Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat > Class Template Reference

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_representationget_protein (unsigned i) const
 Return the ith loaded protein (const). More...
 
Protein_representationget_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
ProteinRepresentationA model of SBL::CSB::T_Protein_representation
MolecularCovalentStructureBuilderBuilder of the covalent structure.
PDBLineFormatFormat 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

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
ParticleTraitsTraits class providing the particle type, see package ParticleTraits
MolecularCovalentStructureGraph representation of a covalent structure.
ConformationTypeRepresentation 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.

Representaiton of a protein with its polypeptide chains.

Template Parameters
PolypeptideChainRepresentation 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_namePath 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
iNumber 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
inumber 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
inumber 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
altcAlternate 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_levelBuilding 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
chainsConcatenated 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
iNumber of the PDB file for which chains are specified
chainsConcatenated 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_hetatomsTag 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_waterTag 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
iOccupancy 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
nNumber 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_ssTag to set with or without disulfide bonds