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IMP Reference Guide  develop.5651aa123e,2024/07/23
The Integrative Modeling Platform
IMP::npctransport::ChainStatisticsOptimizerState Class Reference

#include <IMP/npctransport/ChainStatisticsOptimizerState.h>

+ Inheritance diagram for IMP::npctransport::ChainStatisticsOptimizerState:

Detailed Description

Compute various statistics of a chain.

Definition at line 22 of file ChainStatisticsOptimizerState.h.

Public Member Functions

 ChainStatisticsOptimizerState (const ParticlesTemp &ps, unsigned int periodicity=1)
 
virtual void do_update (unsigned int call_num) override
 
double get_correlation_time () const
 
double get_diffusion_coefficient () const
 
Floats get_local_diffusion_coefficients () const
 
double get_mean_bond_distance () const
 returns the mean bond distance of this chain More...
 
double get_mean_end_to_end_distance () const
 returns the mean end-to-end distance of this chain More...
 
double get_mean_radius_of_gyration () const
 returns the mean Rgyr of this chain More...
 
double get_mean_square_bond_distance () const
 
double get_mean_square_end_to_end_distance () const
 
double get_mean_square_radius_of_gyration () 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...
 
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)
 

Additional Inherited Members

- 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 ()
 

Constructor & Destructor Documentation

IMP::npctransport::ChainStatisticsOptimizerState::ChainStatisticsOptimizerState ( const ParticlesTemp ps,
unsigned int  periodicity = 1 
)
Parameters
psthe particles being wrapped
periodicityframe interval for statistics, equiv. to set_period(1)

Member Function Documentation

virtual void IMP::npctransport::ChainStatisticsOptimizerState::do_update ( unsigned int  )
overridevirtual

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::ChainStatisticsOptimizerState::get_diffusion_coefficient ( ) const

get an estimate of the diffusion coefficient of the entire chain in A^2/fs units

Floats IMP::npctransport::ChainStatisticsOptimizerState::get_local_diffusion_coefficients ( ) const

returns a vector of diffusion coefficients for each particle in the chain, computed in the local reference frame of the chain (by locally aligning the chain)

double IMP::npctransport::ChainStatisticsOptimizerState::get_mean_bond_distance ( ) const

returns the mean bond distance of this chain

Definition at line 97 of file ChainStatisticsOptimizerState.h.

double IMP::npctransport::ChainStatisticsOptimizerState::get_mean_end_to_end_distance ( ) const

returns the mean end-to-end distance of this chain

Definition at line 85 of file ChainStatisticsOptimizerState.h.

double IMP::npctransport::ChainStatisticsOptimizerState::get_mean_radius_of_gyration ( ) const

returns the mean Rgyr of this chain

Definition at line 73 of file ChainStatisticsOptimizerState.h.

double IMP::npctransport::ChainStatisticsOptimizerState::get_mean_square_bond_distance ( ) const

returns the mean square bond distance, which can be used to compute std-dev (but recorded separately so it could be averaged with other chains)

Definition at line 104 of file ChainStatisticsOptimizerState.h.

double IMP::npctransport::ChainStatisticsOptimizerState::get_mean_square_end_to_end_distance ( ) const

returns the mean square end-to-end distance, which can be used to compute std-dev (but recorded separately so it could be averaged with other chains)

Definition at line 92 of file ChainStatisticsOptimizerState.h.

double IMP::npctransport::ChainStatisticsOptimizerState::get_mean_square_radius_of_gyration ( ) const

returns the mean Rgyr^2, which can be used to compute std-dev (but recorded separately so it could be averaged with other chains)

Definition at line 80 of file ChainStatisticsOptimizerState.h.

virtual ::IMP::VersionInfo IMP::npctransport::ChainStatisticsOptimizerState::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 113 of file ChainStatisticsOptimizerState.h.

void IMP::npctransport::ChainStatisticsOptimizerState::reset ( )
overridevirtual

Resets all the statistics about that chain

Reimplemented from IMP::OptimizerState.


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