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"

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

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

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.

Input Accessors
Alpha_complex *&	get_alpha_complex (void)
	Reference to a pointer over the input $\alpha$ -complex.
Is_in_partner &	get_is_in_partner (void)
	Reference to the input predicate.

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

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

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

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.
const std::string &	get_module_instance_name (void) const
	Get the name of this instance of this module.
void	set_report_mode (std::ios_base::openmode report_mode)
	Set a report mode, that is open or append modes.
void	set_report_mode (std::ios_base::openmode &report_mode)
	Set a report mode, that is open or append modes.
const std::ios_base::openmode	get_report_mode (void) const
	Get the report mode to be used when reporting.

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

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

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

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

template<class ModuleTraits>

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

template<class ModuleTraits>

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

Template Parameters

ParticleTraits	Model of the concept ParticleTraits.
FT	Number type used for representing the buried surface area (default is intervals of double).

◆ Is_in_partner

template<class ModuleTraits>

typedef ModuleTraits::Is_in_partner Is_in_partner

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

Member Function Documentation

◆ add_options()

template<class ModuleTraits>

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()

template<class ModuleTraits>

bool check_options ( std::string & message ) const

inlineoverridevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

◆ clone()

template<class Self_>

Self_ * clone ( const Self_ * s ) const

inlineinherited

Clones the object using the copy constructor.

◆ get_alpha_complex()

template<class ModuleTraits>

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]

template<class ModuleTraits>

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]

template<class ModuleTraits>

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()

template<class ModuleTraits>

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()

template<class ModuleTraits>

std::string get_name ( void ) const

inlineoverridevirtual

Returns the name of the package.

Reimplemented from Module_base.

◆ get_options()

template<class Dummy = void>

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

inlinestaticinherited

Access to the options' description of the module.

◆ get_output_prefix()

template<class ModuleTraits>

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()

template<class ModuleTraits>

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()

template<class ModuleTraits>

void report ( const std::string & prefix )

inlineoverridevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

◆ run()

template<class ModuleTraits>

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()

template<class ModuleTraits>

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

Member Typedef Documentation

◆ Alpha_complex

◆ Buried_surface_area

◆ Is_in_partner

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_is_in_partner()

◆ 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()