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

#include "Buried_surface_area_with_labels_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::Particle_BSA_record	Particle_BSA_record
	or SBL::CSB::T_BSA_record_pseudoatom More...

Other Types
typedef SBL::CSB::T_Buried_surface_area_with_labels< typename Alpha_complex::Alpha_complex_of_molecular_model_traits::Particle_traits, Particle_BSA_record >	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...

Output Accessors
const Buried_surface_area &	get_buried_surface_area (void) const
	Const reference to the output buried surface area functor. More...

Buried_surface_area &	get_buried_surface_area (void)
	Reference to the output buried surface area functor. More...

Mandatory Requirements
void	run (unsigned verbose, std::ostream &out) override
	Runs the module following the input options. More...

bool	is_runnable (void) const override
	Checks that all the input options were set. More...

void	statistics (std::ostream &out) override
	Reports high-level statistics on the module. More...

std::string	get_name (void) const override
	Returns the name of the package. More...

Optional Requirements
boost::program_options::options_description	add_options (void) override
	Virtual method for adding options to the module. More...

bool	check_options (std::string &message) const override
	Checks that the input options' values are coherent. More...

std::string	get_output_prefix (void) const override
	Returns a prefix that concatains the input line options used when running the module. More...

void	report (const std::string &prefix) override
	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...

Optional Requirements
void	check_filesystem_directory_exists (const std::string &output_prefix)
	To avoid later crash: check filesystem / existence of directory / directory exists. 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_with_labels_module< ModuleTraits >

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

It builds from an input $\alpha$ -complex of type SBL::Modules::T_Buried_surface_area_with_labels_module::Alpha_complex, an object of type SBL::Modules::T_Buried_surface_area_with_labels_module::Buried_surface_area: it is a functor that returns the buried surface area of the input $\alpha$ -complex restricted to an input partner's label.

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

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

Template Parameters

ModuleTraits Traits class defining the type SBL::Modules::T_Buried_surface_area_with_labels_module::Alpha_complex.

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

ParticleTraits	Traits class defining geometric properties of a particle.
TAlphaComplexVertexBase	Base class for representing a vertex in the 3D $\alpha$ -complex. It has SBL::CSB::T_Alpha_complex_vertex_base_3 as default type.
TAlphaComplexCellBase	Base class for representing a cell in the 3D $\alpha$ -complex. It has SBL::CSB::T_Alpha_complex_cell_base_3 as default type.
TAlphaComplexBase	Base 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_with_labels<typename Alpha_complex::Alpha_complex_of_molecular_model_traits::Particle_traits, Particle_BSA_record> Buried_surface_area

Compute the buried surface area of two given partners

Template Parameters

ParticleWithSystemLabelTraits	Model of the concept ParticleTraits where each particle has a system's label.
FT	Number type used for representing the buried surface area (default is intervals of double).

◆ Particle_BSA_record

typedef ModuleTraits::Particle_BSA_record Particle_BSA_record

or SBL::CSB::T_BSA_record_pseudoatom

Member Function Documentation

◆ add_options()

boost::program_options::options_description add_options ( void )

inlineoverridevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ check_filesystem_directory_exists()

void check_filesystem_directory_exists ( const std::string & output_prefix )

inlineinherited

To avoid later crash: check filesystem / existence of directory / directory exists.

◆ check_options()

bool check_options ( std::string & message ) const

inlineoverridevirtual

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.

◆ get_alpha_complex()

T_Buried_surface_area_with_labels_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_with_labels_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_with_labels_module< ModuleTraits >::Buried_surface_area & get_buried_surface_area ( void ) const

inline

Const reference to the output buried surface area functor.

◆ 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

inlineoverridevirtual

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

inlineoverridevirtual

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.

◆ 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

inlineoverridevirtual

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 )

inlineoverridevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

◆ run()

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

inlineoverridevirtual

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 )

inlineoverridevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.

Static Public Member Functions

Traits Requirements

Other Types

Input Accessors

Output Accessors

Mandatory Requirements

Optional Requirements

Modules Management

Optional Requirements

Others

Detailed Description

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

Member Typedef Documentation

◆ Alpha_complex

◆ Buried_surface_area

◆ Particle_BSA_record

Member Function Documentation

◆ add_options()

◆ check_filesystem_directory_exists()

◆ check_options()

◆ clone()

◆ get_alpha_complex()

◆ get_buried_surface_area() [1/2]

◆ get_buried_surface_area() [2/2]

◆ get_module_instance_name()

◆ get_name()

◆ get_options()

◆ get_output_prefix()

◆ get_report_mode()

◆ is_condition_module()

◆ is_logical_module()

◆ is_modules_collection()

◆ is_runnable()

◆ operator()()

◆ report()

◆ run()

◆ set_module_instance_name()

◆ set_report_mode() [1/2]

◆ set_report_mode() [2/2]

◆ statistics()

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