Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Space_filling_model_interpolated_approximation_module< ModuleTraits > Class Template Reference

Module building the interpolated approximation of an input set of particles from their inner and outer approximations Module building the interpolated approximation of an input set of particles from their inner and outer approximations. More...

#include "Space_filling_model_interpolated_approximation_module.hpp"

Public Types

typedef SBL::Modules::T_Space_filling_model_interpolated_approximation_module< ModuleTraits > Self
 
typedef SBL::Modules::Module_base Base
 

Static Public Member Functions

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)
 

Traits Requirements

typedef ModuleTraits::Alpha_complex Alpha_complex
 $\alpha$-complex type used for computing the volumes of the interpolated approximations built during the algorithm. More...
 

Other Types

typedef T_Space_filling_model_coarse_graining_interpolated_cover< Alpha_complexInterpolated_approximation_builder
 Engine computing the interpolated cover between given inner and outer covers. More...
 
typedef Interpolated_approximation_builder::Sphere_3 Sphere_3
 Representation of a sphere in the interpolated approximation. More...
 

Input Accessors

std::vector< Sphere_3 > & get_inner_approximation (void)
 Reference to the container of spheres of the input inner approximation. More...
 
std::vector< Sphere_3 > & get_outer_approximation (void)
 Reference to the container of spheres of the input outer approximation. More...
 
double & get_volume (void)
 Reference to the volume of the union of the input particles. More...
 

Output Accessors

const std::vector< Sphere_3 > & get_interpolated_approximation (void) const
 Const reference to the output interpolated approximation. More...
 
std::vector< Sphere_3 > & get_interpolated_approximation (void)
 Reference to the output interpolated approximation. More...
 

Mandatory Requirements

void run (unsigned verbose, std::ostream &out)
 Runs the module following the input options. More...
 
bool is_runnable (void) const
 Checks that all the input options were set. More...
 
void statistics (std::ostream &out)
 Reports high-level statistics on the module. More...
 
std::string get_name (void) const
 Returns the name of the package. More...
 

Optional Requirements

boost::program_options::options_description add_options (void) const
 Virtual method for adding options to the module. More...
 
bool check_options (std::string &message) const
 Checks that the input options' values are coherent. More...
 
std::string get_output_prefix (void) const
 Returns a prefix that concatains the input line options used when running the module. More...
 
void report (const std::string &prefix)
 Reports the output and statistics in output files. More...
 

Modules Management

void set_module_instance_name (const std::string &module_instance_name)
 Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules. More...
 
const std::string & get_module_instance_name (void) const
 Get the name of this instance of this module. More...
 
void set_report_mode (std::ios_base::openmode report_mode)
 Set a report mode, that is open or append modes. More...
 
void set_report_mode (std::ios_base::openmode &report_mode)
 Set a report mode, that is open or append modes. More...
 
const std::ios_base::openmode get_report_mode (void) const
 Get the report mode to be used when reporting. More...
 

Others

template<class Self_ >
Self_ * clone (const Self_ *s) const
 Clones the object using the copy constructor. More...
 
virtual bool is_logical_module (void) const
 Checks that this module defines a logical operator. More...
 
virtual bool is_condition_module (void) const
 Checks that this module defines a condition operator. More...
 
virtual bool operator() (void)
 Only for condition modules, for returning the predicate value. More...
 
virtual bool is_modules_collection (void) const
 Checks that this module defines a collection of modules. More...
 

Detailed Description

template<class ModuleTraits>
class SBL::Modules::T_Space_filling_model_interpolated_approximation_module< ModuleTraits >

Module building the interpolated approximation of an input set of particles from their inner and outer approximations Module building the interpolated approximation of an input set of particles from their inner and outer approximations.

It uses the algorithm described in T_Space_filling_model_coarse_graining_interpolated_cover for building the interpolated approximation.

The input are the nested inner and outer approximations of an input set of particles, together with the volume of the union of these input particles.

The input inner and outer approximations can be set using the methods SBL::Modules::T_Space_filling_model_interpolated_approximation_module::get_inner_approximation and SBL::Modules::T_Space_filling_model_interpolated_approximation_module::get_outer_approximation that return respectively a reference to the container of the balls defining the input inner and the outer approximations.

The input volume can be set using the method SBL::Modules::T_Space_filling_model_interpolated_approximation_module::get_volume that returns a reference to the input volume.

The output interpolated approximation is accessible via the method SBL::Modules::T_Space_filling_model_interpolated_approximation_module::get_interpolated_approximation.

Template Parameters
ModuleTraitsTraits class defining the type SBL::Modules::T_Space_filling_model_interpolated_approximation_module::Alpha_complex

Member Typedef Documentation

◆ Alpha_complex

typedef ModuleTraits::Alpha_complex Alpha_complex

$\alpha$-complex type used for computing the volumes of the interpolated approximations built during the algorithm.

◆ Base

◆ Interpolated_approximation_builder

Engine computing the interpolated cover between given inner and outer covers.

Template Parameters
AlphaComplex3Model of an alpha-complex used for computing the volume of the inteprolated covers.

◆ Self

◆ Sphere_3

Representation of a sphere in the interpolated approximation.

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 >.

◆ 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 >.

◆ clone()

Self_* clone ( const Self_ *  s) const
inlineinherited

Clones the object using the copy constructor.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_inner_approximation()

std::vector< typename T_Space_filling_model_interpolated_approximation_module< ModuleTraits >::Sphere_3 > & get_inner_approximation ( void  )
inline

Reference to the container of spheres of the input inner approximation.

◆ get_interpolated_approximation() [1/2]

std::vector< typename T_Space_filling_model_interpolated_approximation_module< ModuleTraits >::Sphere_3 > & get_interpolated_approximation ( void  )
inline

Reference to the output interpolated approximation.

◆ get_interpolated_approximation() [2/2]

const std::vector< typename T_Space_filling_model_interpolated_approximation_module< ModuleTraits >::Sphere_3 > & get_interpolated_approximation ( void  ) const
inline

Const reference to the output interpolated approximation.

◆ get_module_instance_name()

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

Get the name of this instance of this module.

◆ get_name()

std::string get_name ( void  ) const
inlinevirtual

Returns the name of the package.

Reimplemented from Module_base.

◆ get_options()

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

Access to the options' description of the module.

◆ get_outer_approximation()

std::vector< typename T_Space_filling_model_interpolated_approximation_module< ModuleTraits >::Sphere_3 > & get_outer_approximation ( void  )
inline

Reference to the container of spheres of the input outer approximation.

◆ 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_report_mode()

const std::ios_base::openmode get_report_mode ( void  ) const
inlineinherited

Get the report mode to be used when reporting.

◆ get_volume()

double & get_volume ( void  )
inline

Reference to the volume of the union of the input particles.

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

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

◆ is_condition_module()

virtual bool is_condition_module ( void  ) const
inlineprotectedvirtualinherited

Checks that this module defines a condition operator.

◆ is_logical_module()

virtual bool is_logical_module ( void  ) const
inlineprotectedvirtualinherited

Checks that this module defines a logical operator.

◆ is_modules_collection()

virtual bool is_modules_collection ( void  ) const
inlineprotectedvirtualinherited

Checks that this module defines a collection of modules.

◆ is_runnable()

bool is_runnable ( void  ) const
inlinevirtual

Checks that all the input options were set.

Reimplemented from Module_base.

◆ operator()()

virtual bool operator() ( void  )
inlineprotectedvirtualinherited

Only for condition modules, for returning the predicate value.

◆ report()

void report ( const std::string &  prefix)
inlinevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

◆ run()

void run ( unsigned  verbose,
std::ostream &  out 
)
inlinevirtual

Runs the module following the input options.

Implements Module_base.

◆ set_module_instance_name()

void set_module_instance_name ( const std::string &  module_instance_name)
inlineinherited

Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules.

◆ set_report_mode() [1/2]

void set_report_mode ( std::ios_base::openmode &  report_mode)
inlineinherited

Set a report mode, that is open or append modes.

◆ set_report_mode() [2/2]

void set_report_mode ( std::ios_base::openmode  report_mode)
inlineinherited

Set a report mode, that is open or append modes.

◆ statistics()

void statistics ( std::ostream &  out)
inlinevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.