T_Alpha_complex_of_molecular_model_module< ModuleTraits > Class Template Reference

Module building the alpha-complex of an input set of particles. Module building the alpha-complex of an input set of particles. More...

#include "Alpha_complex_of_molecular_model_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::Particles_container	Particles_container
	Representation of the input collection of particles.
typedef ModuleTraits::Alpha_complex	Alpha_complex
	Representation of the output -complex.

Other Types
typedef Alpha_complex::Triangulation	Triangulation
	Underlaying triangulation of the -complex.

Input Accessors
Particles_container *&	get_particles (void)
	Reference to the input particles container.
Triangulation &	get_triangulation (void)
	Reference to the underlying triangulation of the output -complex.

Output Accessors
const Alpha_complex &	get_alpha_complex (void) const
	Const reference to the output -complex.
Alpha_complex &	get_alpha_complex (void)
	Reference to the output -complex.

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_Alpha_complex_of_molecular_model_module< ModuleTraits >

Module building the alpha-complex of an input set of particles. Module building the alpha-complex of an input set of particles.

It is designed such that the input can be either a collection of 3D spheres representing the particles, or a collection of particles with the type derived from ParticleTraits, depending on the type of the output -complex:

• Alpha_shape_3 or Fixed_alpha_shape_3 : the input is a collection of particles represented by weighted points (Weighted_point), that is a 3D point (the center of a particle represented as a 3D sphere) with an associated weight (the squared radius of the 3D sphere).

• SBL::CSB::T_Alpha_complex_of_molecular_model<ParticleTraits>: the input is a collection of particles represented by the class Particle_base defined in ParticleTraits.

The input collection of particles can be set using the method T_Alpha_complex_of_molecular_model_module::get_particles, that return a reference over the container of particles. Note also that the 3D triangulation underlying the output -complex can be parametrized using the method T_Alpha_complex_of_molecular_model_module::get_triangulation. This is particularly useful when an additional radius has to be set to all the particles when using the class SBL::CSB::T_Alpha_complex_of_molecular_model, for example in the case of the Solvent Accessible Model,solvent accessible model.

Template Parameters

ModuleTraits

Traits class defining the types T_Alpha_complex_of_molecular_model_module::Alpha_complex and T_Alpha_complex_of_molecular_model_module::Particles_container.

Member Typedef Documentation

Alpha_complex

template<class ModuleTraits>

typedef ModuleTraits::Alpha_complex Alpha_complex

Representation of the output -complex.

Its type is partially determined by the type of particles:

• when using Weighted_point, it should be Alpha_shape_3 or Fixed_alpha_shape_3
• when using the Particle_base structure defined in ParticleTraits, it should be the class SBL::CSB::T_Alpha_complex_of_molecular_model

Particles_container

template<class ModuleTraits>

typedef ModuleTraits::Particles_container Particles_container

Representation of the input collection of particles.

It could be any of the stl container having the begin(), end() and size() methods. The value type of the elements of the container is the particle type and can be either:

• Weighted_point
• the Particle_base structure defined in ParticleTraits.

Triangulation

template<class ModuleTraits>

typedef Alpha_complex::Triangulation Triangulation

Underlaying triangulation of the -complex.

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() [1/2]

template<class ModuleTraits>

T_Alpha_complex_of_molecular_model_module< ModuleTraits >::Alpha_complex & get_alpha_complex ( void )

inline

Reference to the output -complex.

get_alpha_complex() [2/2]

template<class ModuleTraits>

const T_Alpha_complex_of_molecular_model_module< ModuleTraits >::Alpha_complex & get_alpha_complex ( void ) const

inline

Const reference to the output -complex.

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_particles()

template<class ModuleTraits>

T_Alpha_complex_of_molecular_model_module< ModuleTraits >::Particles_container *& get_particles ( void )

inline

Reference to the input particles container.

get_report_mode()

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

inlineinherited

Get the report mode to be used when reporting.

get_triangulation()

template<class ModuleTraits>

T_Alpha_complex_of_molecular_model_module< ModuleTraits >::Triangulation & get_triangulation ( void )

inline

Reference to the underlying triangulation of the output -complex.

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.