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IMP Reference Guide  2.13.0
The Integrative Modeling Platform
IMP::npctransport::BipartitePairsStatisticsOptimizerState Class Reference

#include <IMP/npctransport/BipartitePairsStatisticsOptimizerState.h>

+ Inheritance diagram for IMP::npctransport::BipartitePairsStatisticsOptimizerState:

Detailed Description

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
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
void reset ()
 
- 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...
 
Optimizerget_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...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_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)
 
- Protected Member Functions inherited from IMP::OptimizerState
virtual ModelObjectsTemp do_get_inputs () const
 
virtual ModelObjectsTemp do_get_outputs () const
 
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 ()
 

Constructor & Destructor Documentation

IMP::npctransport::BipartitePairsStatisticsOptimizerState::BipartitePairsStatisticsOptimizerState ( IMP::npctransport::Statistics statistics_manager,
InteractionType  interaction_type,
const ParticlesTemp particlesI,
const ParticlesTemp particlesII,
double  contact_range = 1.0,
double  slack = 1.0 
)

Constructor

Parameters
[in]mthe model associated with particlesI / II
[in]interaction_typethe pair of interacting particle types, assumed to be the types of all particles in particlesI and particlesII, respectively.
[in]particlesIparticles from one side of the interaction
[in]particlesIIparticles from other side of the interaction
[in]contact_rangedefine a contact for particle pairs whose sphere distances are within contact_range in [A]
[in]slackslack for updating close particles in appropriate CloseBiparyiyrPairContainer, this affects only performance - touch only if you know what you're doing

Member Function Documentation

virtual void IMP::npctransport::BipartitePairsStatisticsOptimizerState::do_update ( unsigned int  )
protectedvirtual

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.

virtual std::string IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_type_name ( ) const
virtual

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.

virtual ::IMP::VersionInfo IMP::npctransport::BipartitePairsStatisticsOptimizerState::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 271 of file BipartitePairsStatisticsOptimizerState.h.

void IMP::npctransport::BipartitePairsStatisticsOptimizerState::reset ( )
virtual

restart accumulation of all averages in the next time that update() is called

Reimplemented from IMP::OptimizerState.


The documentation for this class was generated from the following file: