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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Undefined. Undefined. More...
#include "Iterative_alignment_module.hpp"
Public Types | |
typedef T_Iterative_alignment_module< ModuleTraits > | Self |
typedef ModuleTraits::Iterative_aligner_engine | Iterative_aligner_engine |
typedef Iterative_aligner_engine::Alignment_type | Alignment_type |
typedef ModuleTraits::Shelf | Shelf |
typedef SBL::Modules::T_Alignment_structures_module< ModuleTraits, Iterative_aligner_engine > | Base |
typedef Base::Aligner_algorithm::Seed_type | Seed_type |
typedef Base::Aligner_algorithm::Seeder | Seeder |
typedef ModuleTraits::Structure | Structure |
typedef ModuleTraits::FT | FT |
typedef ModuleTraits::Molecular_distance | Molecular_distance |
typedef ModuleTraits::Iterative_aligner_engine | Alignment_engine |
Base engine for making alignments between structures. Base engine for making alignments between structures. More... | |
typedef Alignment_engine::Aligner_algorithm | Aligner_algorithm |
Core algorithm performing the alignment. More... | |
typedef Alignment_engine::Alignment_unit | Structure_unit |
Type for a unit (e.g residue or nucleotid) More... | |
typedef Alignment_engine::Sequence_length_type | Sequence_length_type |
Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages. More... | |
Public Member Functions | |
void | run (unsigned verbose, std::ostream &out) |
Runs the module following the input options. More... | |
std::vector< Seed_type > & | get_seeds () |
void | report (const std::string &prefix) |
Reports the output and statistics in output files. More... | |
void | write_pymol_script (const std::string &filename) |
boost::program_options::options_description | add_options () const |
Virtual method for adding options to the module. 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 Shelf *& | get_shelf () |
Return the shelf. More... | |
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) |
Input Accessors and modifiers | |
Structure *& | get_first_structure (void) |
Structure *& | get_second_structure (void) |
const Alignment_type & | get_alignment (void) const |
Aligner_algorithm & | get_aligner_algorithm (void) |
const Aligner_algorithm & | get_aligner_algorithm (void) const |
Alignment_engine *& | get_alignment_engine (void) |
const Alignment_engine * | get_alignment_engine (void) const |
void | initialize_engine (void) |
static SBL::CSB::Alignment_substitution_matrix_type & | get_substition_matrix_type (void) |
static string & | get_alignment_viewer_name (void) |
static Sequence_length_type & | get_percentage_length_type (void) |
Mandatory Requirements | |
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... | |
std::string | get_name (void) const |
Returns the name of the package. More... | |
Optional Requirements | |
bool | check_options (std::string &message) const |
Checks that the input options' values are coherent. 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... | |
Undefined. Undefined.
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inherited |
Core algorithm performing the alignment.
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inherited |
Base engine for making alignments between structures. Base engine for making alignments between structures.
It inherits from the generic interface for all alignments and provide its base functionality. It also implements functionality specific to structural alignments, in particular for anaylzing and comparing alignments. The specific functionality concerns:
Due to geometric nature of the structural alignment, the structure type requires that its units define 3D coordinates, i.e the Alignment_unit defines methods x(), y() and z().
StructureType | Representation of a structure : it requires in particular to define the type Alignment_unit for the geometric representation of a unit to align (e.g a residue or a nucleotid with associated 3D coordinates), the type Alignment_unit indexing the units in the structure, the method size() to return the length of the sequence, and the operator [Alignment_unit_rep] for accessing to the corresponding unit of the structure. |
AlignerAlgorithm | Base functor for the algorithm that makes the alignment between the two input structures : it requires to define a type Score_type for the score (e.g a double, or a pair of doubles if two scores are required), to take two input structures and an output iterator over pairs of Alignment_unit_rep for the output alignment, and to return the score of the algorithm |
FT | Number type representation used for all statistics except the algorithm score. |
MolecularDistance | Distance functor between two molecular structures (default is lRMSD). |
typedef Iterative_aligner_engine::Alignment_type Alignment_type |
typedef SBL::Modules::T_Alignment_structures_module<ModuleTraits, Iterative_aligner_engine> Base |
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inherited |
typedef ModuleTraits::Iterative_aligner_engine Iterative_aligner_engine |
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inherited |
typedef Base::Aligner_algorithm::Seed_type Seed_type |
typedef Base::Aligner_algorithm::Seeder Seeder |
typedef T_Iterative_alignment_module<ModuleTraits> Self |
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inherited |
Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages.
typedef ModuleTraits::Shelf Shelf |
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inherited |
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Type for a unit (e.g residue or nucleotid)
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inlinevirtual |
Virtual method for adding options to the module.
Reimplemented from T_Module_option_description< Dummy >.
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inlinevirtualinherited |
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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inlinestaticinherited |
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inlineinherited |
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inlineinherited |
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inlineinherited |
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inlineinherited |
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inlineinherited |
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inlinestaticinherited |
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inlineinherited |
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inlineinherited |
Get the name of this instance of this module.
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inlinevirtualinherited |
Returns the name of the package.
Reimplemented from Module_base.
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inlinestaticinherited |
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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inlinestaticinherited |
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inlineinherited |
Get the report mode to be used when reporting.
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inlineinherited |
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inline |
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inlinestatic |
Return the shelf.
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inlinestaticinherited |
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inlinestaticinherited |
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inlineinherited |
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inlinestaticinherited |
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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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inlinevirtualinherited |
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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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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inlinevirtualinherited |
Reports high-level statistics on the module.
Reimplemented from Module_base.
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inline |