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IMP Reference Guide
develop.1a86c4215a,2024/04/24
The Integrative Modeling Platform
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#include <IMP/npctransport/BipartitePairsStatisticsOptimizerState.h>
Inheritance diagram for IMP::npctransport::BipartitePairsStatisticsOptimizerState:Track the interaction between pairs from one group of particles with particles from another group, within some specified contact range
Definition at line 29 of file BipartitePairsStatisticsOptimizerState.h.
Public Member Functions | |
| BipartitePairsStatisticsOptimizerState (IMP::npctransport::Statistics *statistics_manager, InteractionType interaction_type, const ParticlesTemp &particlesI, const ParticlesTemp &particlesII, double contact_range=1.0, double slack=1.0) | |
| double | get_average_fraction_bound_particle_sites_I () const |
| double | get_average_fraction_bound_particle_sites_II () const |
| double | get_average_fraction_bound_particles_I () const |
| double | get_average_fraction_bound_particles_II () const |
| double | get_average_fraction_nonspecific_interactions_I () const |
| double | get_average_fraction_nonspecific_interactions_II () const |
| double | get_average_number_of_contacts () const |
| double | get_average_off_per_bound_I_per_ns () const |
| double | get_average_off_per_bound_II_per_ns () const |
| double | get_average_off_per_contact_per_ns () const |
| double | get_average_on_per_missing_contact_per_ns () const |
| double | get_average_on_per_unbound_I_per_ns () const |
| double | get_average_on_per_unbound_II_per_ns () const |
| InteractionType | get_interaction_type () const |
| double | get_misc_stats_period_ns () const |
| Int | get_number_of_particles_1 () |
| Int | get_number_of_particles_2 () |
| double | get_off_I_stats_period_ns () const |
| double | get_off_II_stats_period_ns () const |
| double | get_off_stats_period_ns () const |
| double | get_on_I_stats_period_ns () const |
| double | get_on_II_stats_period_ns () const |
| double | get_on_stats_period_ns () const |
| 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 | reset () override |
| Public Member Functions inherited from IMP::OptimizerState | |
| OptimizerState (Model *m, std::string name) | |
| Constructor. More... | |
| unsigned int | get_number_of_updates () const |
| Return the number of times do_update() has been called. More... | |
| Optimizer * | get_optimizer () const |
| unsigned int | get_period () const |
| Get the periodicity of this state. More... | |
| virtual void | set_is_optimizing (bool) |
| Called by an Optimizer to signal begin/end of an optimize run. More... | |
| void | set_number_of_updates (unsigned int n) |
| Set the counter of number of times do_update() has been called. More... | |
| void | set_period (unsigned int p) |
| Set the periodicity of this state. More... | |
| virtual void | update () |
| Called when the Optimizer accepts a new conformation. More... | |
| void | update_always () |
| Force the state to perform its action now, ignoring the periodicity. More... | |
| 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 | |
| virtual void | do_update (unsigned int call_num) override |
| Protected Member Functions inherited from IMP::OptimizerState | |
| virtual ModelObjectsTemp | do_get_inputs () const override |
| virtual ModelObjectsTemp | do_get_outputs () const override |
| virtual void | do_set_is_optimizing (bool) |
| 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 () |
| IMP::npctransport::BipartitePairsStatisticsOptimizerState::BipartitePairsStatisticsOptimizerState | ( | IMP::npctransport::Statistics * | statistics_manager, |
| InteractionType | interaction_type, | ||
| const ParticlesTemp & | particlesI, | ||
| const ParticlesTemp & | particlesII, | ||
| double | contact_range = 1.0, |
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| double | slack = 1.0 |
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| ) |
Constructor
| [in] | m | the model associated with particlesI / II |
| [in] | interaction_type | the pair of interacting particle types, assumed to be the types of all particles in particlesI and particlesII, respectively. |
| [in] | particlesI | particles from one side of the interaction |
| [in] | particlesII | particles from other side of the interaction |
| [in] | contact_range | define a contact for particle pairs whose sphere distances are within contact_range in [A] |
| [in] | slack | slack for updating close particles in appropriate CloseBiparyiyrPairContainer, this affects only performance - touch only if you know what you're doing |
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overrideprotectedvirtual |
This method is called every get_period() update calls. The number of times this method has been called since the last reset or start of the optimization run is passed.
Reimplemented from IMP::OptimizerState.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_fraction_bound_particle_sites_I | ( | ) | const |
returns the average fraction of particle sites from group I that are bound in each update round
Definition at line 192 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_fraction_bound_particle_sites_II | ( | ) | const |
returns the average fraction of particle sites from group II that are bound in each update round
Definition at line 198 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_fraction_bound_particles_I | ( | ) | const |
returns the average fraction of particles from group I that are bound in each update round
Definition at line 178 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_fraction_bound_particles_II | ( | ) | const |
returns the average fraction of particles from group II that are bound in each update round
Definition at line 186 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_fraction_nonspecific_interactions_I | ( | ) | const |
returns the average fraction of particles from type I that are nonspecifically interaction with particles of type II (= non-zero contribution)
Definition at line 205 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_fraction_nonspecific_interactions_II | ( | ) | const |
returns the average fraction of particles from type II that are nonspecifically interaction with particles of type I (= non-zero contribution)
Definition at line 212 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_number_of_contacts | ( | ) | const |
returns the average number of interacting pairs of particles per update
Definition at line 135 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_off_per_bound_I_per_ns | ( | ) | const |
returns the average off rate per bound particles of type I since last reset()
Definition at line 146 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_off_per_bound_II_per_ns | ( | ) | const |
returns the average off rate per bound particles of type II since last reset()
Definition at line 152 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_off_per_contact_per_ns | ( | ) | const |
returns the average off rate per bound complex per nanosecond since last reset()
Definition at line 140 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_on_per_missing_contact_per_ns | ( | ) | const |
returns the average on rate per missing possible contact (out of all theoretically possible contacts between particlesI and particles II)
Definition at line 159 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_on_per_unbound_I_per_ns | ( | ) | const |
returns the average on rate per unbound particles of type I since last resetI()
Definition at line 165 of file BipartitePairsStatisticsOptimizerState.h.
| double IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_average_on_per_unbound_II_per_ns | ( | ) | const |
returns the average on rate per unbound particles of type II since last resetII()
Definition at line 171 of file BipartitePairsStatisticsOptimizerState.h.
| InteractionType IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_interaction_type | ( | ) | const |
returns the particle types of the first and second group of particles, respectively. This might change in the future, since types can be mixed
Definition at line 129 of file BipartitePairsStatisticsOptimizerState.h.
| Int IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_number_of_particles_1 | ( | ) |
return the total number of particles in the first group
Definition at line 219 of file BipartitePairsStatisticsOptimizerState.h.
| Int IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_number_of_particles_2 | ( | ) |
return the total number of particles in the second group
Definition at line 224 of file BipartitePairsStatisticsOptimizerState.h.
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overridevirtual |
update fraction bound with n1 bound particles of type I; and n2 bound particles of type II, assuming old_updates for the old average
Reimplemented from IMP::Object.
Definition at line 271 of file BipartitePairsStatisticsOptimizerState.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 271 of file BipartitePairsStatisticsOptimizerState.h.
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overridevirtual |
restart accumulation of all averages in the next time that update() is called
Reimplemented from IMP::OptimizerState.