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 Types

typedef T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius > Self
 
typedef SBL::IO::Loader_base Base
 
typedef NT FT
 

Public Member Functions

 T_Radius_annotator_for_particles_with_annotated_name (void)
 
 ~T_Radius_annotator_for_particles_with_annotated_name (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)
 
FT 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 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 Typedef Documentation

◆ Base

◆ FT

typedef NT FT

◆ Self

Constructor & Destructor Documentation

◆ T_Radius_annotator_for_particles_with_annotated_name()

◆ ~T_Radius_annotator_for_particles_with_annotated_name()

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<>.

◆ 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<>.

◆ 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[]()

FT 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