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. More...

Constructors
	T_XTC_file_loader (void)
	Default Constructor. More...

Parameters
boost::program_options::options_description	add_options (void) override
	Virtual method for adding options to the module. More...

const std::string &	get_input_file_name (void) const
	Return the name of the input file when only one is given. More...

const std::string &	get_input_file_name (unsigned i) const
	Return the name of the ith input file. More...

unsigned	get_model_number (void) const
	Return the number of the model used in the PDB files. More...

bool	is_loaded_water (void) const
	Check that water molecules are loaded. More...

bool	is_loaded_hydrogen (void) const
	Check that hydrogen are loaded. More...

void	set_loaded_chains (const std::string &loaded_chains)

Access
unsigned	get_number_of_loaded_geometric_model_ensembles (void) const
	Number of loaded XTC ensembles. More...

const Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (unsigned i) const
	ith XTC ensemble (const). More...

Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (unsigned i)
	ith XTC ensemble. More...

const Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (void) const
	XTC ensemble. (use only if one input file was provided) (const). More...

Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (void)
	onformations ensemble. (use only if one input file was provided). More...

Requirements
bool	load (unsigned verbose=false, std::ostream &out=std::cout)
	Load function. More...

std::string	get_output_prefix (void) const override
	Returns a prefix that concatains the input line options used when running the module. More...

std::string	get_name (void) const override
	Return the name of the class itself. More...

bool	check_options (std::string &message) const override
	Checks that the input options' values are coherent. 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 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()

T_XTC_file_loader ( void )

inline

Default Constructor.

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_geometric_model_ensemble() [1/4]

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]

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]

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]

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]

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]

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()

unsigned get_model_number ( void ) const

inline

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

◆ get_name()

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()

unsigned get_number_of_loaded_geometric_model_ensembles ( void ) const

inline

Number of loaded XTC ensembles.

◆ 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 >.

◆ is_loaded_hydrogen()

bool is_loaded_hydrogen ( void ) const

inline

Check that hydrogen are loaded.

◆ is_loaded_water()

bool is_loaded_water ( void ) const

inline

Check that water molecules are loaded.

◆ load()

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.

Static Public Member Functions

Constructors

Parameters

Access

Requirements

Management

Detailed Description

Constructor & Destructor Documentation

◆ T_XTC_file_loader()

Member Function Documentation

◆ add_options()

◆ check_options()

◆ get_geometric_model_ensemble() [1/4]

◆ get_geometric_model_ensemble() [2/4]

◆ get_geometric_model_ensemble() [3/4]

◆ get_geometric_model_ensemble() [4/4]

◆ get_input_file_name() [1/2]

◆ get_input_file_name() [2/2]

◆ get_model_number()

◆ get_name()

◆ get_number_of_loaded_geometric_model_ensembles()

◆ get_options()

◆ get_output_prefix()

◆ is_loaded_hydrogen()

◆ is_loaded_water()

◆ load()