T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader > Class Template Reference

Loader for proteins from PDB and mmCIF files using SBL. More...

#include <Biomolecule_representation_loader.hpp>

Public Member Functions
virtual	~T_Biomolecule_representation_loader (void)
	Default destructor.
virtual boost::program_options::options_description	add_options (void) override
	Virtual method for adding options to the module.
virtual bool	check_options (std::string &message) const override
	Checks that the input options' values are coherent.
bool	load (unsigned verbose, std::ostream &out) override
	Load function.
std::string	get_name (void) const override
	Return the name of the class itself.
std::string	get_output_prefix (void) const override
	Returns a prefix that concatains the input line options used when running the module.
const std::vector< Protein_representation * > &	get_protein_representations (void) const
	Get the protein representations.
std::vector< Protein_representation * > &	get_protein_representations (void)
	Get the protein representations.
Molecular_covalent_structure_loader &	get_molecular_covalent_structure_loader (void)
	Get the molecular covalent structure loader.
void	statistics (std::ostream &out)
	Prints statistics about the loaded protein representations.

Static Public Member Functions
static boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module.

Detailed Description

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>
class SBL::IO::T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >

Loader for proteins from PDB and mmCIF files using SBL.

Template Parameters

ProteinRepresentation	A model of SBL::CSB::T_Protein_representation
MolecularCovalentStructureBuilder	Builder of the covalent structure.

Constructor & Destructor Documentation

~T_Biomolecule_representation_loader()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

~T_Biomolecule_representation_loader ( void )

virtual

Default destructor.

Member Function Documentation

add_options()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

boost::program_options::options_description add_options ( void )

overridevirtual

Virtual method for adding options to the module.

Adds the options of the molecular system loader (under "PDB Loader") to the option parser and also as command line arguments.

Reimplemented from T_Module_option_description< Dummy >.

check_options()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

bool check_options ( std::string & message ) const

overridevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

get_molecular_covalent_structure_loader()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

T_Biomolecule_representation_loader< ProteinRepresentation, NucleicAcidRepresentation, MCSLoader >::Molecular_covalent_structure_loader & get_molecular_covalent_structure_loader

(

void

)

Get the molecular covalent structure loader.

Returns

A reference to the molecular covalent structure loader.

get_name()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

std::string get_name ( void ) const

overridevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

get_options()

template<class Dummy = void>

boost::program_options::options_description *& get_options ( void )

inlinestaticinherited

Access to the options' description of the module.

get_output_prefix()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

std::string get_output_prefix ( void ) const

overridevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

get_protein_representations() [1/2]

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

std::vector< Protein_representation * > & get_protein_representations ( void )

inline

Get the protein representations.

Returns

A reference to the vector of protein representations.

get_protein_representations() [2/2]

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

const std::vector< Protein_representation * > & get_protein_representations ( void ) const

inline

Get the protein representations.

Returns

A constant reference to the vector of protein representations.

load()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

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

overridevirtual

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

Load protein representations. This function loads the protein representations.

Reimplemented from Loader_base.

statistics()

template<class ProteinRepresentation, class NucleicAcidRepresentation, class MCSLoader>

void statistics

(

std::ostream &

out

)

Prints statistics about the loaded protein representations.

Parameters

[out]

out

Output stream for printing the statistics.