 |
|
IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
|
A Monte Carlo optimizer. More...
#include <IMP/core/MonteCarlo.h>
Inheritance diagram for IMP::core::MonteCarlo:A Monte Carlo optimizer.
The optimizer uses a set of Mover objects to propose steps. At each sampling iteration, all Movers added to MonteCarlo are called to generate a new proposed configuration.
The movers propose some modification, which is then accepted or rejected based on the Metropolis criterion. Optionally, a number of local optimization steps are taken before the MonteCarlo step is accepted or rejected.
If you want to sequentially call one mover at every iteration, wrap all movers into a SerialMover first, and then add the SerialMover to MonteCarlo.
By default, the lowest score state encountered is returned.
Definition at line 44 of file MonteCarlo.h.
Public Member Functions | |
| MonteCarlo (Model *m) | |
| double | get_best_accepted_energy () const |
| If return best is on, returns the best energy found so far. More... | |
| double | get_last_accepted_energy () const |
| Return the energy of the last accepted state. More... | |
| double | get_maximum_difference () const |
| double | get_score_threshold () const |
| Get the score threshold. More... | |
| virtual std::string | get_type_name () const override |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| Get information about the module and version of the object. More... | |
| void | set_maximum_difference (double d) |
| void | set_return_best (bool tf) |
| void | set_score_moved (bool mv) |
| If set true (default false), only rescore moved particles. More... | |
| void | set_score_threshold (double s) |
| Set the score threshold. More... | |
| Public Member Functions inherited from IMP::Optimizer | |
| Optimizer (Model *m, std::string name="Optimizer %1%") | |
| double | get_last_score () const |
| Return the score found in the last evaluate. More... | |
| ScoringFunction * | get_scoring_function () const |
| Return the scoring function that is being used. More... | |
| bool | get_stop_on_good_score () const |
| double | optimize (unsigned int max_steps) |
| Optimize the model for up to max_steps iterations. More... | |
| virtual void | set_scoring_function (ScoringFunctionAdaptor sf) |
| Set the scoring function to use. More... | |
| void | set_stop_on_good_score (bool tf) |
| 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 | erase_optimizer_state (unsigned int i) |
| void | reserve_optimizer_states (unsigned int sz) |
| Public Member Functions inherited from IMP::ModelObject | |
| ModelObject (Model *m, std::string name) | |
| bool | get_has_dependencies () const |
| Return whether this object has dependencies computed. More... | |
| bool | get_has_required_score_states () const |
| Return whether score states are computed. More... | |
| ModelObjectsTemp | get_inputs () const |
| ModelObjectsTemps | get_interactions () const |
| Get the interacting sets induced by this ModelObject. More... | |
| Model * | get_model () const |
| ModelObjectsTemp | get_outputs () const |
| const ScoreStatesTemp & | get_required_score_states () const |
| Get the score states that are ancestors of this in the dependency graph. More... | |
| void | set_has_dependencies (bool tf) |
| Either invalidate the dependencies or ensure they are correct. More... | |
| void | set_has_required_score_states (bool tf) |
| Compute the required score states. More... | |
| Public Member Functions inherited from IMP::Object | |
| virtual void | clear_caches () |
| 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) |
Protected Member Functions | |
| bool | do_accept_or_reject_move (double score, double last, const MonteCarloMoverResult &moved) |
| bool | do_accept_or_reject_move (double score, const MonteCarloMoverResult &moved) |
| virtual double | do_evaluate (const ParticleIndexes &moved, bool force_full_score) const |
| Get the current energy. More... | |
| MonteCarloMoverResult | do_move () |
| virtual Float | do_optimize (unsigned int max_steps) override |
| override this function to do actual optimization More... | |
| virtual void | do_step () |
| a class that inherits from this should override this method More... | |
| ParticleIndexes | get_movable_particles () const |
| Protected Member Functions inherited from IMP::Optimizer | |
| virtual ModelObjectsTemp | do_get_inputs () const override |
| virtual ModelObjectsTemp | do_get_outputs () const override |
| don't return anything here to avoid pointless dependencies More... | |
| 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::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
Protected Attributes | |
| ParticleIndexes | reset_pis_ |
kT | |
The kT value has to be on the same scale as the differences in energy between good and bad states (and so the default is likely to not be a good choice). | |
| void | set_kt (Float t) |
| Float | get_kt () const |
Statistics | |
| unsigned int | get_number_of_downward_steps () const |
| Return how many times the optimizer has stepped to lower score. More... | |
| unsigned int | get_number_of_upward_steps () const |
| Return how many times the optimizer has stepped to higher score. More... | |
| unsigned int | get_number_of_proposed_steps () const |
| Get number of proposed moves. More... | |
| unsigned int | get_number_of_accepted_steps () const |
| Get number of accepted moves. More... | |
| void | reset_statistics () |
Movers | |
The following methods are used to manipulate the list of Movers. Each mover is called at each optimization step, giving it a chance to change the current configuration. | |
| list | movers |
| A Python list of Movers More... | |
| void | remove_mover (MonteCarloMover *d) |
| void | remove_movers (const MonteCarloMovers &d) |
| void | set_movers (const MonteCarloMovers &ps) |
| void | set_movers_order (const MonteCarloMovers &objs) |
| unsigned int | add_mover (MonteCarloMover *obj) |
| void | add_movers (const MonteCarloMovers &objs) |
| void | clear_movers () |
| unsigned int | get_number_of_movers () const |
| bool | get_has_movers () |
| MonteCarloMover * | get_mover (unsigned int i) const |
| MonteCarloMovers | get_movers () const |
| void | erase_mover (unsigned int i) |
| void | reserve_movers (unsigned int sz) |
|
protected |
Note that if return best is true, this will save the current state of the model. Also, if the move is accepted, the optimizer states will be updated.
|
protectedvirtual |
Get the current energy.
By default it just calls Optimizer::get_scoring_function()->evaluate(false). However, if an incremental scoring function is used, the list of moved particles will be used to evaluate the score more efficiently. Also, if there is a maximum allowed difference in scores Optimizer::get_scoring_function()->evaluate_if_below() will be called instead, allowing more efficient evaluation. Classes which override this method should be similarly aware for efficiency.
The list of moved particles is passed.
Reimplemented in IMP::isd::HybridMonteCarlo.
Definition at line 182 of file MonteCarlo.h.
Here is the call graph for this function:
|
overrideprotectedvirtual |
override this function to do actual optimization
Implements IMP::Optimizer.
|
protectedvirtual |
a class that inherits from this should override this method
Reimplemented in IMP::core::MonteCarloWithBasinHopping, IMP::core::MonteCarloWithLocalOptimization, IMP::spb::MonteCarloWithWte, and IMP::isd::HybridMonteCarlo.
| double IMP::core::MonteCarlo::get_best_accepted_energy | ( | ) | const |
If return best is on, returns the best energy found so far.
Definition at line 91 of file MonteCarlo.h.
| double IMP::core::MonteCarlo::get_last_accepted_energy | ( | ) | const |
Return the energy of the last accepted state.
Definition at line 88 of file MonteCarlo.h.
|
protected |
Get all movable particles (those that can be moved by the current movers.
| unsigned int IMP::core::MonteCarlo::get_number_of_accepted_steps | ( | ) | const |
Get number of accepted moves.
Definition at line 113 of file MonteCarlo.h.
| unsigned int IMP::core::MonteCarlo::get_number_of_downward_steps | ( | ) | const |
Return how many times the optimizer has stepped to lower score.
Definition at line 100 of file MonteCarlo.h.
| unsigned int IMP::core::MonteCarlo::get_number_of_proposed_steps | ( | ) | const |
Get number of proposed moves.
Definition at line 108 of file MonteCarlo.h.
| unsigned int IMP::core::MonteCarlo::get_number_of_upward_steps | ( | ) | const |
Return how many times the optimizer has stepped to higher score.
Definition at line 104 of file MonteCarlo.h.
| double IMP::core::MonteCarlo::get_score_threshold | ( | ) | const |
Get the score threshold.
Definition at line 129 of file MonteCarlo.h.
|
overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Reimplemented in IMP::core::MonteCarloWithBasinHopping, IMP::core::MonteCarloWithLocalOptimization, IMP::spb::MonteCarloWithWte, and IMP::isd::HybridMonteCarlo.
Definition at line 51 of file MonteCarlo.h.
| void IMP::core::MonteCarlo::set_maximum_difference | ( | double | d | ) |
Computations can be accelerated by throwing out the tails of the distribution of accepted moves. To do this, specify a maximum acceptable difference between the before and after scores.
Definition at line 136 of file MonteCarlo.h.
| void IMP::core::MonteCarlo::set_return_best | ( | bool | tf | ) |
By default, the optimizer returns the lowest scoring state found so far. If, instead, you wish to return the last accepted state, set return best to false.
Definition at line 57 of file MonteCarlo.h.
| void IMP::core::MonteCarlo::set_score_moved | ( | bool | mv | ) |
If set true (default false), only rescore moved particles.
By default, on each move the score of the entire system is calculated. If it is guaranteed that only Movers and ScoreStates move the system, then the score can potentially be calculated more quickly by caching the scores on parts of the system that don't move. This is still experimental.
Definition at line 73 of file MonteCarlo.h.
| void IMP::core::MonteCarlo::set_score_threshold | ( | double | s | ) |
Set the score threshold.
Definition at line 126 of file MonteCarlo.h.
| list IMP::core::MonteCarlo::movers |
A Python list of Movers
Definition at line 147 of file MonteCarlo.h.