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

#include <Tripeptide_loop_closure_module.hpp>

Public Types

typedef SBL::Models::T_Conformation_traits< std::vector< CGAL::Gmpfr > > Conformation_traits
 [typedefs] More...
 
typedef Conformation_traits::Conformation Conformation
 
typedef CGAL::Algebraic_kernel_d_1< CGAL::Gmpq > K
 
typedef SBL::CSB::T_Tripeptide_loop_closure< Kget_loop_solutions
 
typedef CGAL::Gmpfr NT
 
typedef CGAL::Point_3< CGAL::Cartesian< CGAL::Gmpfr > > Point
 
typedef CGAL::Point_3< CGAL::Cartesian< double > > Point_d
 
typedef CGAL::Vector_3< CGAL::Cartesian< CGAL::Gmpfr > > Vector
 
typedef CGAL::Vector_3< CGAL::Cartesian< double > > Vector_d
 
typedef SBL::GT::T_Point_cloud_rigid_registration_3< double > registration
 
typedef SBL::Models::T_Atom_with_hierarchical_info_traits Particle_traits
 
typedef SBL::CSB::T_Particle_info_for_proteins< Particle_traitsParticle_info
 
typedef SBL::CSB::T_Particle_info_traits< Particle_infoParticle_info_traits
 
typedef SBL::CSB::Molecular_coordinates_utilities MCU
 
typedef SBL::CSB::T_Molecular_covalent_structure< Particle_infoCovalent_structure
 
typedef SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins< Covalent_structureCovalent_structure_builder
 
typedef SBL::CSB::T_Polypeptide_chain_representation< Particle_traits, Covalent_structure, ConformationPolypeptide_chain_representation
 
typedef SBL::CSB::T_Protein_representation< Polypeptide_chain_representationProtein_representation
 
typedef SBL::IO::T_Protein_representation_loader< Protein_representation, Covalent_structure_builderProtein_representation_loader
 
typedef SBL::CSB::T_Tripeptide_loop_closure< Kget_polynomial
 
typedef Module_base Self
 
typedef T_Module_option_description Base
 

Public Member Functions

bool & show_whole_protein ()
 
bool & show_side_chains ()
 
std::string & get_pdb_file_path ()
 
std::string & get_prefix ()
 
std::string & get_outputfolder ()
 
std::vector< std::string > & get_res_ids ()
 
char & get_chain_id ()
 
SBL::CSB::T_Tripeptide_constraints< NT > & get_constraints ()
 
std::vector< Point > & get_P0 ()
 
void run (unsigned verbose, std::ostream &out)
 Runs the module following the input options. More...
 
virtual boost::program_options::options_description add_options (void) const
 Virtual method for adding options to the module. More...
 
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)
 

Protected Attributes

std::string m_pdb_file_path
 [typedefs] More...
 
std::string m_prefix
 
std::string m_outputfolder
 
std::vector< std::string > m_resids
 
char m_chainid
 
Protein_representationm_prot
 
std::vector< Pointm_P0
 
SBL::CSB::T_Tripeptide_constraints< NTm_Constraints
 
bool m_show_whole_protein
 
bool m_show_side_chains
 

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...
 

Optional Requirements

virtual bool is_runnable (void) const
 Checks that all the input options were set. More...
 
virtual void statistics (std::ostream &out)
 Reports high-level statistics on the module. More...
 
virtual std::string get_name (void) const
 Returns the name of the package. More...
 
void check_filesystem_directory_exists (const std::string &output_prefix)
 To avoid later crash: check filesystem / existence of directory / directory exists. More...
 
virtual void report (const std::string &output_prefix)
 Reports the output and statistics in output files. 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...
 

Member Typedef Documentation

◆ Base

typedef T_Module_option_description Base
inherited

◆ Conformation

typedef Conformation_traits::Conformation Conformation

◆ Conformation_traits

typedef SBL::Models::T_Conformation_traits<std::vector<CGAL::Gmpfr> > Conformation_traits

[typedefs]

◆ Covalent_structure

◆ Covalent_structure_builder

◆ get_loop_solutions

◆ get_polynomial

◆ K

typedef CGAL::Algebraic_kernel_d_1<CGAL::Gmpq> K

◆ MCU

◆ NT

typedef CGAL::Gmpfr NT

◆ Particle_info

◆ Particle_info_traits

◆ Particle_traits

◆ Point

typedef CGAL::Point_3<CGAL::Cartesian<CGAL::Gmpfr> > Point

◆ Point_d

typedef CGAL::Point_3<CGAL::Cartesian<double> > Point_d

◆ Polypeptide_chain_representation

◆ Protein_representation

◆ Protein_representation_loader

◆ registration

◆ Self

typedef Module_base Self
inherited

◆ Vector

typedef CGAL::Vector_3<CGAL::Cartesian<CGAL::Gmpfr> > Vector

◆ Vector_d

typedef CGAL::Vector_3<CGAL::Cartesian<double> > Vector_d

Member Function Documentation

◆ add_options()

virtual boost::program_options::options_description add_options ( void  ) const
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_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_interfaces_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Earth_mover_distance_module< ModuleTraits >, T_D_Family_matching_module< ModuleTraits, TSolutionComputer >, 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 >, 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 >, Tripeptide_constraints_loader_from_pdb, 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 >, T_Archive_file_loader< InputArchive, SerializedData >, Internal_cartesian_file_converter, 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_filesystem_directory_exists()

void check_filesystem_directory_exists ( const std::string &  output_prefix)
inlineinherited

To avoid later crash: check filesystem / existence of directory / directory exists.

◆ check_options()

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 >.

◆ clone()

Self_* clone ( const Self_ *  s) const
inlineinherited

Clones the object using the copy constructor.

◆ delete_options()

static void delete_options ( void  )
inlinestaticinherited

◆ get_chain_id()

char& get_chain_id ( )
inline

◆ get_constraints()

SBL::CSB::T_Tripeptide_constraints<NT>& get_constraints ( )
inline

◆ 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()

virtual std::string get_name ( void  ) const
inlinevirtualinherited

Returns the name of the package.

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_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_vertex_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_NNG_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_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 >, and T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >.

◆ 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 >.

◆ get_outputfolder()

std::string& get_outputfolder ( )
inline

◆ get_P0()

std::vector<Point>& get_P0 ( )
inline

◆ get_pdb_file_path()

std::string& get_pdb_file_path ( )
inline

◆ get_prefix()

std::string& get_prefix ( )
inline

◆ get_report_mode()

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

Get the report mode to be used when reporting.

◆ get_res_ids()

std::vector<std::string>& get_res_ids ( )
inline

◆ has_options()

static bool has_options ( void  )
inlinestaticinherited

◆ initialize_options()

static void initialize_options ( const std::string &  caption)
inlinestaticinherited

◆ 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()

virtual bool is_runnable ( void  ) const
inlinevirtualinherited

Checks that all the input options were set.

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_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_vertex_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_NNG_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_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_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >, T_RST_MST_D_Family_matching_module< ModuleTraits >, and T_D_Family_matching_module< ModuleTraits, TSolutionComputer >.

◆ operator()()

virtual bool operator() ( void  )
inlineprotectedvirtualinherited

Only for condition modules, for returning the predicate value.

◆ report()

virtual void report ( const std::string &  output_prefix)
inlinevirtualinherited

Reports the output and statistics in output files.

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_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_vertex_weighted_graph_module< ModuleTraits, GraphType, GetWeight >, T_Morse_theory_based_analyzer_for_NNG_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_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, and T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >.

◆ run()

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

Runs the module following the input options.

Implements Module_base.

◆ 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.

◆ show_side_chains()

bool& show_side_chains ( )
inline

◆ show_whole_protein()

bool& show_whole_protein ( )
inline

◆ statistics()

virtual void statistics ( std::ostream &  out)
inlinevirtualinherited

Reports high-level statistics on 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_RST_MST_D_Family_matching_module< ModuleTraits >, T_RMSD_comb_edge_weighted_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_Earth_mover_distance_module< ModuleTraits >, 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 >, and T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >.

Member Data Documentation

◆ m_chainid

char m_chainid
protected

◆ m_Constraints

SBL::CSB::T_Tripeptide_constraints<NT> m_Constraints
protected

◆ m_outputfolder

std::string m_outputfolder
protected

◆ m_P0

std::vector<Point> m_P0
protected

◆ m_pdb_file_path

std::string m_pdb_file_path
protected

[typedefs]

◆ m_prefix

std::string m_prefix
protected

◆ m_prot

Protein_representation* m_prot
protected

◆ m_resids

std::vector<std::string> m_resids
protected

◆ m_show_side_chains

bool m_show_side_chains
protected

◆ m_show_whole_protein

bool m_show_whole_protein
protected