Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius > Class Template Reference

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

#include <Radius_annotator_for_particles_with_annotated_name.hpp>

Public Member Functions

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...
 

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 NT = double, class SetRadius = Radius_annotator_for_particles_with_annotated_name_setter_default>
class SBL::Models::T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >

Model of ParticleAnnotator for attributing a radius to an atom.

Annotations' file loaded by this annotator has no header information. The key is an annotated atom name (not the one from PDB, if any). By default, the radii for atoms are the van der Walls radii, while the radii for pseudo-atoms representing residues are approximations of radii of residues without their side-chain. The following radii are provided for atoms:

  • Cali 1.87
  • Caro 1.76
  • Cpep 1.76
  • Nhbd 1.65
  • Naro 1.65
  • NchP 1.50
  • Ohbd 1.4
  • Opep 1.4
  • OchM 1.4
  • Owat 1.4
  • Sh 1.85
  • Pdna 1.9
  • Opd 1.4
  • Orib 1.4
  • Unk 2.0

and for pseudo-atoms:

  • ALA 2.75
  • VAL 3.25
  • LEU 3.45
  • ILE 3.45
  • CYS 2.95
  • MET 3.4
  • MSE 3.4
  • PRO 3.15
  • PHE 3.675
  • TYR 3.7
  • TRP 3.85
  • ASP 3.15
  • ASN 3.2
  • GLU 3.35
  • GLN 3.35
  • HIS 3.4
  • SER 2.85
  • THR 3.15
  • ARG 3.675
  • LYS 3.45
  • GLY 2.5
Template Parameters
NTNumber type used for representing the radius.
SetRadiusFunctor setting the radius of an input particle

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<>.

◆ check_options()

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

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description<>.

◆ 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<>.

◆ load()

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

Loads the data.

Reimplemented from Loader_base.