs) |
| Simulate for a given time in fs. More... | |
| double | simulate_wave (double time_in_fs, double max_time_step_factor=10.0, double base=1.5) |
| void | set_maximum_time_step (double ts) |
| double | get_maximum_time_step () const |
| double | get_last_time_step () const |
| void | remove_particle (kernel::Particle *d) |
| void | remove_particles (const kernel::Particles &d) |
| void | set_particles (const kernel::Particles &ps) |
| void | set_particles_order (const kernel::Particles &objs) |
| unsigned int | add_particle (kernel::Particle *obj) |
| void | add_particles (const kernel::Particles &objs) |
| void | clear_particles () |
| unsigned int | get_number_of_particles () const |
| bool | get_has_particles () |
| kernel::Particle * | get_particle (unsigned int i) const |
| kernel::Particles | get_particles () const |
| void | reserve_particles (unsigned int sz) |
| Public Member Functions inherited from IMP::kernel::Optimizer | |
| Optimizer (kernel::Model *m, std::string name="Optimizer %1%") | |
| Optimizer () | |
| void | clear_range_cache () |
| Float | get_derivative (FloatIndex fi) const |
| double | get_last_score () const |
| Return the score found in the last evaluate. | |
| FloatIndexes | get_optimized_attributes () const |
| Restraints | get_restraints () const |
| double | get_scaled_derivative (FloatIndex fi) const |
| double | get_scaled_value (FloatIndex fi) const |
| double | get_score_threshold () const |
| ScoringFunction * | get_scoring_function () const |
| Return the scoring function that is being used. | |
| bool | get_stop_on_good_score () const |
| Float | get_value (FloatIndex fi) const |
| double | get_width (FloatKey k) const |
| double | optimize (unsigned int max_steps) |
| Optimize the model for up to max_steps iterations. More... | |
| void | set_restraints (const RestraintsTemp &rs) |
| void | set_scaled_value (FloatIndex fi, Float v) const |
| void | set_score_threshold (double s) |
| virtual void | set_scoring_function (ScoringFunctionAdaptor sf) |
| void | set_stop_on_good_score (bool tf) |
| void | set_value (FloatIndex fi, double v) const |
| double | width (FloatKey k) const |
| void | remove_optimizer_state (OptimizerState *d) |
| void | remove_optimizer_states (const OptimizerStates &d) |
| void | set_optimizer_states (const OptimizerStates &ps) |
| void | set_optimizer_states_order (const OptimizerStates &objs) |
| unsigned int | add_optimizer_state (OptimizerState *obj) |
| void | add_optimizer_states (const OptimizerStates &objs) |
| void | clear_optimizer_states () |
| unsigned int | get_number_of_optimizer_states () const |
| bool | get_has_optimizer_states () |
| OptimizerState * | get_optimizer_state (unsigned int i) const |
| OptimizerStates | get_optimizer_states () const |
| void | reserve_optimizer_states (unsigned int sz) |
| Public Member Functions inherited from IMP::kernel::ModelObject | |
| ModelObject (kernel::Model *m, std::string name) | |
| ModelObject (std::string name) | |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. | |
| bool | get_has_required_score_states () const |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| bool | get_is_part_of_model () const |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| void | set_has_dependencies (bool tf) |
| void | set_has_required_score_states (bool tf) |
| virtual void | set_model (kernel::Model *m) |
| Public Member Functions inherited from IMP::base::Object | |
| virtual void | clear_caches () |
| virtual void | do_destroy () |
| CheckLevel | get_check_level () const |
| LogLevel | get_log_level () const |
| void | set_check_level (CheckLevel l) |
| void | set_log_level (LogLevel l) |
| Set the logging level used in this object. More... | |
| void | set_was_used (bool tf) const |
| void | show (std::ostream &out=std::cout) const |
| const std::string & | get_name () const |
| void | set_name (std::string name) |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::atom::Simulator | |
| virtual Float | do_optimize (unsigned int max_steps) |
| override this function to do actual optimization | |
| Protected Member Functions inherited from IMP::kernel::Optimizer | |
| virtual ModelObjectsTemp | do_get_inputs () const |
| virtual ModelObjectsTemp | do_get_outputs () const |
| don't return anything here to avoid pointless dependencies | |
| ModelObjectsTemp | get_optimizer_state_inputs () const |
| void | update_states () const |
| Update optimizer states, should be called at each successful step. More... | |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| Object () | |
The particles to be optimized must have optimizable x,y,z attributes and a non-optimizable "Stokes radius"; this optimizer assumes the score to be energy in kcal/mol, the xyz coordinates to be in angstroms and the diffusion coefficent be in cm^2/s
kernel::Particles without optimized x,y,z and nonoptimized D are skipped.
Rigid bodies are supported.
BrownianDynamics uses a SimulationParameters particle to store the parameters of the simulation. Such a particle must be passed on creation. The BrownianDynamics object will at least see updates to the SimulationParamters particle which occur before the call to BrownianDynamics::optimize() or BrownianDynamics::simulate(), changing the the parameters during optimization has undefined results.
The optimizer can either automatically determine which particles to use from the model or be passed a SingletonContainer for the particles. If such a container is passed, particles added to it during optimization state updates are handled properly.
Definition at line 51 of file BrownianDynamics.h.
| IMP::atom::BrownianDynamics::BrownianDynamics | ( | kernel::Model * | m, |
| std::string | name = "BrownianDynamics%1%", |
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| double | wave_factor = 1.0 |
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| ) |
If sc is not null, that container will be used to find particles to move, otherwise the model will be searched.
| m | model associated with bd |
| name | name of bd object |
| wave_factor | for wave step function, see Simulator object, if >1.001 or so, creates a wave of time steps that are larger by up to wave_factor from formal maximal time step |