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IMP
2.3.1
The Integrative Modeling Platform
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IMP
2.3.1
The Integrative Modeling Platform
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This variant of Monte Carlo uses basis hopping. More...
#include <IMP/core/MonteCarlo.h>
Inheritance diagram for IMP::core::MonteCarloWithBasinHopping:This variant of Monte Carlo uses basis hopping.
Basin hopping is where, after a move, a local optimizer is used to relax the model before the energy computation. However, the pre-relaxation state of the model is used as the starting point for the next step. The idea is that models are accepted or rejected based on the score of the nearest local minima, but they can still climb the barriers in between as the model is not reset to the minima after each step.
Definition at line 243 of file MonteCarlo.h.
Public Member Functions | |
| MonteCarloWithBasinHopping (Optimizer *opt, unsigned int ns) | |
| 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. More... | |
| Public Member Functions inherited from IMP::core::MonteCarloWithLocalOptimization | |
| MonteCarloWithLocalOptimization (Optimizer *opt, unsigned int steps) | |
| Optimizer * | get_local_optimizer () const |
| unsigned int | get_number_of_steps () const |
| Public Member Functions inherited from IMP::core::MonteCarlo | |
| MonteCarlo (kernel::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... | |
| void | set_maximum_difference (double d) |
| void | set_return_best (bool tf) |
| void | set_score_threshold (double s) |
| Set the score threshold. More... | |
| void | set_kt (Float t) |
| Float | get_kt () const |
| unsigned int | get_number_of_forward_steps () const |
| Return how many times the optimizer has succeeded in taking a step. More... | |
| 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 () |
| 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 | reserve_movers (unsigned int sz) |
| void | set_incremental_scoring_function (IncrementalScoringFunction *isf) |
| bool | get_use_incremental_scoring_function () const |
| IncrementalScoringFunction * | get_incremental_scoring_function () const |
| Public Member Functions inherited from IMP::kernel::Optimizer | |
| Optimizer (kernel::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) |
| 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 | reserve_optimizer_states (unsigned int sz) |
| Public Member Functions inherited from IMP::kernel::ModelObject | |
| ModelObject (kernel::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::base::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 | |
| virtual void | do_step () |
| a class that inherits from this should override this method More... | |
| Protected Member Functions inherited from IMP::core::MonteCarlo | |
| bool | do_accept_or_reject_move (double score, double last, double proposal_ratio) |
| bool | do_accept_or_reject_move (double score, double proposal_ratio) |
| virtual double | do_evaluate (const kernel::ParticleIndexes &moved) const |
| Get the current energy. More... | |
| MonteCarloMoverResult | do_move () |
| virtual Float | do_optimize (unsigned int max_steps) |
| override this function to do actual optimization More... | |
| kernel::ParticleIndexes | get_movable_particles () const |
| 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 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::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... | |
| virtual void | do_destroy () |
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protectedvirtual |
a class that inherits from this should override this method
Reimplemented from IMP::core::MonteCarloWithLocalOptimization.
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virtual |
Get information about the module and version of the object.
Reimplemented from IMP::core::MonteCarloWithLocalOptimization.
Definition at line 250 of file MonteCarlo.h.