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>

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...

Parameters
boost::program_options::options_description	add_options (void) const
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)
	Load function. 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 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

ParticleTraits	Traits class providing the particle type
MolecularCovalentStructure	Graph representation of a covalent structure.
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 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()

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 >.

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_covalent_structure() [1/2]

MolecularCovalentStructure & get_covalent_structure ( unsigned  i )

inline

ith covalent structure.

get_covalent_structure() [2/2]

const MolecularCovalentStructure & get_covalent_structure ( unsigned  i ) const

inline

ith covalent structure (const).

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.

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.

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< Dummy >.

load()

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

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_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_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.