T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat > Class Template Reference

Loader for one or more PDB files, even listed in a file. Loader for one or more PDB files, even listed in a file. More...

#include "PDB_file_loader.hpp"

Public Types
typedef T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >	Self
typedef SBL::IO::Loader_base	Base
typedef ESBTLMolecularSystem	ESBTL_molecular_system

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)

Other Types
typedef ESBTL_molecular_system::Model	Molecular_geometric_model

Accessors
static const std::string &	get_input_file_name (void)
	Name of the input PDB file. More...
static const std::string &	get_input_file_name (unsigned i)
	Name of the ith input PDB file. More...
static void	add_input_file_name (const std::string &file_name)
	Add manually the name of an input PDB file. More...
static unsigned	get_model_number (void)
	Number of the model used in the PDB files. More...
static bool	is_loaded_water (void)
	Checks that water molecules are loaded. More...
static bool	is_loaded_hydrogen (void)
	Checks that hydrogen are loaded. More...
static std::string	get_loaded_chains (void)
	Loaded chains (if only one or none were given) More...
static std::string	get_loaded_chains (unsigned i)
	Loaded chains (if as many as loaded PDB files) More...
unsigned	get_number_of_loaded_geometric_models (void) const
	Number of loaded PDB files. More...
unsigned	get_number_of_models_in_loaded_PDB (unsigned i) const
	Number of models in the ith PDB file. More...
const Molecular_geometric_model &	get_geometric_model (unsigned i, unsigned n) const
Molecular_geometric_model &	get_geometric_model (unsigned i, unsigned n)
const Molecular_geometric_model &	get_geometric_model (unsigned i) const
Molecular_geometric_model &	get_geometric_model (unsigned i)
const Molecular_geometric_model &	get_geometric_model (void) const
Molecular_geometric_model &	get_geometric_model (void)

Modifiers
static void	set_occupancy_factor (unsigned i)
	Set the occupancy factor for all input PDB. More...
static void	set_loaded_chains (const std::string &chains)
	Set the loaded chains (if only one or none were given) More...
static void	set_loaded_chains (unsigned i, const std::string &chains)
	Set the loaded chains (if as many as loaded PDB files) More...
static void	set_loaded_water (bool b)
	Checks that water molecules are loaded. More...
static void	set_loaded_hetatoms (bool b)
	Checks that water molecules are loaded. More...

Mandatory Requirements
boost::program_options::options_description	add_options (void) const
	Virtual method for adding options to the module. More...
bool	load (unsigned verbose, std::ostream &out)
	Loads the data. More...
bool	check_options (std::string &message) const
	Checks that the input options' values are coherent. 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...

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 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_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >

Loader for one or more PDB files, even listed in a file. Loader for one or more PDB files, even listed in a file.

The different options are:

• Load of one, n or a list of PDB files,

• Possibility to discard or not the hydrogen atoms (discarded by default) are discarded,

• Possibility to select atoms following their occupancy factor. By default, the atoms are loaded regardless their occupancy factor.

• In case of alternates, the first occurrence is the one selected.

• if several models of the structure coexist, which one do we consider. Important Note about hetero atoms: When dealing with hetero atoms, these ones may be associated to a chain. If the chain is associated to a partner, these hetero atoms will be also associated to this partner.

• The classification of atoms used is such that hydrogen atoms are discarded, see Atomic Radii and Group Radii, atomic group radii above.

• For PDB models, all occupancy factors to be equal to 1. If not and for a more elaborate processing, the user should retrieve the binary program, learn about the strategies offered in case of factors < 1, and proceed accordingly.

• In case of alternates, the first occurrence is the one selected.

Template Parameters

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::PDB::Line_format<>)

Member Typedef Documentation

Base

typedef SBL::IO::Loader_base Base

ESBTL_molecular_system

typedef ESBTLMolecularSystem ESBTL_molecular_system

Molecular_geometric_model

typedef ESBTL_molecular_system::Model Molecular_geometric_model

Self

typedef T_PDB_file_loader<ESBTLMolecularSystem, PDBLineFormat> Self

Member Function Documentation

add_input_file_name()

void add_input_file_name ( const std::string &  file_name )

inlinestatic

Add manually the name of an input PDB 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() [1/6]

T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model & get_geometric_model ( unsigned  i )

inline

ith ESBTL system corresponding to the ith loaded PDB file.

Precondition

there are at least (i+1) loaded PDB files.

get_geometric_model() [2/6]

const T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model & get_geometric_model ( unsigned  i ) const

inline

ith ESBTL system corresponding to the ith loaded PDB file (const).

Precondition

there are at least (i+1) loaded PDB files.

get_geometric_model() [3/6]

T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model & get_geometric_model ( unsigned  i, unsigned  n  )

inline

n-th ESBTL molecular model from the ith ESBTL system corresponding to the ith loaded PDB file (const).

Precondition

there are at least (i+1) loaded PDB files.

there are at least n models in the i-th loaded PDB file.

get_geometric_model() [4/6]

const T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model & get_geometric_model ( unsigned  i, unsigned  n  ) const

inline

n-th ESBTL molecular model from the ith ESBTL system corresponding to the ith loaded PDB file (const).

Precondition

there are at least (i+1) loaded PDB files.

there are at least n models in the i-th loaded PDB file.

get_geometric_model() [5/6]

T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model & get_geometric_model ( void  )

inline

ESBTL system containing the atoms of the loaded PDB file.

Precondition

Only one PDB file name was given.

get_geometric_model() [6/6]

const T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >::Molecular_geometric_model & get_geometric_model ( void  ) const

inline

ESBTL system containing the atoms of the loaded PDB file (const).

Precondition

Only one PDB file name was given.

get_input_file_name() [1/2]

const std::string & get_input_file_name ( unsigned  i )

inlinestatic

Name of the ith input PDB file.

Precondition

there are at least (i+1) loaded PDB files.

get_input_file_name() [2/2]

const std::string & get_input_file_name ( void  )

inlinestatic

Name of the input PDB file.

Precondition

Only one PDB file name was given.

get_loaded_chains() [1/2]

std::string get_loaded_chains ( unsigned  i )

inlinestatic

Loaded chains (if as many as loaded PDB files)

get_loaded_chains() [2/2]

std::string get_loaded_chains ( void  )

inlinestatic

Loaded chains (if only one or none were given)

get_loader_instance_name()

const std::string& get_loader_instance_name ( void  ) const

inlineinherited

get_model_number()

unsigned get_model_number ( void  )

inlinestatic

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_models()

unsigned get_number_of_loaded_geometric_models ( void  ) const

inline

Number of loaded PDB files.

get_number_of_models_in_loaded_PDB()

unsigned get_number_of_models_in_loaded_PDB ( unsigned  i ) const

inline

Number of models in the ith PDB file.

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  )

inlinestatic

Checks that hydrogen are loaded.

is_loaded_water()

bool is_loaded_water ( void  )

inlinestatic

Checks that water molecules are loaded.

load()

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

inlinevirtual

Loads the data.

Reimplemented from Loader_base.

set_loaded_chains() [1/2]

void set_loaded_chains ( const std::string &  chains )

inlinestatic

Set the loaded chains (if only one or none were given)

set_loaded_chains() [2/2]

void set_loaded_chains ( unsigned  i, const std::string &  chains  )

inlinestatic

Set the loaded chains (if as many as loaded PDB files)

set_loaded_hetatoms()

void set_loaded_hetatoms ( bool  b )

inlinestatic

Checks that water molecules are loaded.

set_loaded_water()

void set_loaded_water ( bool  b )

inlinestatic

Checks that water molecules are loaded.

set_loader_instance_name()

void set_loader_instance_name ( const std::string &  loader_instance_name )

inlineinherited

set_occupancy_factor()

void set_occupancy_factor ( unsigned  i )

inlinestatic

Set the occupancy factor for all input PDB.