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 Member Functions
virtual boost::program_options::options_description	add_options (void)
	Virtual method for adding options to the module. More...

Static Public Member Functions
static boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module. More...

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)
	Load function. 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 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() [1/2]

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

inlinevirtualinherited

Virtual method for adding options to the module.

Reimplemented in T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_vertex_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< typename ModuleTraits::Graph, typename ModuleTraits::Get_weight >::Morse_Smale_Witten_chain_complex >, T_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_NNG_builder< ModuleTraits::Nearest_neighbors_graph, ModuleTraits::Morse_function, ModuleTraits::Distance_graph_function >::Morse_Smale_Witten_chain_complex >, T_Molecular_interfaces_module< ModuleTraits >, T_Earth_mover_distance_module< ModuleTraits >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Points_d_file_loader< PointD >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Protein_representation_loader< Protein_representation_ >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Numbers_file_loader< FT, Tag >, T_Molecular_system_loader< Molecular_system_ >, T_Molecular_system_loader< Molecular_system >, T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins< typename Protein_representation_::Polypeptide_chain::Molecular_covalent_structure > >, T_Conformation_loader< Conformation_builder_ >, T_Archive_file_loader< InputArchive, SerializedData >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Domain_annotator_for_particles< Annotations >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, and T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >.

add_options() [2/2]

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

inline

Virtual method for adding options to the module.

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 >.

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_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 >.

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

Load function.

Parameters

	verbose	Verbosity level.
[out]	out	Output stream.

Returns

True if loading is successful, false otherwise. Function to call to execute the main function of a Loader

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_occupancy_factor()

void set_occupancy_factor ( unsigned  i )

inlinestatic

Set the occupancy factor for all input PDB.