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

SetAnnotatedName

Functor 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

	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.