Loader for proteins from PDB files using ESBTL Loader for proteins from PDB files using ESBTL. More...

#include <Protein_representation_loader.hpp>

Public Types
typedef T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >	Self
	The class itself. More...

typedef SBL::IO::Loader_base	Base
	Base loader from which any loader should inherit. More...

typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT	FT
	Representation of the number type. More...

typedef ProteinRepresentation	Protein_representation
	Representaiton of a protein with its polypeptide chains. More...

typedef ProteinRepresentation::Polypeptide_chain	Polypeptide_chain
	Reprenstation of a single polypeptidic chain within a protein representation. More...

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)

Parameters
boost::program_options::options_description	add_options (void) const
	Build the command line options related to this loader and return them. More...

static void	add_input_pdb_file (const std::string &file_name)
	Add manually the name of an input PDB file for loading a covalent structure. More...

static void	set_coarse_level (unsigned coarse_level)
	Configure the loader to build the covalent structure at different levels. More...

static void	set_max_bond_distance (double max_bond_distance)
	Set the maximal bond distance between the C of a residue and the N of its next residue. More...

static void	set_loaded_water (bool with_water)
	Configure the loader to load or not the water molecules. More...

static bool	is_loaded_water (void)

static void	set_loaded_hetatoms (bool with_hetatoms)
	Configure the loader to load or not the hetero-atoms. More...

static bool	is_loaded_hetatoms (void)

static void	set_allow_incomplete_chains (bool with_incomplete_chains)
	Set the load incomplete residues tag. More...

static void	set_without_disulfide_bonds (bool without_ss)
	Configure the loader not to build disulfide bonds. More...

static void	set_occupancy_factor (unsigned i)
	Selection policy for atoms in the input PDB files with no alternate location and occupancy not equal to 1. More...

static unsigned	get_occupancy_factor (void)

static void	set_alternate_coordinate (char altc)
	Alternate coordinates: alternative to be used. More...

static void	set_PDB_model_number (unsigned n)
	ID of the model to be loaded frome the PDB file (default is 1) More...

static void	set_loaded_chains (const std::string &chains)
	Subset of chains to be loaded : do it for all input PDB files. More...

static std::string	get_loaded_chains (void)

static void	set_loaded_chains (unsigned i, const std::string &chains)
	Subset of chains to be loaded : do it for the ith input PDB file. More...

static std::string	get_loaded_chains (unsigned i)

Access
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_number_of_loaded_proteins (void) const
	Return the number of successfuly loaded PDB files. More...

const Protein_representation &	get_protein (unsigned i) const
	Return the ith loaded protein (const). More...

Protein_representation &	get_protein (unsigned i)
	Return the ith loaded protein . More...

static unsigned	get_model_number (void)
	Return the number of the selected model for the input PDB files. More...

Requirements
bool	load (unsigned verbose=0, 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 ProteinRepresentation, class MolecularCovalentStructureBuilder = SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins<typename ProteinRepresentation::Polypeptide_chain::Molecular_covalent_structure>, class PDBLineFormat = ESBTL::PDB::Line_format<>>
class SBL::IO::T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >

Loader for proteins from PDB files using ESBTL Loader for proteins from PDB files using ESBTL.

Template Parameters

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

Base loader from which any loader should inherit.

Requirements are...

◆ FT

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

Representation of the number type.

◆ Polypeptide_chain

typedef ProteinRepresentation::Polypeptide_chain Polypeptide_chain

Reprenstation of a single polypeptidic chain within a protein representation.

Template Parameters

ParticleTraits	Traits class providing the particle type, see package ParticleTraits
MolecularCovalentStructure	Graph representation of a covalent structure.
ConformationType	Representation of a conformation as a point in dimension D, where D is three times the number of particles in the conformation.

◆ Protein_representation

typedef ProteinRepresentation Protein_representation

Representaiton of a protein with its polypeptide chains.

Template Parameters

PolypeptideChain Representation of a polypeptide chain (see SBL::CSB::T_Polypeptide_chain_representation)

◆ Self

typedef T_Protein_representation_loader<ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat> Self

The class itself.

Member Function Documentation

◆ add_input_pdb_file()

void add_input_pdb_file ( const std::string & file_name )

inlinestatic

Add manually the name of an input PDB file for loading a covalent structure.

Parameters

file_name Path to the PDB file to add

◆ add_options()

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

inlinevirtual

Build the command line options related to this loader and return them.

Returns: The command line options as defined in the Boost Program Options library

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_input_file_name() [1/2]

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

inline

Return the name of the ith input file.

Parameters

i	Number of the input PDB file

Returns: The name of the ith input PDB 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.

Returns: The name of the input PDB file.

◆ get_loaded_chains() [1/2]

std::string get_loaded_chains ( unsigned i )

inlinestatic

◆ get_loaded_chains() [2/2]

std::string get_loaded_chains ( void )

inlinestatic

◆ get_loader_instance_name()

const std::string& get_loader_instance_name ( void ) const

inlineinherited

◆ get_model_number()

unsigned get_model_number ( void )

inlinestatic

Return the number of the selected model for the input PDB files.

Returns: Number of the model.

◆ get_name()

std::string get_name ( void ) const

inlinevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

◆ get_number_of_loaded_proteins()

unsigned get_number_of_loaded_proteins ( void ) const

inline

Return the number of successfuly loaded PDB files.

Returns: Number of loaded proteins

◆ get_occupancy_factor()

unsigned get_occupancy_factor ( void )

inlinestatic

◆ 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 >.

◆ get_protein() [1/2]

ProteinRepresentation & get_protein ( unsigned i )

inline

Return the ith loaded protein .

Parameters

i	number of the protein to return

Returns: a built instance of SBL::CSB::T_Protein_representation

◆ get_protein() [2/2]

const ProteinRepresentation & get_protein ( unsigned i ) const

inline

Return the ith loaded protein (const).

Parameters

i	number of the protein to return

Returns: a built instance of SBL::CSB::T_Protein_representation

◆ has_options()

static bool has_options ( void )

inlinestaticinherited

◆ initialize_options()

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

inlinestaticinherited

◆ is_loaded_hetatoms()

bool is_loaded_hetatoms ( void )

inlinestatic

◆ is_loaded_water()

bool is_loaded_water ( void )

inlinestatic

◆ load()

bool load	(	unsigned	verbose = `0`,
		std::ostream &	out = `std::cout`
	)

inlinevirtual

Loads the data.

Reimplemented from Loader_base.

◆ set_allow_incomplete_chains()

void set_allow_incomplete_chains ( bool with_incomplete_chains )

inlinestatic

Set the load incomplete residues tag.

◆ set_alternate_coordinate()

void set_alternate_coordinate ( char altc )

inlinestatic

Alternate coordinates: alternative to be used.

Parameters

altc	Alternate coordinate value

◆ set_coarse_level()

void set_coarse_level ( unsigned coarse_level )

inlinestatic

Configure the loader to build the covalent structure at different levels.

Parameters

coarse_level Building level of the covalent structure (0 : all atoms, 1 : heavy atoms only, 2 : c-alpha only)

◆ set_loaded_chains() [1/2]

void set_loaded_chains ( const std::string & chains )

inlinestatic

Subset of chains to be loaded : do it for all input PDB files.

Parameters

chains Concatenated list of chains

◆ set_loaded_chains() [2/2]

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

inlinestatic

Subset of chains to be loaded : do it for the ith input PDB file.

Parameters

i	Number of the PDB file for which chains are specified
chains	Concatenated list of chains

◆ set_loaded_hetatoms()

void set_loaded_hetatoms ( bool with_hetatoms )

inlinestatic

Configure the loader to load or not the hetero-atoms.

Parameters

with_hetatoms Tag to set with or without hetero-atoms

◆ set_loaded_water()

void set_loaded_water ( bool with_water )

inlinestatic

Configure the loader to load or not the water molecules.

Parameters

with_water Tag to set with or without water

◆ set_loader_instance_name()

void set_loader_instance_name ( const std::string & loader_instance_name )

inlineinherited

◆ set_max_bond_distance()

void set_max_bond_distance ( double max_bond_distance )

inlinestatic

Set the maximal bond distance between the C of a residue and the N of its next residue.

◆ set_occupancy_factor()

void set_occupancy_factor ( unsigned i )

inlinestatic

Selection policy for atoms in the input PDB files with no alternate location and occupancy not equal to 1.

Parameters

i	Occupancy value. Allowed values are: 1 (all), 2 (forbbiden, default), 3 (none), 4 (max), 5 (min)

◆ set_PDB_model_number()

void set_PDB_model_number ( unsigned n )

inlinestatic

ID of the model to be loaded frome the PDB file (default is 1)

Parameters

n	Number of the model

◆ set_without_disulfide_bonds()

void set_without_disulfide_bonds ( bool without_ss )

inlinestatic

Configure the loader not to build disulfide bonds.

Parameters

without_ss Tag to set with or without disulfide bonds

Public Types

Static Public Member Functions

Parameters

Access

Requirements

Management

Detailed Description

Member Typedef Documentation

◆ Base

◆ FT

◆ Polypeptide_chain

◆ Protein_representation

◆ Self

Member Function Documentation

◆ add_input_pdb_file()

◆ add_options()

◆ check_options()

◆ delete_options()

◆ get_input_file_name() [1/2]

◆ get_input_file_name() [2/2]

◆ get_loaded_chains() [1/2]

◆ get_loaded_chains() [2/2]

◆ get_loader_instance_name()

◆ get_model_number()

◆ get_name()

◆ get_number_of_loaded_proteins()

◆ get_occupancy_factor()

◆ get_options()

◆ get_output_prefix()

◆ get_protein() [1/2]

◆ get_protein() [2/2]

◆ has_options()

◆ initialize_options()

◆ is_loaded_hetatoms()

◆ is_loaded_water()

◆ load()

◆ set_allow_incomplete_chains()

◆ set_alternate_coordinate()

◆ set_coarse_level()

◆ set_loaded_chains() [1/2]

◆ set_loaded_chains() [2/2]

◆ set_loaded_hetatoms()

◆ set_loaded_water()

◆ set_loader_instance_name()

◆ set_max_bond_distance()

◆ set_occupancy_factor()

◆ set_PDB_model_number()

◆ set_without_disulfide_bonds()