IMP Reference Guide
develop.714915d50b,2024/12/07
The Integrative Modeling Platform
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#include <IMP/npctransport/ChainStatisticsOptimizerState.h>
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... | |
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) |
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 () |
IMP::npctransport::ChainStatisticsOptimizerState::ChainStatisticsOptimizerState | ( | const ParticlesTemp & | ps, |
unsigned int | periodicity = 1 |
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ps | the particles being wrapped |
periodicity | frame interval for statistics, equiv. to set_period(1) |
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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.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 113 of file ChainStatisticsOptimizerState.h.
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overridevirtual |
Resets all the statistics about that chain
Reimplemented from IMP::OptimizerState.