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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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#include <IMP/npctransport/ChainStatisticsOptimizerState.h>
Inheritance diagram for IMP::npctransport::ChainStatisticsOptimizerState: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.