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

Model of ParticleAnnotator for attributing a name to a pseudo-atom. More...

#include <Name_annotator_for_pseudo_atoms.hpp>

Public Types

typedef T_Name_annotator_for_pseudo_atoms< SetAnnotatedName > Self
 
typedef SBL::IO::Loader_base Base
 

Public Member Functions

 T_Name_annotator_for_pseudo_atoms (void)
 
 ~T_Name_annotator_for_pseudo_atoms (void)
 
bool set_options (boost::program_options::options_description &options) const
 
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...
 
bool load (unsigned verbose, std::ostream &out)
 Loads the data. More...
 
std::string get_name (void) const
 Return the name of the class itself. More...
 
Baseget_annotator (const std::string &name)
 
std::string operator[] (const std::string &name) const
 
template<class Particle >
void operator() (Particle &p) const
 

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)
 

Management

void set_loader_instance_name (const std::string &loader_instance_name)
 
const std::string & get_loader_instance_name (void) const
 

Detailed Description

template<class SetAnnotatedName = Name_annotator_for_pseudo_atoms_setter_default>
class SBL::Models::T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >

Model of ParticleAnnotator for attributing a name to a pseudo-atom.

It loads the annotations from a file without header information. In this annotator, pseudo-atoms are supposed to represent residues, so that the key of a pseudo-atom is the 3 letters code of the residue it presents. By default, the associated name is the name os the residue.

Template Parameters
SetAnnotatedNameFunctor taking a particle and a name and setting the name to the particle.

Member Typedef Documentation

◆ Base

◆ Self

typedef T_Name_annotator_for_pseudo_atoms<SetAnnotatedName> Self

Constructor & Destructor Documentation

◆ T_Name_annotator_for_pseudo_atoms()

◆ ~T_Name_annotator_for_pseudo_atoms()

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 >.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_annotator()

Base* get_annotator ( const std::string &  name)
inline

◆ get_loader_instance_name()

const std::string& get_loader_instance_name ( void  ) const
inlineinherited

◆ get_name()

std::string get_name ( void  ) const
inlinevirtual

Return the name of the class itself.

Reimplemented from Loader_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 >.

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

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

◆ load()

bool load ( unsigned  verbose,
std::ostream &  out 
)
inlinevirtual

Loads the data.

Reimplemented from Loader_base.

◆ operator()()

void operator() ( Particle &  p) const
inline

◆ operator[]()

std::string operator[] ( const std::string &  name) const
inline

◆ set_loader_instance_name()

void set_loader_instance_name ( const std::string &  loader_instance_name)
inlineinherited

◆ set_options()

bool set_options ( boost::program_options::options_description &  options) const
inline