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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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#include <Subdomain_comparator_module.hpp>
Public Types | |
enum | Run_type { ONEPNC , TWOPONEC , TWOPNC , NPONEC , NPNC } |
An enum to keep track of which run type the module is on. More... | |
typedef T_Subdomain_comparator_module< ModuleTraits > | Self |
typedef SBL::Modules::Module_base | Base |
typedef ModuleTraits::Molecular_distance | Molecular_distance |
The molecular distance used to compare the structures. More... | |
typedef ModuleTraits::Label_traits | Label_traits |
The labels to load the SSEs we wish to compare. More... | |
typedef ModuleTraits::Protein_representation | Protein_representation |
A protein representation. More... | |
typedef ModuleTraits::Alignment_engine | Molecular_aligner |
The structures aren't always the same: they require a molecular aligner to compute an alignment. More... | |
typedef ModuleTraits::Residue | Residue |
Representation of a residue in the input representation. More... | |
typedef ModuleTraits::Structure | Structure |
The structure in which sub domains will be stored (to perform an alignment and compute distances) More... | |
typedef ModuleTraits::Structure_builder | Structure_builder |
Builder of the structure, particularly important when used with Kpax that requires the built of cannonized segments. More... | |
typedef Structure::value_type | Alignment_residue |
An alignment residue (used for the particle aligner and as our primitive residue type) More... | |
typedef Label_traits::Primitive_label_classifier | Label_classifier |
A label classifier, to determine the sub domain a particular atom belongs to. More... | |
typedef Label_traits::Label | Label |
The label defining a sub domain. More... | |
typedef Molecular_distance::Point | Conformation |
A Conformation (used for computing the molecular distance) More... | |
typedef Molecular_aligner::Alignment_type | Alignment_type |
The alignment type (usually just a vector of pairings) More... | |
typedef std::map< std::string, Structure > | Subdomains_map |
A multimap which associates to a sub domain label all the residues it contains. More... | |
typedef std::map< char, Subdomains_map > | Chain_map |
A multimap which associates to a sub domain label all the residues it contains. More... | |
Public Member Functions | |
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 bool | has_options (void) |
static void | delete_options (void) |
static void | initialize_options (const std::string &caption) |
Attributes | |
T_Subdomain_comparator_module (void) | |
T_Subdomain_comparator_module (const Self &other) | |
Input Accessors | |
std::vector< const Protein_representation * > & | get_proteins () |
void | initialize_proteins (const Label_classifier &classifier) |
static void | set_conformations_flag (void) |
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... | |
Self * | clone (void) const |
Clones the object using the copy constructor. More... | |
std::string | get_name (void) const |
Returns the name of the package. More... | |
Optional Requirements | |
const boost::program_options::options_description * | get_options (void) const |
Access to the options' description of the module. More... | |
boost::program_options::options_description *& | get_options (void) |
Access to the options' description of the module. More... | |
boost::program_options::options_description | add_options () const |
Virtual method for adding options to the module. More... | |
bool | check_options (std::string &message) const |
Checks that the input options' values are coherent. More... | |
void | report (const std::string &prefix) |
Reports the output and statistics in output files. 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... | |
typedef Structure::value_type Alignment_residue |
An alignment residue (used for the particle aligner and as our primitive residue type)
typedef Molecular_aligner::Alignment_type Alignment_type |
The alignment type (usually just a vector of pairings)
typedef SBL::Modules::Module_base Base |
typedef std::map<char, Subdomains_map> Chain_map |
A multimap which associates to a sub domain label all the residues it contains.
A Conformation (used for computing the molecular distance)
typedef Label_traits::Label Label |
The label defining a sub domain.
A label classifier, to determine the sub domain a particular atom belongs to.
typedef ModuleTraits::Label_traits Label_traits |
The labels to load the SSEs we wish to compare.
typedef ModuleTraits::Alignment_engine Molecular_aligner |
The structures aren't always the same: they require a molecular aligner to compute an alignment.
typedef ModuleTraits::Molecular_distance Molecular_distance |
The molecular distance used to compare the structures.
typedef ModuleTraits::Protein_representation Protein_representation |
A protein representation.
typedef ModuleTraits::Residue Residue |
Representation of a residue in the input representation.
typedef T_Subdomain_comparator_module<ModuleTraits> Self |
typedef ModuleTraits::Structure Structure |
The structure in which sub domains will be stored (to perform an alignment and compute distances)
typedef ModuleTraits::Structure_builder Structure_builder |
Builder of the structure, particularly important when used with Kpax that requires the built of cannonized segments.
typedef std::map<std::string, Structure> Subdomains_map |
A multimap which associates to a sub domain label all the residues it contains.
enum Run_type |
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inline |
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inline |
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inlinevirtual |
Virtual method for adding options to the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlinevirtual |
Checks that the input options' values are coherent.
Reimplemented from T_Module_option_description< Dummy >.
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inlineinherited |
Clones the object using the copy constructor.
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inline |
Clones the object using the copy constructor.
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inlinestaticinherited |
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inlineinherited |
Get the name of this instance of this module.
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inlinevirtual |
Returns the name of the package.
Reimplemented from Module_base.
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inline |
Access to the options' description of the module.
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inline |
Access to the options' description of the module.
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inlinevirtualinherited |
Returns a prefix that concatains the input line options used when running the module.
Reimplemented in T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, T_Space_filling_model_shelling_diagram_comparison_module< ModuleTraits >, T_Space_filling_model_interface_finder_module< ModuleTraits >, T_Space_filling_model_outer_approximation_module< ModuleTraits >, T_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Space_filling_model_inner_approximation_module< ModuleTraits >, T_Weights_file_loader< FT >, T_Graph_loader< GraphType, FT >, T_Stop_criterion_module< ModuleTraits >, T_Sample_selector_module< ModuleTraits >, T_Sample_extender_module< ModuleTraits >, T_Exploration_parameters_update_module< ModuleTraits >, T_Exploration_parameters_with_layers< NumberType, Distance >, T_Exploration_parameters_default< NumberType, Distance >, T_Acceptance_test_module< ModuleTraits >, T_Graph_loader< GraphType, FT >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Weighted_points_d_loader< PointD, WeightType >, T_Sequences_loader< FT >, T_Graph_loader< Graph >, T_Correlated_motions_by_domain_module< ModuleTraits >, T_Point_cloud_hausdorff_distance_d_module< ModuleTraits >, T_Conformational_ensemble_symmetric_difference_module< ModuleTraits >, T_Graph_loader< GraphType, FT >, 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_PDB_file_loader< Molecular_system >, 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_Transition_graph_loader< boost::archive::xml_iarchive, typename Traits::Transition_graph_traits >, 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 >, T_Archive_file_loader< InputArchive, SerializedData >, and T_Archive_file_loader< boost::archive::xml_iarchive, typename Traits::Atom_shelling_forest >.
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inline |
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inlineinherited |
Get the report mode to be used when reporting.
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inlinestaticinherited |
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inlinestaticinherited |
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inline |
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inlineprotectedvirtualinherited |
Checks that this module defines a condition operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a logical operator.
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inlineprotectedvirtualinherited |
Checks that this module defines a collection of modules.
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inlinevirtual |
Checks that all the input options were set.
Reimplemented from Module_base.
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inlineprotectedvirtualinherited |
Only for condition modules, for returning the predicate value.
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inlinevirtual |
Reports the output and statistics in output files.
Reimplemented from Module_base.
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inlinevirtual |
Runs the module following the input options.
Implements Module_base.
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inlinestatic |
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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.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlineinherited |
Set a report mode, that is open or append modes.
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inlinevirtual |
Reports high-level statistics on the module.
Reimplemented from Module_base.