Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat > Class Template Reference

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_modelMolecular_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)
 

Management

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

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_ensembleget_geometric_model_ensemble (unsigned i) const
 ith Conformations ensemble (const). More...
 
Molecular_geometric_model_ensembleget_geometric_model_ensemble (unsigned i)
 ith Conformations ensemble. More...
 
const Molecular_geometric_model_ensembleget_geometric_model_ensemble (void) const
 Conformations ensemble. (use only if one input file was provided) (const). More...
 
Molecular_geometric_model_ensembleget_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...
 

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
ConformationTypeRepresentation of a conformation as a point in dimension D, where D is three times the number of particles in the conformation.
ConformationBuilderFunctor building a conformation from a dD point or a molecular model from the ESBTL.
ESBTLMolecularSystemRepresentation of a molecular system in ESBTL (default is ESBTL::Default_system)
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

◆ Molecular_geometric_model

typedef ConformationType 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<>.

◆ 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_geometric_model_ensemble() [1/4]

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() [2/4]

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() [3/4]

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_geometric_model_ensemble() [4/4]

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_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_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<>.

◆ 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