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. More...

#include "Buried_surface_area_without_label_module.hpp"

Static Public Member Functions

static boost::program_options::options_description *& get_options (void)
 Access to the options' description of the module. More...
 

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_traits > Buried_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.

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.

 \tparam ModuleTraits Traits 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.

◆ Buried_surface_area

typedef SBL::CSB::T_Buried_surface_area_without_label<typename Alpha_complex::Alpha_complex_of_molecular_model_traits::Particle_traits> Buried_surface_area

Compute the buried surface area of two given partners.

Compute the buried surface area of two given partners

  \tparam ParticleTraits Model of the concept \ref ParticleTraits-package.

  \tparam FT Number 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.

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<>.

◆ check_options()

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

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description<>.

◆ clone()

Self_* clone ( const Self_ *  s) const
inlineinherited

Clones the object using the copy constructor.

◆ 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]

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_buried_surface_area() [2/2]

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_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<>.

◆ get_report_mode()

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

Get the report mode to be used when reporting.

◆ 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.