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 <Conformations_file_loader.hpp>

Classes
struct	Is_loaded_atom

Public Types
typedef T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >	Self

typedef SBL::IO::Loader_base	Base

typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT	FT

typedef ConformationType	Molecular_geometric_model

typedef std::vector< Molecular_geometric_model >	Molecular_geometric_model_ensemble

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

static bool	has_options (void)

static void	delete_options (void)

static void	initialize_options (const std::string &caption)

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

Parameters
boost::program_options::options_description	add_options (void) const
	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...

void	set_occupancy_policy (unsigned policy)

void	set_loaded_water (bool b)

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

void	set_loaded_hydrogen (bool b)

void	set_loaded_chains (const std::string &loaded_chains)

void	save_ensembles (void)

static void	add_input_pdb_file_name (const std::string &file_name)
	Add manually the name of an input PDB file. More...

static void	add_input_points_file_name (const std::string &file_name)
	Add manually the name of an input Points file. More...

static void	set_model_number (unsigned i)

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

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

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

const Molecular_geometric_model_ensemble &	get_geometric_model_ensemble (void) const
	Conformations 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)
	Loads the data. More...

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

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

bool	check_options (std::string &message) const
	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_Conformations_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<>)

Member Typedef Documentation

◆ Base

typedef SBL::IO::Loader_base Base

◆ FT

typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT FT

◆ Molecular_geometric_model

typedef ConformationType Molecular_geometric_model

◆ Molecular_geometric_model_ensemble

typedef std::vector<Molecular_geometric_model> Molecular_geometric_model_ensemble

◆ Self

typedef T_Conformations_file_loader<ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat> Self

Constructor & Destructor Documentation

◆ T_Conformations_file_loader()

T_Conformations_file_loader ( void )

inline

Default Constructor.

Member Function Documentation

◆ add_input_pdb_file_name()

void add_input_pdb_file_name ( const std::string & file_name )

inlinestatic

Add manually the name of an input PDB file.

◆ add_input_points_file_name()

void add_input_points_file_name ( const std::string & file_name )

inlinestatic

Add manually the name of an input Points file.

◆ add_options()

boost::program_options::options_description add_options ( void ) const

inlinevirtual

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ check_options()

bool check_options ( std::string & message ) const

inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

◆ delete_options()

static void delete_options ( void )

inlinestaticinherited

◆ get_geometric_model_ensemble() [1/4]

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

inline

ith Conformations ensemble.

◆ get_geometric_model_ensemble() [2/4]

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

inline

ith Conformations ensemble (const).

◆ get_geometric_model_ensemble() [3/4]

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

inline

Conformations 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_loader_instance_name()

const std::string& get_loader_instance_name ( void ) const

inlineinherited

◆ 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

inlinevirtual

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 Conformations 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

inlinevirtual

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

Reimplemented from T_Module_option_description< Dummy >.

◆ has_options()

static bool has_options ( void )

inlinestaticinherited

◆ initialize_options()

static void initialize_options ( const std::string & caption )

inlinestaticinherited

◆ 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

Loads the data.

Reimplemented from Loader_base.

◆ save_ensembles()

void save_ensembles ( void )

inline

◆ set_loaded_chains()

void set_loaded_chains ( const std::string & loaded_chains )

inline

◆ set_loaded_hydrogen()

void set_loaded_hydrogen ( bool b )

inline

◆ set_loaded_water()

void set_loaded_water ( bool b )

inline

◆ set_loader_instance_name()

void set_loader_instance_name ( const std::string & loader_instance_name )

inlineinherited

◆ set_model_number()

void set_model_number ( unsigned i )

inlinestatic

◆ set_occupancy_policy()

void set_occupancy_policy ( unsigned policy )

inline

Classes

Public Types

Static Public Member Functions

Constructors

Parameters

Access

Requirements

Management

Detailed Description

Member Typedef Documentation

◆ Base

◆ FT

◆ Molecular_geometric_model

◆ Molecular_geometric_model_ensemble

◆ Self

Constructor & Destructor Documentation

◆ T_Conformations_file_loader()

Member Function Documentation

◆ add_input_pdb_file_name()

◆ add_input_points_file_name()

◆ add_options()

◆ check_options()

◆ delete_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_loader_instance_name()

◆ get_model_number()

◆ get_name()

◆ get_number_of_loaded_geometric_model_ensembles()

◆ get_options()

◆ get_output_prefix()

◆ has_options()

◆ initialize_options()

◆ is_loaded_hydrogen()

◆ is_loaded_water()

◆ load()

◆ save_ensembles()

◆ set_loaded_chains()

◆ set_loaded_hydrogen()

◆ set_loaded_water()

◆ set_loader_instance_name()

◆ set_model_number()

◆ set_occupancy_policy()