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) 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 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 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

	verbose	Verbosity level.
[out]	out	Output stream.

Returns

True if loading is successful, false otherwise. Function to call to execute the main function of a Loader

Reimplemented from Loader_base.