T_Tertiary_quaternary_structure_annotator_module< ModuleTraits > Class Template Reference

Module building the Biochemical Interfaces Graph of a molecular structure. More...

#include <Tertiary_quaternary_structure_annotator_module.hpp>

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

Input Accessors
const Molecular_model *&	get_molecular_model (void)

Output Accessors
Interfaces_graph &	get_interfaces_graph (void)
	Const reference to the output Interfaces Graph. More...
const Interfaces_graph &	get_interfaces_graph (void) const
	Reference to the output Interfaces Graph. 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...
Self *	clone (void) const
	Clones the object using the copy constructor. 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_Tertiary_quaternary_structure_annotator_module< ModuleTraits >

Module building the Biochemical Interfaces Graph of a molecular structure.

Template Parameters

ModuleTraits

Traits class defining the types T_Tertiary_quaternary_structure_annotator_module::Particle_traits from the concept ParticleTraits , and T_Tertiary_quaternary_structure_annotator_module::Label_traits from the concept MolecularSystemLabelsTraits .

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() [1/2]

Self_* clone ( const Self_ *  s ) const

inlineinherited

Clones the object using the copy constructor.

clone() [2/2]

T_Tertiary_quaternary_structure_annotator_module< ModuleTraits > * clone ( void  ) const

inline

Clones the object using the copy constructor.

get_interfaces_graph() [1/2]

T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >::Interfaces_graph & get_interfaces_graph ( void  )

inline

Const reference to the output Interfaces Graph.

get_interfaces_graph() [2/2]

const T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >::Interfaces_graph & get_interfaces_graph ( void  ) const

inline

Reference to the output Interfaces Graph.

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.