T_Subdomain_comparator_module< ModuleTraits > Class Template Reference

#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
The loaded partners (which we will compare)
	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...

Member Typedef Documentation

Alignment_residue

typedef Structure::value_type Alignment_residue

An alignment residue (used for the particle aligner and as our primitive residue type)

Alignment_type

typedef Molecular_aligner::Alignment_type Alignment_type

The alignment type (usually just a vector of pairings)

Base

typedef SBL::Modules::Module_base Base

Chain_map

typedef std::map<char, Subdomains_map> Chain_map

A multimap which associates to a sub domain label all the residues it contains.

Conformation

typedef Molecular_distance::Point Conformation

A Conformation (used for computing the molecular distance)

Label

typedef Label_traits::Label Label

The label defining a sub domain.

Label_classifier

typedef Label_traits::Primitive_label_classifier Label_classifier

A label classifier, to determine the sub domain a particular atom belongs to.

Label_traits

typedef ModuleTraits::Label_traits Label_traits

The labels to load the SSEs we wish to compare.

Molecular_aligner

typedef ModuleTraits::Alignment_engine Molecular_aligner

The structures aren't always the same: they require a molecular aligner to compute an alignment.

Molecular_distance

typedef ModuleTraits::Molecular_distance Molecular_distance

The molecular distance used to compare the structures.

Protein_representation

typedef ModuleTraits::Protein_representation Protein_representation

A protein representation.

Residue

typedef ModuleTraits::Residue Residue

Representation of a residue in the input representation.

Self

typedef T_Subdomain_comparator_module<ModuleTraits> Self

Structure

typedef ModuleTraits::Structure Structure

The structure in which sub domains will be stored (to perform an alignment and compute distances)

Structure_builder

typedef ModuleTraits::Structure_builder Structure_builder

Builder of the structure, particularly important when used with Kpax that requires the built of cannonized segments.

Subdomains_map

typedef std::map<std::string, Structure> Subdomains_map

A multimap which associates to a sub domain label all the residues it contains.

Member Enumeration Documentation

Run_type

enum Run_type

An enum to keep track of which run type the module is on.

Enumerator
ONEPNC
TWOPONEC
TWOPNC
NPONEC
NPNC

Constructor & Destructor Documentation

T_Subdomain_comparator_module() [1/2]

T_Subdomain_comparator_module ( void  )

inline

T_Subdomain_comparator_module() [2/2]

T_Subdomain_comparator_module ( const Self &  other )

inline

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< Dummy >.

check_options()

bool check_options ( std::string &  message ) const

inlinevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

clone() [1/2]

Self_* clone ( const Self_ *  s ) const

inlineinherited

Clones the object using the copy constructor.

clone() [2/2]

T_Subdomain_comparator_module< ModuleTraits >::Self * clone ( void  ) const

inline

Clones the object using the copy constructor.

delete_options()

static void delete_options ( void  )

inlinestaticinherited

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

inlinevirtual

Returns the name of the package.

Reimplemented from Module_base.

get_options() [1/2]

boost::program_options::options_description *& get_options ( void  )

inline

Access to the options' description of the module.

get_options() [2/2]

const boost::program_options::options_description * get_options ( void  ) const

inline

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_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 >.

get_proteins()

std::vector<const Protein_representation*>& get_proteins ( )

inline

get_report_mode()

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

inlineinherited

Get the report mode to be used when reporting.

has_options()

static bool has_options ( void  )

inlinestaticinherited

initialize_options()

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

inlinestaticinherited

initialize_proteins()

void initialize_proteins ( const Label_classifier &  classifier )

inline

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

inlinevirtual

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_conformations_flag()

static void set_conformations_flag ( void  )

inlinestatic

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 )

inlinevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.