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

Loader for covalent structures from PDB files using ESBTL. More...

#include <Molecular_covalent_structure_loader_from_PDB.hpp>

Classes

struct  Is_loaded_atom
 

Public Types

typedef T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat > Self
 
typedef SBL::IO::Loader_base Base
 
typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT FT
 

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)
 

Management

void set_loader_instance_name (const std::string &loader_instance_name)
 
const std::string & get_loader_instance_name (void) const
 

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...
 
static void add_input_file_name (const std::string &file_name)
 Add manually the name of an input PDB file. More...
 
static void set_coarse_level (unsigned coarse_level)
 Set the coarse level. 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)
 Set the loaded water tag. More...
 
static void set_loaded_hetatoms (bool with_hetatoms)
 Set the loaded hetatoms tag. More...
 
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)
 Set the without disulfide bonds tag. More...
 
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...
 

Access

unsigned get_number_of_loaded_covalent_structures (void) const
 Number of loaded covalent structures. More...
 
const MolecularCovalentStructure & get_covalent_structure (unsigned i) const
 ith covalent structure (const). More...
 
MolecularCovalentStructure & get_covalent_structure (unsigned i)
 ith covalent structure. 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...
 

Detailed Description

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_for_proteins<ParticleTraits> >, class MolecularCovalentStructureBuilder = SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins<MolecularCovalentStructure>, class PDBLineFormat = ESBTL::PDB::Line_format<>>
class SBL::IO::T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >

Loader for covalent structures from PDB files using ESBTL.

Loader for covalent structures from PDB files using ESBTL; For now, it loads everything except heteroatoms and water molecules.

Template Parameters
ParticleTraitsTraits class providing the particle type
MolecularCovalentStructureGraph representation of a covalent structure.
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

◆ FT

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

◆ Self

typedef T_Molecular_covalent_structure_loader_from_PDB<ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, 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<>.

◆ check_options()

bool check_options ( std::string &  message) const
inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description<>.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_covalent_structure() [1/2]

const MolecularCovalentStructure & get_covalent_structure ( unsigned  i) const
inline

ith covalent structure (const).

◆ get_covalent_structure() [2/2]

MolecularCovalentStructure & get_covalent_structure ( unsigned  i)
inline

ith covalent structure.

◆ get_input_file_name() [1/2]

const std::string& get_input_file_name ( void  ) const
inline

Return the name of the input file when only one is given.

◆ get_input_file_name() [2/2]

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

Return the name of the ith input file.

◆ get_loader_instance_name()

const std::string& get_loader_instance_name ( void  ) const
inlineinherited

◆ get_name()

std::string get_name ( void  ) const
inlinevirtual

Return the name of the class itself.

Reimplemented from Loader_base.

◆ get_number_of_loaded_covalent_structures()

unsigned get_number_of_loaded_covalent_structures ( void  ) const
inline

Number of loaded covalent structures.

◆ 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<>.

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

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

◆ load()

bool load ( unsigned  verbose = false,
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_coarse_level()

void set_coarse_level ( unsigned  coarse_level)
inlinestatic

Set the coarse level.

◆ 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  with_hetatoms)
inlinestatic

Set the loaded hetatoms tag.

◆ set_loaded_water()

void set_loaded_water ( bool  with_water)
inlinestatic

Set the loaded water tag.

◆ 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

Set the occupancy factor for all input PDB.

◆ set_without_disulfide_bonds()

void set_without_disulfide_bonds ( bool  without_ss)
inlinestatic

Set the without disulfide bonds tag.