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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Module which computes a pairwise structural alignment of two protein structures Module which computes a pairwise structural alignment of two protein structures. More...
#include "Pairwise_structural_alignment_module.hpp"
Public Types | |
enum | run_type { SCORE , LRMSD , RANDOM } |
The run type for the module. More... | |
typedef SBL::Modules::T_Alignment_structures_module< ModuleTraits, AlignmentEngine > | Base |
typedef T_Pairwise_structural_alignment_module< ModuleTraits, AlignmentEngine > | Self |
typedef AlignmentEngine | Alignment_engine |
typedef Alignment_engine::Aligned_pair | Aligned_pair |
typedef Alignment_engine::Alignment_type | Alignment_type |
typedef Base::Sequence_length_type | Sequence_length_type |
typedef Base::Structure | Structure |
typedef ModuleTraits::Residue_set | Residue_set |
typedef ModuleTraits::Alignment_residue | Alignment_residue |
typedef ModuleTraits::Atom | Atom |
typedef ModuleTraits::Molecular_system | Molecular_system |
typedef ModuleTraits::Shelf | Shelf |
typedef SBL::CSB::T_Score_ordering_computer< Structure, Alignment_engine > | Score_ordering_computer |
typedef ModuleTraits::FT | FT |
typedef ModuleTraits::Molecular_distance | Molecular_distance |
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... | |
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_Pairwise_structural_alignment_module (void) | |
T_Pairwise_structural_alignment_module (const Self &other) | |
Mandatory Requirements | |
void | run (unsigned verbose, std::ostream &out) |
Runs the module following the input options. 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... | |
Printers | |
void | print_alignment (const std::string &filename) |
Print the alignment (as a pairing of residue sequence numbers) More... | |
void | write_pymol_script (const std::string &filename) |
Write a PyMol script. More... | |
template<class Archive > | |
void | serialize (Archive &ar, const unsigned BOOST_PFTO int version) |
Serialize. More... | |
Accessors | |
Structure *& | get_aligned_structure_1 () |
Return the aligned residues belonging to the first chain. More... | |
Structure *& | get_aligned_structure_2 () |
Return the aligned residues belonging to the second chain More... | |
double | get_alignment_lRMSD () const |
Return the least RMSD. More... | |
double | get_distance_RMSD () const |
Return the distance RMSD. More... | |
unsigned | get_size () const |
Return the alignment size. More... | |
double | get_similarity_percentage () const |
Return the sequence similarity percentage. More... | |
double | get_identity_percentage () const |
Return the sequence identity percentage. More... | |
Residue_set | get_first_chain_motif_as_residue_set (void) |
Return the first motif as a residue set (as defined in the traits class). More... | |
Residue_set | get_second_chain_motif_as_residue_set (void) |
Return the second motif as a residue set (as defined in the traits class). More... | |
double | get_lrmsd_ratio (void) |
bool | is_structural_motif (void) const |
template<class OutputIterator > | |
void | get_first_structure_score_ordering (OutputIterator out) |
template<class OutputIterator > | |
void | get_second_structure_score_ordering (OutputIterator out) |
static unsigned | get_size_threshold (void) |
static Shelf *& | get_shelf () |
Return the shelf. More... | |
Modifiers | |
void | set_persistence_one (std::pair< double, double > persistence) |
Set the persistence values for the blocks. More... | |
void | set_persistence_two (std::pair< double, double > persistence) |
void | set_run_type (run_type new_type) |
Set the run type of the module. More... | |
static void | set_reference_lrmsd (double lrmsd) |
Set the reference lRMSD (used to determine if a motif is interesting) More... | |
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... | |
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... | |
Module which computes a pairwise structural alignment of two protein structures Module which computes a pairwise structural alignment of two protein structures.
It is designed such that the input can be either a collection of 3D spheres representing the particles, or a collection of particles with the type derived from ParticleTraits, depending on the type of the output -complex:
ModuleTraits | Traits class defining the types T_Alpha_complex_of_molecular_model_module::Alpha_complex and T_Alpha_complex_of_molecular_model_module::Particles_container. |
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inherited |
Core algorithm performing the alignment.
typedef AlignmentEngine Alignment_engine |
typedef ModuleTraits::Alignment_residue Alignment_residue |
typedef ModuleTraits::Atom Atom |
typedef SBL::Modules::T_Alignment_structures_module<ModuleTraits, AlignmentEngine> Base |
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inherited |
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inherited |
typedef ModuleTraits::Molecular_system Molecular_system |
typedef ModuleTraits::Residue_set Residue_set |
typedef T_Pairwise_structural_alignment_module<ModuleTraits, AlignmentEngine> Self |
typedef ModuleTraits::Shelf Shelf |
typedef Base::Structure Structure |
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inherited |
Type for a unit (e.g residue or nucleotid)
enum run_type |
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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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inlinestaticinherited |
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Return the aligned residues belonging to the first chain.
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Return the aligned residues belonging to the second chain
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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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Return the least RMSD.
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inlinestaticinherited |
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Return the distance RMSD.
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Return the first motif as a residue set (as defined in the traits class).
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inlineinherited |
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Return the sequence identity percentage.
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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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Access to the options' description of the module.
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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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Return the second motif as a residue set (as defined in the traits class).
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inlineinherited |
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inline |
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inlinestatic |
Return the shelf.
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inline |
Return the sequence similarity percentage.
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Return the alignment size.
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inlinestatic |
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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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inline |
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inlineprotectedvirtualinherited |
Only for condition modules, for returning the predicate value.
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inline |
Print the alignment (as a pairing of residue sequence numbers)
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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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inline |
Serialize.
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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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inline |
Set the persistence values for the blocks.
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inline |
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inlinestatic |
Set the reference lRMSD (used to determine if a motif is interesting)
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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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Set the run type of the module.
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inlinevirtualinherited |
Reports high-level statistics on the module.
Reimplemented from Module_base.
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Write a PyMol script.