Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Internal_cartesian_file_converter Class Reference

#include <Internal_cartesian_coordinates_file_converter.hpp>

Public Types

typedef Internal_cartesian_file_converter Self
 
typedef SBL::Models::T_Atom_with_hierarchical_info_traits Particle_traits
 
typedef Particle_traits::Molecular_system Molecular_system
 
typedef SBL::CSB::T_Particle_info_for_proteins< Particle_traits > Particle_info
 
typedef SBL::CSB::T_Particle_info_traits< Particle_info > Particle_info_traits
 
typedef SBL::CSB::T_Molecular_covalent_structure< Particle_info > Covalent_structure
 
typedef SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins< Covalent_structure > Covalent_structure_builder
 
typedef std::vector< double > Conformation
 
typedef SBL::CSB::T_Molecular_primitive_internal_coordinates< Conformation, Covalent_structure > Internal_coordinates
 
typedef SBL::CSB::T_Molecular_cartesian_coordinates< Conformation, Covalent_structure > Cartesian_coordinates
 
typedef SBL::CSB::T_Polypeptide_chain_representation< Particle_traits, Covalent_structure, Conformation > Polypeptide_chain_representation
 
typedef SBL::CSB::T_Protein_representation< Polypeptide_chain_representation > Protein_representation
 
typedef SBL::IO::T_Protein_representation_loader< Protein_representation, Covalent_structure_builder > Protein_representation_loader
 
typedef double FT
 
typedef SBL::Models::T_Unit_system_traits_AKMA< FT > UST_base
 
typedef SBL::Models::T_Unit_system_traits_for_potential_energy< UST_base > Unit_system_traits
 
typedef SBL::IO::T_Potential_energy_parameters< Covalent_structure, Unit_system_traits, FT > Potential_energy_parameters_loader
 
typedef SBL::Modules::T_Module_option_description Base
 

Public Member Functions

boost::program_options::options_description add_options (void) const
 Virtual method for adding options to the module. More...
 
bool load (unsigned verbose=false, std::ostream &out=std::cout)
 Loads the data. More...
 
bool check_options (std::string &message)
 
virtual bool check_options (std::string &message) const
 Checks that the input options' values are coherent. More...
 
virtual std::string get_output_prefix (void) const
 Returns a prefix that concatains the input line options used when running 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...
 
static bool has_options (void)
 
static void delete_options (void)
 
static void initialize_options (const std::string &caption)
 

Requirements

virtual 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
 

Member Typedef Documentation

◆ Base

typedef SBL::Modules::T_Module_option_description Base
inherited

◆ Cartesian_coordinates

typedef SBL::CSB::T_Molecular_cartesian_coordinates<Conformation, Covalent_structure> Cartesian_coordinates

◆ Conformation

typedef std::vector<double> Conformation

◆ Covalent_structure

typedef SBL::CSB::T_Molecular_covalent_structure<Particle_info> Covalent_structure

◆ Covalent_structure_builder

typedef SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins<Covalent_structure> Covalent_structure_builder

◆ FT

typedef double FT

◆ Internal_coordinates

typedef SBL::CSB::T_Molecular_primitive_internal_coordinates<Conformation, Covalent_structure> Internal_coordinates

◆ Molecular_system

typedef Particle_traits::Molecular_system Molecular_system

◆ Particle_info

typedef SBL::CSB::T_Particle_info_for_proteins<Particle_traits> Particle_info

◆ Particle_info_traits

typedef SBL::CSB::T_Particle_info_traits<Particle_info> Particle_info_traits

◆ Particle_traits

typedef SBL::Models::T_Atom_with_hierarchical_info_traits Particle_traits

◆ Polypeptide_chain_representation

typedef SBL::CSB::T_Polypeptide_chain_representation<Particle_traits, Covalent_structure, Conformation> Polypeptide_chain_representation

◆ Potential_energy_parameters_loader

typedef SBL::IO::T_Potential_energy_parameters<Covalent_structure, Unit_system_traits, FT> Potential_energy_parameters_loader

◆ Protein_representation

typedef SBL::CSB::T_Protein_representation<Polypeptide_chain_representation> Protein_representation

◆ Protein_representation_loader

typedef SBL::IO::T_Protein_representation_loader<Protein_representation, Covalent_structure_builder> Protein_representation_loader

◆ Self

typedef Internal_cartesian_file_converter Self

◆ Unit_system_traits

typedef SBL::Models::T_Unit_system_traits_for_potential_energy<UST_base> Unit_system_traits

◆ UST_base

typedef SBL::Models::T_Unit_system_traits_AKMA<FT> UST_base

Member Function Documentation

◆ add_options()

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

Virtual method for adding options to the module.

Reimplemented from T_Module_option_description< Dummy >.

◆ check_options() [1/2]

bool check_options ( std::string &  message)
inline

◆ check_options() [2/2]

virtual bool check_options ( std::string &  message) const
inlinevirtualinherited

Checks that the input options' values are coherent.

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_RST_MST_D_Family_matching_module< ModuleTraits >, 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_structure_classifier_module< ModuleTraits >, T_Molecular_interfaces_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Module_condition< void, Predicate >, T_Module_condition< Module, Predicate >, T_Module_based_workflow< Dummy >, T_Minimal_oriented_spanning_forest_module< ModuleTraits, SpatialSearchEngine >, T_D_Family_matching_module< ModuleTraits, TSolutionComputer >, T_Cluster_engine_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_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, 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_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, No_particle_annotator, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, Space_filling_model_loader, Conformations_loader, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Domain_annotator_for_particles< Annotations >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Numbers_file_loader< FT, Tag >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, T_Clustering_loader< Graph, Clustering >, and T_Archive_file_loader< InputArchive, SerializedData >.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_loader_instance_name()

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

◆ get_name()

virtual std::string get_name ( void  ) const
inlinevirtualinherited

Return the name of the class itself.

Reimplemented in 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_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, No_particle_annotator, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, Space_filling_model_loader, Conformations_loader, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Domain_annotator_for_particles< Annotations >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Numbers_file_loader< FT, Tag >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, T_Clustering_loader< Graph, Clustering >, and T_Archive_file_loader< InputArchive, SerializedData >.

◆ get_options()

static boost::program_options::options_description*& get_options ( void  )
inlinestaticinherited

Access to the options' description of the module.

◆ get_output_prefix()

virtual std::string get_output_prefix ( void  ) const
inlinevirtualinherited

Returns a prefix that concatains the input line options used when running 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_structure_classifier_module< ModuleTraits >, T_Molecular_interfaces_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Module_condition< void, Predicate >, T_Module_condition< Module, Predicate >, T_Module_based_workflow< Dummy >, T_Minimal_oriented_spanning_forest_module< ModuleTraits, SpatialSearchEngine >, T_Earth_mover_distance_module< ModuleTraits >, T_Cluster_engine_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_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, No_particle_annotator, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, Space_filling_model_loader, Conformations_loader, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Domain_annotator_for_particles< Annotations >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Numbers_file_loader< FT, Tag >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, T_Clustering_loader< Graph, Clustering >, and T_Archive_file_loader< InputArchive, SerializedData >.

◆ 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.

[Loading force field parameters]

Reimplemented from Loader_base.

◆ set_loader_instance_name()

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