Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Correlated_motions_by_domain_module< ModuleTraits > Class Template Reference

Module computing the rigid motion between domains and comparing the rotations of the rigid motions. More...

#include <Correlated_motions_by_domain_module.hpp>

Public Types

typedef T_Correlated_motions_by_domain_module< ModuleTraits > Self
 
typedef SBL::Modules::Module_base Base
 
typedef ModuleTraits::Particle_traits Particle_traits
 Traits class for particles. More...
 
typedef ModuleTraits::Particles_container Particles_container
 Container for the input particles (atoms or pseudo-atoms). More...
 
typedef ModuleTraits::Label_traits Label_traits
 Traits class defining system's labels attached to particles. More...
 
typedef ModuleTraits::Get_label_identifier Get_label_identifier
 Functor returning the identifier of the primitive label of a particle. More...
 

Static Public Member Functions

static boost::program_options::options_description *& get_options (void)
 Access to the options' description of the module. More...
 
static bool has_options (void)
 
static void delete_options (void)
 
static void initialize_options (const std::string &caption)
 

Input Accessors

Particles_container *& get_first_particles (void)
 Reference to the first container of particles. More...
 
Particles_container *& get_second_particles (void)
 Reference to the second container of particles. More...
 
Get_label_identifierget_label_identifier (void)
 Reference to the functor labeling the particles in the first container. 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...
 
Selfclone (void) const
 Clones the object using the copy constructor. 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 T_Correlated_motions_by_domain_module< ModuleTraits >

Module computing the rigid motion between domains and comparing the rotations of the rigid motions.

Module computing the rigid motion between domains and comparing the rotations of the rigid motions.

Template Parameters
ModuleTraitsTraits class defining the types T_Correlated_motions_by_domain_module::Particle_traits, T_Correlated_motions_by_domain_module::Particles_container, T_Correlated_motions_by_domain_module::Get_label_identifier.

Member Typedef Documentation

◆ Base

◆ Get_label_identifier

typedef ModuleTraits::Get_label_identifier Get_label_identifier

Functor returning the identifier of the primitive label of a particle.

It takes as argument a particle, and return the identifier of its primitive label. The type of the identifier is named result_type and has to be a concatenable type (e.g a string).

◆ Label_traits

typedef ModuleTraits::Label_traits Label_traits

Traits class defining system's labels attached to particles.

◆ Particle_traits

typedef ModuleTraits::Particle_traits Particle_traits

Traits class for particles.

◆ Particles_container

typedef ModuleTraits::Particles_container Particles_container

Container for the input particles (atoms or pseudo-atoms).

See ParticleTraits for more details.

◆ Self

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< Dummy >.

◆ check_options()

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

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_Correlated_motions_by_domain_module< ModuleTraits > * clone ( void  ) const
inline

Clones the object using the copy constructor.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_first_particles()

Particles_container*& get_first_particles ( void  )
inline

Reference to the first container of particles.

◆ get_label_identifier()

Get_label_identifier& get_label_identifier ( void  )
inline

Reference to the functor labeling the particles in the first container.

◆ 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< Dummy >.

◆ get_report_mode()

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

Get the report mode to be used when reporting.

◆ get_second_particles()

Particles_container*& get_second_particles ( void  )
inline

Reference to the second container of particles.

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

static void initialize_options ( const std::string &  caption)
inlinestaticinherited

◆ 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.