Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_RMSD_comb_edge_weighted_module< ModuleTraits > Class Template Reference

Undefined. More...

#include "RMSD_comb_edge_weighted_module.hpp"

Public Member Functions

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...
 

Modules Management

void set_module_instance_name (const std::string &module_instance_name)
 Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules. More...
 
const std::string & get_module_instance_name (void) const
 Get the name of this instance of this module. More...
 
void set_report_mode (std::ios_base::openmode report_mode)
 Set a report mode, that is open or append modes. More...
 
void set_report_mode (std::ios_base::openmode &report_mode)
 Set a report mode, that is open or append modes. More...
 
const std::ios_base::openmode get_report_mode (void) const
 Get the report mode to be used when reporting. More...
 

Others

template<class Self_ >
Self_ * clone (const Self_ *s) const
 Clones the object using the copy constructor. More...
 
virtual bool is_logical_module (void) const
 Checks that this module defines a logical operator. More...
 
virtual bool is_condition_module (void) const
 Checks that this module defines a condition operator. More...
 
virtual bool operator() (void)
 Only for condition modules, for returning the predicate value. More...
 
virtual bool is_modules_collection (void) const
 Checks that this module defines a collection of modules. More...
 

Traits Requirements

typedef Module_traits::Structure Structure
 Representation of the input structure. More...
 
typedef ModuleTraits::RMSD_comb_edge_weighted RMSD_comb_edge_weighted
 Builds the motif graph and computes the combined motif lRMSD. More...
 
typedef std::pair< Structure *, Structure * > Motif_pairing
 brief A pair of structural motifs More...
 
typedef boost::archive::xml_oarchive Archive_type
 brief To serialize the results More...
 

Mandatory Requirements

void run (unsigned verbose, std::ostream &out)
 Runs the module following the input options. More...
 
bool is_runnable (void) const
 Checks that all the input options were set. More...
 
void statistics (std::ostream &out)
 Reports high-level statistics on the module. More...
 
Selfclone (void) const
 Clones the object using the copy constructor. More...
 
boost::program_options::options_description add_options () const
 Virtual method for adding options to the module. More...
 
std::string get_name (void) const
 Returns the name of the package. More...
 

Optional Requirements

void report (const std::string &prefix)
 Reports the output and statistics in output files. More...
 
template<class Archive >
void serialize (Archive &ar, const unsigned BOOST_PFTO int version)
 Serialize the output of this module. More...
 

Detailed Description

template<class ModuleTraits>
class SBL::Modules::T_RMSD_comb_edge_weighted_module< ModuleTraits >

Undefined.

Undefined

Member Typedef Documentation

◆ Archive_type

typedef boost::archive::xml_oarchive Archive_type

brief To serialize the results

◆ Motif_pairing

typedef std::pair<Structure*, Structure*> Motif_pairing

brief A pair of structural motifs

◆ RMSD_comb_edge_weighted

typedef ModuleTraits::RMSD_comb_edge_weighted RMSD_comb_edge_weighted

Builds the motif graph and computes the combined motif lRMSD.

◆ Structure

typedef Module_traits::Structure Structure

Representation of the input structure.

Member Function Documentation

◆ 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()

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

Checks that the input options' values are coherent.

Reimplemented in T_Exploration_parameters_with_layers< NumberType, Distance >, T_Module_based_workflow< Dummy >, T_Module_based_workflow<>, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Molecular_interfaces_module< ModuleTraits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, T_Space_filling_model_outer_approximation_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< GraphType, GetWeight >::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_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Sample_extender_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >, T_Alignment_structures_module< ModuleTraits, AlignmentEngine >, T_Exploration_parameters_update_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Filtration_graph_module< ModuleTraits, GraphBuilder >, T_Acceptance_test_module< ModuleTraits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Sample_selector_module< ModuleTraits >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Cluster_engine_module< ModuleTraits >, T_Exploration_parameters_default< NumberType, Distance >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Archive_file_loader< InputArchive, SerializedData >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Domain_annotator_for_particles< Annotations >, T_Graph_loader< GraphType, FT >, T_Module_condition< Module, Predicate >, T_Sequences_loader< FT >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Weights_file_loader< FT >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Points_d_file_loader< PointD >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Numbers_file_loader< FT, Tag >, T_Graph_loader< Graph >, and No_particle_annotator.

◆ clone() [1/2]

T_RMSD_comb_edge_weighted_module< ModuleTraits >::Self * clone ( void  ) const
inline

Clones the object using the copy constructor.

◆ clone() [2/2]

Self_* clone ( const Self_ *  s) const
inlineinherited

Clones the object using the copy constructor.

◆ get_module_instance_name()

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

Get the name of this instance of this module.

◆ get_name()

std::string get_name ( void  ) const
inlinevirtual

Returns the name of the package.

Reimplemented from Module_base.

◆ 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_Exploration_parameters_with_layers< NumberType, Distance >, T_Module_based_workflow< Dummy >, T_Module_based_workflow<>, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, T_Molecular_interfaces_module< ModuleTraits >, T_Union_of_balls_surface_volume_3_module< ModuleTraits, OutputArchive >, T_Conformations_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Radius_annotator_for_particles_with_annotated_name< NT, SetRadius >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Molecular_covalent_structure_loader_from_PDB< ParticleTraits, MolecularCovalentStructure, MolecularCovalentStructureBuilder, PDBLineFormat >, 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< GraphType, GetWeight >::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_Morse_theory_based_analyzer_module< ModuleTraits, SBL::GT::T_Morse_Smale_Witten_chain_complex_from_weighted_graph_builder< GraphType, GetWeight >::Morse_Smale_Witten_chain_complex >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, T_XTC_file_loader< ConformationType, ConformationBuilder, ESBTLMolecularSystem, PDBLineFormat >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Sample_extender_module< ModuleTraits >, T_Stop_criterion_module< ModuleTraits >, T_Alpha_complex_of_molecular_model_module< ModuleTraits >, T_Molecular_structure_classifier_module< ModuleTraits >, T_Exploration_parameters_update_module< ModuleTraits >, T_Earth_mover_distance_module< ModuleTraits >, T_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Buried_surface_area_without_label_module< ModuleTraits >, T_Tertiary_quaternary_structure_annotator_module< ModuleTraits >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Buried_surface_area_with_labels_module< ModuleTraits >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Exploration_parameters_default< NumberType, Distance >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Acceptance_test_module< ModuleTraits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, T_Sample_selector_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Archive_file_loader< InputArchive, SerializedData >, T_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >, T_Domain_annotator_for_particles< Annotations >, T_Multiple_archives_xml_archive_file_loader< SecondaryArchive, SecondaryData, SerializedData >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Graph_loader< GraphType, FT >, T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, T_Sequences_loader< FT >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Weights_file_loader< FT >, T_Points_d_file_loader< PointD >, T_Module_condition< Module, Predicate >, T_Conformational_ensemble_symmetric_difference_module< ModuleTraits >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, T_Numbers_file_loader< FT, Tag >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Point_cloud_hausdorff_distance_d_module< ModuleTraits >, T_Graph_loader< Graph >, and No_particle_annotator.

◆ get_report_mode()

const std::ios_base::openmode get_report_mode ( void  ) const
inlineinherited

Get the report mode to be used when reporting.

◆ is_condition_module()

virtual bool is_condition_module ( void  ) const
inlineprotectedvirtualinherited

Checks that this module defines a condition operator.

◆ is_logical_module()

virtual bool is_logical_module ( void  ) const
inlineprotectedvirtualinherited

Checks that this module defines a logical operator.

◆ is_modules_collection()

virtual bool is_modules_collection ( void  ) const
inlineprotectedvirtualinherited

Checks that this module defines a collection of modules.

◆ is_runnable()

bool is_runnable ( void  ) const
inlinevirtual

Checks that all the input options were set.

Reimplemented from Module_base.

◆ operator()()

virtual bool operator() ( void  )
inlineprotectedvirtualinherited

Only for condition modules, for returning the predicate value.

◆ report()

void report ( const std::string &  prefix)
inlinevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

◆ run()

void run ( unsigned  verbose,
std::ostream &  out 
)
inlinevirtual

Runs the module following the input options.

Implements Module_base.

◆ serialize()

void serialize ( Archive &  ar,
const unsigned BOOST_PFTO int  version 
)
inline

Serialize the output of this module.

◆ set_module_instance_name()

void set_module_instance_name ( const std::string &  module_instance_name)
inlineinherited

Sets a name for this instance of this module. In particular, it will be used in the prefix of output files generated by a collection of modules.

◆ set_report_mode() [1/2]

void set_report_mode ( std::ios_base::openmode  report_mode)
inlineinherited

Set a report mode, that is open or append modes.

◆ set_report_mode() [2/2]

void set_report_mode ( std::ios_base::openmode &  report_mode)
inlineinherited

Set a report mode, that is open or append modes.

◆ statistics()

void statistics ( std::ostream &  out)
inlinevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.