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...
Base *	get_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

NT	Number type used for representing the radius.
SetRadius	Functor setting the radius of an input particle

Member Typedef Documentation

Base

typedef SBL::IO::Loader_base Base

FT

typedef NT FT

Self

typedef T_Radius_annotator_for_particles_with_annotated_name<NT, SetRadius> Self

Constructor & Destructor Documentation

T_Radius_annotator_for_particles_with_annotated_name()

T_Radius_annotator_for_particles_with_annotated_name ( void  )

inline

~T_Radius_annotator_for_particles_with_annotated_name()

~T_Radius_annotator_for_particles_with_annotated_name ( void  )

inline

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[]()

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