T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat > Class Template Reference

Application allowing to load conformations from a list of PDB files using ESBTL, or from a plain txt file listing the conformations as Point_d. More...

#include <XTC_file_loader.hpp>

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

Constructors
	T_XTC_file_loader (void)
	Default Constructor.

Parameters
boost::program_options::options_description	add_options (void) override
	Virtual method for adding options to the module.
const std::string &	get_input_file_name (void) const
	Return the name of the input file when only one is given.
const std::string &	get_input_file_name (unsigned i) const
	Return the name of the ith input file.
unsigned	get_model_number (void) const
	Return the number of the model used in the PDB files.
bool	is_loaded_water (void) const
	Check that water molecules are loaded.
bool	is_loaded_hydrogen (void) const
	Check that hydrogen are loaded.

Access
unsigned	get_number_of_loaded_geometric_model_ensembles (void) const
	Number of loaded XTC ensembles.
const Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (unsigned i) const
	ith XTC ensemble (const).
Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (unsigned i)
	ith XTC ensemble.
const Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (void) const
	XTC ensemble. (use only if one input file was provided) (const).
Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (void)
	onformations ensemble. (use only if one input file was provided).

Requirements
bool	load (unsigned verbose=false, std::ostream &out=std::cout)
	Load function.
std::string	get_output_prefix (void) const override
	Returns a prefix that concatains the input line options used when running the module.
std::string	get_name (void) const override
	Return the name of the class itself.
bool	check_options (std::string &message) const override
	Checks that the input options' values are coherent.

Detailed Description

template<class ConformationType = CGAL::Cartesian_d<ESBTL::CGAL::EPIC_kernel_with_atom::FT>::Point_d, class ConformationBuilder = T_Conformation_builder_cartesian_default<ConformationType>, class ESBTLMolecularSystem = ESBTL::Molecular_system<ESBTL::Default_system_items, ESBTL::CGAL::EPIC_kernel_with_atom::Point_3>, class PDBLineFormat = ESBTL::PDB::Line_format<>>
class SBL::Models::T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >

Application allowing to load conformations from a list of PDB files using ESBTL, or from a plain txt file listing the conformations as Point_d.

It combines the options from the SBL::Models::T_PDB_file_loader and the SBL::Models::T_Points_d_file_loader

Template Parameters

ConformationType	Representation of a conformation as a point in dimension D, where D is three times the number of particles in the conformation.
ConformationBuilder	Functor building a conformation from a dD point or a molecular model from the ESBTL.
ESBTLMolecularSystem	Representation of a molecular system in ESBTL (default is ESBTL::Default_system)
PDBLineFormat	Format of a line in a PDB file, determining wether a field of a line is mandatory or not (default is ESBTL::Line_format<>)

Constructor & Destructor Documentation

T_XTC_file_loader()

template<class ConformationType, class ESBTLMolecularSystem, class PDBLineSelector, class PDBLineFormat>

T_XTC_file_loader ( void )

inline

Default Constructor.

Member Function Documentation

add_options()

template<class ConformationType, class ESBTLMolecularSystem, class PDBLineSelector, class PDBLineFormat>

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()

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

bool check_options ( std::string & message ) const

inlineoverridevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

get_geometric_model_ensemble() [1/4]

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model_ensemble & get_geometric_model_ensemble ( unsigned i )

inline

ith XTC ensemble.

get_geometric_model_ensemble() [2/4]

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

const T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model_ensemble & get_geometric_model_ensemble ( unsigned i ) const

inline

ith XTC ensemble (const).

get_geometric_model_ensemble() [3/4]

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model_ensemble & get_geometric_model_ensemble ( void )

inline

onformations ensemble. (use only if one input file was provided).

get_geometric_model_ensemble() [4/4]

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

const T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model_ensemble & get_geometric_model_ensemble ( void ) const

inline

XTC ensemble. (use only if one input file was provided) (const).

get_input_file_name() [1/2]

template<class ConformationType = CGAL::Cartesian_d<ESBTL::CGAL::EPIC_kernel_with_atom::FT>::Point_d, class ConformationBuilder = T_Conformation_builder_cartesian_default<ConformationType>, class ESBTLMolecularSystem = ESBTL::Molecular_system<ESBTL::Default_system_items, ESBTL::CGAL::EPIC_kernel_with_atom::Point_3>, class PDBLineFormat = ESBTL::PDB::Line_format<>>

const std::string & get_input_file_name ( unsigned i ) const

inline

Return the name of the ith input file.

get_input_file_name() [2/2]

template<class ConformationType = CGAL::Cartesian_d<ESBTL::CGAL::EPIC_kernel_with_atom::FT>::Point_d, class ConformationBuilder = T_Conformation_builder_cartesian_default<ConformationType>, class ESBTLMolecularSystem = ESBTL::Molecular_system<ESBTL::Default_system_items, ESBTL::CGAL::EPIC_kernel_with_atom::Point_3>, class PDBLineFormat = ESBTL::PDB::Line_format<>>

const std::string & get_input_file_name ( void ) const

inline

Return the name of the input file when only one is given.

get_model_number()

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

unsigned get_model_number ( void ) const

inline

Return the number of the model used in the PDB files.

get_name()

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

std::string get_name ( void ) const

inlineoverridevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

get_number_of_loaded_geometric_model_ensembles()

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

unsigned get_number_of_loaded_geometric_model_ensembles ( void ) const

inline

Number of loaded XTC ensembles.

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 ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

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 >.

is_loaded_hydrogen()

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

bool is_loaded_hydrogen ( void ) const

inline

Check that hydrogen are loaded.

is_loaded_water()

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

bool is_loaded_water ( void ) const

inline

Check that water molecules are loaded.

load()

template<class ConformationType, class ConformationBuilder, class ESBTLMolecularSystem, class PDBLineFormat>

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

inlinevirtual

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.