T_Iterative_alignment_module< ModuleTraits > Class Template Reference

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...

Detailed Description

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

Undefined. Undefined.

Member Typedef Documentation

Aligner_algorithm

typedef Alignment_engine::Aligner_algorithm Aligner_algorithm

inherited

Core algorithm performing the alignment.

Alignment_engine

typedef ModuleTraits::Iterative_aligner_engine Alignment_engine

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:

• the molecular distance between the two aligned structures (e.g the lRMSD),
• the Distance Difference Matrix (DDM),
• the dRMSD of the alignment.

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().

Template Parameters

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).

Alignment_type

typedef Iterative_aligner_engine::Alignment_type Alignment_type

Base

typedef SBL::Modules::T_Alignment_structures_module<ModuleTraits, Iterative_aligner_engine> Base

FT

typedef ModuleTraits::FT FT

inherited

Iterative_aligner_engine

typedef ModuleTraits::Iterative_aligner_engine Iterative_aligner_engine

Molecular_distance

typedef ModuleTraits::Molecular_distance Molecular_distance

inherited

Seed_type

typedef Base::Aligner_algorithm::Seed_type Seed_type

Seeder

typedef Base::Aligner_algorithm::Seeder Seeder

Self

typedef T_Iterative_alignment_module<ModuleTraits> Self

Sequence_length_type

typedef Alignment_engine::Sequence_length_type Sequence_length_type

inherited

Enum for selecting the length of the sequence to consider when computing the similarity / identity percentages.

Shelf

typedef ModuleTraits::Shelf Shelf

Structure

typedef ModuleTraits::Structure Structure

inherited

Structure_unit

typedef Alignment_engine::Alignment_unit Structure_unit

inherited

Type for a unit (e.g residue or nucleotid)

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()

bool check_options ( std::string &  message ) const

inlinevirtualinherited

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description<>.

clone()

Self_* clone ( const Self_ *  s ) const

inlineinherited

Clones the object using the copy constructor.

delete_options()

static void delete_options ( void  )

inlinestaticinherited

get_aligner_algorithm() [1/2]

T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >::Aligner_algorithm & get_aligner_algorithm ( void  )

inlineinherited

get_aligner_algorithm() [2/2]

const T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >::Aligner_algorithm & get_aligner_algorithm ( void  ) const

inlineinherited

get_alignment()

const T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >::Alignment_type & get_alignment ( void  ) const

inlineinherited

get_alignment_engine() [1/2]

T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >::Alignment_engine *& get_alignment_engine ( void  )

inlineinherited

get_alignment_engine() [2/2]

const T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >::Alignment_engine * get_alignment_engine ( void  ) const

inlineinherited

get_alignment_viewer_name()

static string& get_alignment_viewer_name ( void  )

inlinestaticinherited

get_first_structure()

T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >::Structure *& get_first_structure ( void  )

inlineinherited

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

inlinevirtualinherited

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_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, T_Module_based_workflow< Dummy >, T_Module_based_workflow<>, T_Molecular_interfaces_module< ModuleTraits >, T_Potential_energy_parameters< CovalentStructure, UnitSystemTraits, FT >, 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_Correlated_motions_by_domain_module< ModuleTraits >, T_Protein_representation_loader< ProteinRepresentation, MolecularCovalentStructureBuilder, PDBLineFormat >, T_PDB_file_loader< ESBTLMolecularSystem, PDBLineFormat >, T_PDB_file_loader< Molecular_system >, 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_Space_filling_model_interpolated_approximation_module< ModuleTraits >, T_Morse_theory_based_analyzer_module< ModuleTraits, MorseSmaleWittenChainComplex >, T_Union_of_balls_boundary_patch_shelling_3_module< ModuleTraits, OutputArchive >, 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_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_Union_of_balls_boundary_3_module< ModuleTraits, ExactNT >, T_Earth_mover_distance_module< ModuleTraits >, T_Modules_collection< Module, SetIndividualInput >, T_Union_of_balls_mesh_3_module< ModuleTraits >, T_Module_condition< void, Predicate >, 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_Buried_surface_area_with_labels_module< ModuleTraits >, T_Spatial_search_module< ModuleTraits, ApproximatedSpatialSearchEngine >, T_Nearest_neighbors_graph_builder_module< ModuleTraits >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Energy_landscape_transition_graph_landmarks_paths_module< ModuleTraits >, T_Exploration_parameters_default< NumberType, Distance >, T_Minimal_oriented_spanning_forest_module< ModuleTraits, SpatialSearchEngine >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Acceptance_test_module< ModuleTraits >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Sample_selector_module< ModuleTraits >, T_Spheres_3_file_loader< Sphere3, Point3 >, 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_Sequences_loader< FT >, T_Weighted_vertex_graph_loader< PointD, WeightType, GraphType >, T_Graph_loader< GraphType, FT >, T_Graph_loader< Graph >, T_Graph_loader< GraphType, FT >, T_Weights_file_loader< FT >, T_Transition_graph_builder_from_DB_of_critical_points_module< ModuleTraits >, 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_Weighted_points_d_loader< PointD, WeightType >, T_Numbers_file_loader< FT, Tag >, T_Module_conjunction< ModuleOrLoader1, ModuleOrLoader2 >, T_Point_cloud_hausdorff_distance_d_module< ModuleTraits >, T_Clustering_loader< Graph, Clustering >, T_Graph_loader< Graph >, T_Clustering_loader< Graph, Clustering >, No_particle_annotator, Conformations_loader, and Space_filling_model_loader.

get_percentage_length_type()

static Sequence_length_type& get_percentage_length_type ( void  )

inlinestaticinherited

get_report_mode()

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

inlineinherited

Get the report mode to be used when reporting.

get_second_structure()

T_Alignment_structures_module< ModuleTraits, ModuleTraits::Iterative_aligner_engine >::Structure *& get_second_structure ( void  )

inlineinherited

get_seeds()

std::vector<Seed_type>& get_seeds ( )

inline

get_shelf()

static Shelf*& get_shelf ( )

inlinestatic

Return the shelf.

get_substition_matrix_type()

static SBL::CSB::Alignment_substitution_matrix_type& get_substition_matrix_type ( void  )

inlinestaticinherited

has_options()

static bool has_options ( void  )

inlinestaticinherited

initialize_engine()

void initialize_engine ( void  )

inlineinherited

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()

bool is_runnable ( void  ) const

inlinevirtualinherited

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.

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 )

inlinevirtualinherited

Reports high-level statistics on the module.

Reimplemented from Module_base.

write_pymol_script()

void write_pymol_script ( const std::string &  filename )

inline