Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Exploration_algorithm_basins_hopping< ELSampleType, SampleSelector, SampleExtender > Class Template Reference

Model of exploration algorithm for basins hopping. More...

#include <Exploration_algorithm_basins_hopping.hpp>

Public Types

typedef T_Exploration_algorithm_basins_hopping< ELSampleType, SampleSelector, SampleExtender > Self
typedef SampleSelector Sample_selector
typedef SampleExtender Sample_extender
typedef ELSampleType EL_sample_type
typedef SBL::Models::T_Conformation_traits< ELSampleType > Conformation_traits
typedef Conformation_traits::FT FT
typedef std::vector< EL_sample_type * > Samples_container
typedef unsigned EL_sample_rep

Public Member Functions

 T_Exploration_algorithm_basins_hopping (void)
Sample_selectorget_selector (void)
EL_sample_typeget_last_generated_sample (void)
EL_sample_rep get_selection (void) const
void set_selection (EL_sample_rep s)
Sample_extenderget_extender (void)
unsigned get_number_of_samples (void) const
EL_sample_rep get_last_sample (void) const
EL_sample_typeget_last_minimum (void)
EL_sample_typeget_sample (EL_sample_rep s)
unsigned get_number_of_connected_components (void) const
template<class ExplorationParameters >
bool insert (ExplorationParameters &parameters, EL_sample_type *s)
template<class OutputIterator >
OutputIterator get_samples (OutputIterator out) const
template<class OutputIterator >
OutputIterator get_minima (OutputIterator out) const

Detailed Description

template<class ELSampleType, class SampleSelector, class SampleExtender>
class T_Exploration_algorithm_basins_hopping< ELSampleType, SampleSelector, SampleExtender >

Model of exploration algorithm for basins hopping.

It implements the basins hopping algorithm as an exploration algorithm. It maintains a database of conformations using a simple vector. When a conformation is about to be inserted, the selector engine first checks if it already exists: if not, it is inserted in the vector. Note that due to the extender engine of basins hopping, all conformations that are inserted are minima.

Template Parameters
ELSampleTypeRepresentation of an elevated conformation (has to define a method get_point returning its representation as a D-dimensional point).
SampleSelectorSelector engine used with the base TRRT algorithm – see T_Sample_selector_for_BH .
SampleExtenderExtender engine used with the base TRRT algorithm – see T_Sample_extender_for_BH .

Member Typedef Documentation

◆ Conformation_traits

◆ EL_sample_rep

typedef unsigned EL_sample_rep

◆ EL_sample_type

typedef ELSampleType EL_sample_type

◆ FT

typedef Conformation_traits::FT FT

◆ Sample_extender

typedef SampleExtender Sample_extender

◆ Sample_selector

typedef SampleSelector Sample_selector

◆ Samples_container

typedef std::vector<EL_sample_type*> Samples_container

◆ Self

typedef T_Exploration_algorithm_basins_hopping<ELSampleType, SampleSelector, SampleExtender> Self

Constructor & Destructor Documentation

◆ T_Exploration_algorithm_basins_hopping()

Member Function Documentation

◆ get_extender()

Sample_extender& get_extender ( void  )

◆ get_last_generated_sample()

EL_sample_type* get_last_generated_sample ( void  )

◆ get_last_minimum()

EL_sample_type* get_last_minimum ( void  )

◆ get_last_sample()

EL_sample_rep get_last_sample ( void  ) const

◆ get_minima()

OutputIterator get_minima ( OutputIterator  out) const

◆ get_number_of_connected_components()

unsigned get_number_of_connected_components ( void  ) const

◆ get_number_of_samples()

unsigned get_number_of_samples ( void  ) const

◆ get_sample()

EL_sample_type* get_sample ( EL_sample_rep  s)

◆ get_samples()

OutputIterator get_samples ( OutputIterator  out) const

◆ get_selection()

EL_sample_rep get_selection ( void  ) const

◆ get_selector()

Sample_selector& get_selector ( void  )

◆ insert()

bool insert ( ExplorationParameters &  parameters,
EL_sample_type s 

◆ set_selection()

void set_selection ( EL_sample_rep  s)