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

Module building the buried surface area of a partner from the alpha-complex of a molecular model. Module building the buried surface area of a partner from the alpha-complex of a molecular model. More...

#include "Buried_surface_area_without_label_module.hpp"

Public Types

typedef T_Buried_surface_area_without_label_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
 Derived class from CGAL alpha-complex for filling it with particles. More...
 
typedef ModuleTraits::Is_in_partner Is_in_partner
 Predicate checking that an input particle is in a given partner. More...
 

Other Types

typedef SBL::CSB::T_Buried_surface_area_without_label< typename Alpha_complex::Alpha_complex_of_molecular_model_traits::Particle_traitsBuried_surface_area
 Compute the buried surface area of two given partners. More...
 

Input Accessors

Alpha_complex *& get_alpha_complex (void)
 Reference to a pointer over the input $\alpha$-complex. More...
 
Is_in_partnerget_is_in_partner (void)
 Reference to the input predicate. More...
 

Output Accessors

const Buried_surface_areaget_buried_surface_area (void) const
 Const reference to the output buried surface area functor. More...
 
Buried_surface_areaget_buried_surface_area (void)
 Reference to the output buried surface area functor. 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_Buried_surface_area_without_label_module< ModuleTraits >

Module building the buried surface area of a partner from the alpha-complex of a molecular model. Module building the buried surface area of a partner from the alpha-complex of a molecular model.

It builds from an input $\alpha$-complex of type SBL::Modules::T_Buried_surface_area_without_label_module::Alpha_complex, an object of type SBL::Modules::T_Buried_surface_area_without_label_module::Buried_surface_area: it is a functor that returns the buried surface area of the input $\alpha$-complex restricted to a partner defined by an input predicate of type SBL::Modules::T_Buried_surface_area_without_label_module::Is_in_partner. This predicate simply checks that an input particle is in the requested partner. Note that contrarily to the module SBL::Modules::T_Buried_surface_area_with_labels_module, this module computes the buried surface area of only one partner.

The input $\alpha$-complex can be set using the method SBL::Modules::T_Buried_surface_area_without_label_module::get_alpha_complex, that returns a reference over a pointer on the input $\alpha$-complex.

The input partner's predicate be set using the method SBL::Modules::T_Buried_surface_area_without_label_module::get_is_in_partner, that returns a reference over a pointer on the input predicate.

The built functor for computing the buried surfacve area is accessible with the method SBL::Modules::T_Buried_surface_area_without_label_module::get_buried_surface_area.

Template Parameters
ModuleTraitsTraits class defining the types SBL::Modules::T_Buried_surface_area_without_label_module::Alpha_complex and SBL::Modules::T_Buried_surface_area_without_label_module::Is_in_partner.

Member Typedef Documentation

◆ Alpha_complex

typedef ModuleTraits::Alpha_complex Alpha_complex

Derived class from CGAL alpha-complex for filling it with particles.

It uses ParticleTraits for determining the geometrical kernel used for the representation and computation of the $\alpha$-complex, and for attaching atom data to their corresponding vertex.

Template Parameters
ParticleTraitsTraits class defining geometric properties of a particle.
TAlphaComplexVertexBaseBase class for representing a vertex in the 3D $\alpha$-complex. It has SBL::CSB::T_Alpha_complex_vertex_base_3 as default type.
TAlphaComplexCellBaseBase class for representing a cell in the 3D $\alpha$-complex. It has SBL::CSB::T_Alpha_complex_cell_base_3 as default type.
TAlphaComplexBaseBase template representation of the $\alpha$-complex it-self without biological context. It allows to switch easily between the class CGAL::Fixed_alpha_shape_3 and the class CGAL::Alpha_shape_3. It has SBL::CSB::T_Alpha_complex_base_3 as default type, that is a wrapper for using both CGAL data structures.

◆ Base

◆ Buried_surface_area

Compute the buried surface area of two given partners.

Compute the buried surface area of two given partners

Template Parameters
ParticleTraitsModel of the concept ParticleTraits.
FTNumber type used for representing the buried surface area (default is intervals of double).

◆ Is_in_partner

typedef ModuleTraits::Is_in_partner Is_in_partner

Predicate checking that an input particle is in a given partner.

◆ 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 >.

◆ 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_alpha_complex()

T_Buried_surface_area_without_label_module< ModuleTraits >::Alpha_complex *& get_alpha_complex ( void  )
inline

Reference to a pointer over the input $\alpha$-complex.

◆ get_buried_surface_area() [1/2]

T_Buried_surface_area_without_label_module< ModuleTraits >::Buried_surface_area & get_buried_surface_area ( void  )
inline

Reference to the output buried surface area functor.

◆ get_buried_surface_area() [2/2]

const T_Buried_surface_area_without_label_module< ModuleTraits >::Buried_surface_area & get_buried_surface_area ( void  ) const
inline

Const reference to the output buried surface area functor.

◆ get_is_in_partner()

T_Buried_surface_area_without_label_module< ModuleTraits >::Is_in_partner & get_is_in_partner ( void  )
inline

Reference to the input predicate.

◆ 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_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.

◆ 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.