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

Model of ParticleAnnotator for attributing a name to an atom. More...

#include <Name_annotator_for_atoms.hpp>

Public Member Functions

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...
 
bool load (unsigned verbose, std::ostream &out) override
 Load function. More...
 
std::string get_name (void) const override
 Return the name of the class itself. More...
 

Static Public Member Functions

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

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_atoms_setter_default>
class SBL::Models::T_Name_annotator_for_atoms< SetAnnotatedName >

Model of ParticleAnnotator for attributing a name to an atom.

The file containing the annotations loaded by this annotator has no header information. The key is a composition of the residue name with the atom name from the PDB file. By default, the following names are provided, depending on the key (residue name, PDB atom name):

  • Cali (Carbon aliphatic)
  • Caro (Carbon aromatic)
  • Cpep (Carbon peptide)
  • Nhbd (Nitrate H-bond)
  • Naro (Nitrate aromatic)
  • NchP (???)
  • Ohbd (Oxygen H-bond)
  • Opep (Oxygen peptide)
  • OchM (???)
  • Owat (Oxygen water)
  • Sh (???)
  • Pdna (Phospate dna)
  • Opd (???)
  • Orib (Oxygen ribosom)
  • Unk (Other atoms)
Template Parameters
SetAnnotatedNameFunctor taking a particle and a name and setting the name to the particle.

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_options()

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

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

◆ get_name()

std::string get_name ( void  ) const
inlineoverridevirtual

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
inlineoverridevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ load()

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

Load function.

Parameters
verboseVerbosity level.
[out]outOutput stream.
Returns
True if loading is successful, false otherwise. Function to call to execute the main function of a Loader

Reimplemented from Loader_base.