Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Exploration_parameters_default< NumberType, Distance > Class Template Reference

Default representation of the parameters of the exploration algorithm. More...

#include <Exploration_parameters.hpp>

Classes

class  Is_lower_sample
 

Public Types

typedef NumberType FT
 
typedef T_Exploration_parameters_default< FT, Distance > Self
 
typedef SBL::IO::Loader_base Base
 
typedef SBL::Models::T_Conformation_traits< typename std::remove_pointer< typename Distance::Point >::type > Conformation_traits
 

Public Member Functions

boost::program_options::options_description add_options (void) const
 Virtual method for adding options to the module. More...
 
bool load (unsigned verbose, std::ostream &out)
 Loads the data. More...
 
bool check_options (std::string &message) const
 Checks that the input options' values are coherent. More...
 
std::string get_name (void) const
 Return the name of the class itself. More...
 
std::string get_output_prefix (void) const
 Returns a prefix that concatains the input line options used when running the module. More...
 
template<class ExplorationAlgorithm >
void update_after_selection (ExplorationAlgorithm &explorer, typename ExplorationAlgorithm::EL_sample_rep s)
 
template<class ExplorationAlgorithm >
void update_after_insertion (ExplorationAlgorithm &explorer, typename ExplorationAlgorithm::EL_sample_rep s)
 
template<class ExplorationAlgorithm >
void update_after_tuning (ExplorationAlgorithm &explorer, typename ExplorationAlgorithm::EL_sample_rep s)
 
template<class ExplorationAlgorithm >
const FTget_initial_temperature (ExplorationAlgorithm &explorer) const
 
template<class ExplorationAlgorithm >
const FTget_initial_displace_delta (ExplorationAlgorithm &explorer) const
 
template<class ExplorationAlgorithm >
const FTget_temperature (ExplorationAlgorithm &explorer) const
 
template<class ExplorationAlgorithm >
void set_temperature (ExplorationAlgorithm &explorer, const FT &temperature)
 
template<class ExplorationAlgorithm >
const FTget_lambda_T (ExplorationAlgorithm &explorer) const
 
template<class ExplorationAlgorithm >
const FTget_displace_delta (ExplorationAlgorithm &explorer) const
 
template<class ExplorationAlgorithm >
void set_displace_delta (ExplorationAlgorithm &explorer, const FT &displace_delta)
 
template<class ExplorationAlgorithm >
const FTget_lambda_D (ExplorationAlgorithm &explorer) const
 
template<class ExplorationAlgorithm >
const FTget_epsilon_height (ExplorationAlgorithm &explorer) const
 
template<class ExplorationAlgorithm >
const FTget_epsilon_distance (ExplorationAlgorithm &explorer) const
 
template<class Archive >
void serialize (Archive &ar, const unsigned BOOST_PFTO int version)
 

Static Public Member Functions

static bool is_lower (const typename Distance::Point &p, const typename Distance::Point &q)
 
static bool are_identical (const typename Distance::Point &p, const typename Distance::Point &q)
 
static boost::program_options::options_description *& get_options (void)
 Access to the options' description of the module. More...
 
static bool has_options (void)
 
static void delete_options (void)
 
static void initialize_options (const std::string &caption)
 

Management

void set_loader_instance_name (const std::string &loader_instance_name)
 
const std::string & get_loader_instance_name (void) const
 

Detailed Description

template<class NumberType, class Distance>
class T_Exploration_parameters_default< NumberType, Distance >

Default representation of the parameters of the exploration algorithm.

The default parameters are the temperature, lambda_T, the displace delta and lambda_D. There are also epsilon values on the energies and distances between conformations when checking if two conformations are similar. In order to initialize the parameters when starting the algorithm, this class is a loader (see package Module_base)Only the temperature and the displace delta evolves during the algorithm: all values are stored in a list for possible analysis of temperature and displace delta evolution during the algorithm. Note that parameters can be updated after the selection, after the extension or after the insertion. By default, they are updated after the insertion. This does not prevent the algorithm to update part of the parameters for its own purpose.

Template Parameters
NumberTypeOutput number type of the distance.
DistanceDistance functor between two conformations.

Member Typedef Documentation

◆ Base

◆ Conformation_traits

typedef SBL::Models::T_Conformation_traits<typename std::remove_pointer<typename Distance::Point>::type> Conformation_traits

◆ FT

typedef NumberType FT

◆ Self

Member Function Documentation

◆ add_options()

boost::program_options::options_description add_options ( void  ) const
inlinevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ are_identical()

static bool are_identical ( const typename Distance::Point &  p,
const typename Distance::Point &  q 
)
inlinestatic

◆ check_options()

bool check_options ( std::string &  message) const
inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_displace_delta()

const FT& get_displace_delta ( ExplorationAlgorithm &  explorer) const
inline

◆ get_epsilon_distance()

const FT& get_epsilon_distance ( ExplorationAlgorithm &  explorer) const
inline

◆ get_epsilon_height()

const FT& get_epsilon_height ( ExplorationAlgorithm &  explorer) const
inline

◆ get_initial_displace_delta()

const FT& get_initial_displace_delta ( ExplorationAlgorithm &  explorer) const
inline

◆ get_initial_temperature()

const FT& get_initial_temperature ( ExplorationAlgorithm &  explorer) const
inline

◆ get_lambda_D()

const FT& get_lambda_D ( ExplorationAlgorithm &  explorer) const
inline

◆ get_lambda_T()

const FT& get_lambda_T ( ExplorationAlgorithm &  explorer) const
inline

◆ get_loader_instance_name()

const std::string& get_loader_instance_name ( void  ) const
inlineinherited

◆ get_name()

std::string get_name ( void  ) const
inlinevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

◆ get_options()

static boost::program_options::options_description*& get_options ( void  )
inlinestaticinherited

Access to the options' description of the module.

◆ get_output_prefix()

std::string get_output_prefix ( void  ) const
inlinevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ get_temperature()

const FT& get_temperature ( ExplorationAlgorithm &  explorer) const
inline

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

static void initialize_options ( const std::string &  caption)
inlinestaticinherited

◆ is_lower()

static bool is_lower ( const typename Distance::Point &  p,
const typename Distance::Point &  q 
)
inlinestatic

◆ load()

bool load ( unsigned  verbose,
std::ostream &  out 
)
inlinevirtual

Loads the data.

Reimplemented from Loader_base.

◆ serialize()

void serialize ( Archive &  ar,
const unsigned BOOST_PFTO int  version 
)
inline

◆ set_displace_delta()

void set_displace_delta ( ExplorationAlgorithm &  explorer,
const FT displace_delta 
)
inline

◆ set_loader_instance_name()

void set_loader_instance_name ( const std::string &  loader_instance_name)
inlineinherited

◆ set_temperature()

void set_temperature ( ExplorationAlgorithm &  explorer,
const FT temperature 
)
inline

◆ update_after_insertion()

void update_after_insertion ( ExplorationAlgorithm &  explorer,
typename ExplorationAlgorithm::EL_sample_rep  s 
)
inline

◆ update_after_selection()

void update_after_selection ( ExplorationAlgorithm &  explorer,
typename ExplorationAlgorithm::EL_sample_rep  s 
)
inline

◆ update_after_tuning()

void update_after_tuning ( ExplorationAlgorithm &  explorer,
typename ExplorationAlgorithm::EL_sample_rep  s 
)
inline