T_Molecular_structure_classifier_module< ModuleTraits > Class Template Reference

Module classifying the particles of a molecular structure following their system's labels. Module classifying the particles of a molecular structure following their system's labels. More...

#include "Molecular_structure_classifier_module.hpp"

Public Member Functions
virtual boost::program_options::options_description	add_options (void)
	Virtual method for adding options to the module. More...

Static Public Member Functions
static boost::program_options::options_description *&	get_options (void)
	Access to the options' description of the module. More...

Traits Requirements
typedef ModuleTraits::Molecular_structure_classifier	Molecular_structure_classifier
	Classify the particles of molecular systems that are at a given interface. More...

Other Types
typedef Molecular_structure_classifier::Molecular_geometric_model_classifier	Molecular_geometric_model_classifier
	Alias for the model classifier. More...
typedef Molecular_geometric_model_classifier::Molecular_model	Molecular_model
	Type of molecular model for the model classifier. More...
typedef Molecular_structure_classifier::Partner_label_classifier	Partner_label_classifier
	Model of MolecularSystemLabelsTraits partners. More...
typedef Molecular_structure_classifier::Mediator_label_classifier	Mediator_label_classifier
	Model of MolecularSystemLabelsTraits mediators. More...
typedef Molecular_structure_classifier::Extra_label_classifier	Extra_label_classifier
	Model of MolecularSystemLabelsTraits extra. More...

Input Accessors
Molecular_model *&	get_molecular_model (void)
	Reference to a pointer over the input molecular model. More...
Partner_label_classifier *&	get_partner_classifier (void)
	Reference to a pointer over the input partner's labels classifier. More...
Mediator_label_classifier *&	get_mediator_classifier (void)
	Reference to a pointer over the input mediator's labels classifier. More...
Extra_label_classifier *&	get_extra_classifier (void)
	Reference to a pointer over the input extra's labels classifier. More...

Output Accessors
const Molecular_structure_classifier &	get_classifier (void) const
	Const reference to the output structure classifier. More...
Molecular_structure_classifier &	get_classifier (void)
	Reference to the output structure classifier. More...

Mandatory Requirements
void	run (unsigned verbose, std::ostream &out) override
	Runs the module following the input options. More...
bool	is_runnable (void) const override
	Checks that all the input options were set. More...
void	statistics (std::ostream &out) override
	Reports high-level statistics on the module. More...
std::string	get_name (void) const override
	Returns the name of the package. More...

Optional Requirements
bool	check_options (std::string &message) const override
	Checks that the input options' values are coherent. More...
std::string	get_output_prefix (void) const override
	Returns a prefix that concatains the input line options used when running the module. More...
void	report (const std::string &prefix) override
	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...

Optional Requirements
void	check_filesystem_directory_exists (const std::string &output_prefix)
	To avoid later crash: check filesystem / existence of directory / directory exists. 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_Molecular_structure_classifier_module< ModuleTraits >

Module classifying the particles of a molecular structure following their system's labels. Module classifying the particles of a molecular structure following their system's labels.

Classifying atoms and contacts between atoms has two aspects:

• the geometric models level: one wishes to find all the contacts in a molecular model. The Molecular_geometric_model_classifier provides different geometric model classifiers. In particular, the SBL::CSB::T_Molecular_geometric_model_classifier_for_alpha_complex class is used when the geometric model is an -complex.

• the systems level: one wishes to find all the particles belonging to a given partner, or all contacts between particles of two different partners. The Molecular_structure_classifier provides the SBL::CSB::T_Molecular_structure_classifier< ParticleWithSystemLabelTraits , MolecularModelClassifier > class to classify the particles endowed with a partner's label. The second template parameter is a model classifier used to classify the contacts in the molecular model.

The input molecular model can be set using the method T_Molecular_structure_classifier_module::get_molecular_model, that returns a reference over a pointer on the input geometric moel.

The system's label of a particle is determined by a system's label classifier. There is one classifier for each category of system's label, that are partners, mediators and extras. These can be set using the methods T_Molecular_structure_classifier_module::get_partner_classifier, T_Molecular_structure_classifier_module::get_mediator_classifier and T_Molecular_structure_classifier_module::get_extra_classifier . For moredetails on these primitive labels classifier, see MolecularSystemLabelsTraits.

Template Parameters

ModuleTraits

Traits class defining the type T_Molecular_structure_classifier_module::Molecular_structure_classifier.

Member Typedef Documentation

Extra_label_classifier

typedef Molecular_structure_classifier::Extra_label_classifier Extra_label_classifier

Model of MolecularSystemLabelsTraits extra.

Mediator_label_classifier

typedef Molecular_structure_classifier::Mediator_label_classifier Mediator_label_classifier

Model of MolecularSystemLabelsTraits mediators.

Molecular_geometric_model_classifier

typedef Molecular_structure_classifier::Molecular_geometric_model_classifier Molecular_geometric_model_classifier

Alias for the model classifier.

Molecular_model

typedef Molecular_geometric_model_classifier::Molecular_model Molecular_model

Type of molecular model for the model classifier.

Molecular_structure_classifier

typedef ModuleTraits::Molecular_structure_classifier Molecular_structure_classifier

Classify the particles of molecular systems that are at a given interface.

Data structure classifying the set of vertices and edges located at the interface between the partners. It also finalizes the labelling of vertices of an alpha-complex designed for a molecular system with several partners. In particular, it marks water molecules that are at the interface between the partners (interface water molecules), and the ones that are not (bulked water molecules).

Template Parameters

ParticleWithSystemLabelTraits	model of ParticleTraits where particles have an attached system\'s label.
MolecularModelClassifier	Classify a molecular model, i.e the geometric embedding of a molecular structure.

Partner_label_classifier

typedef Molecular_structure_classifier::Partner_label_classifier Partner_label_classifier

Model of MolecularSystemLabelsTraits partners.

Member Function Documentation

add_options()

virtual boost::program_options::options_description add_options ( void  )

inlinevirtualinherited

Virtual method for adding options to the module.

Reimplemented in 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_interfaces_module< ModuleTraits >, T_Earth_mover_distance_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_Particle_annotator_collector< ParticleAnnotator1, ParticleAnnotator2 >, T_Name_annotator_for_atoms< SetAnnotatedName >, T_Dynamic_annotator_for_residues< SetDynamicAnnotation >, T_Dynamic_annotator_for_atoms< SetDynamicAnnotation >, T_Transition_graph_loader< InputArchive, TransitionGraphTraits >, T_Protein_representation_loader< Protein_representation_ >, T_Primitive_labels_loader< PartnerLabelsTraits, MediatorLabelsTraits, ExtraLabelsTraits >, T_Numbers_file_loader< FT, Tag >, T_Molecular_system_loader< Molecular_system_ >, T_Molecular_system_loader< Molecular_system >, T_Molecular_system_loader< Molecular_covalent_structure_builder_::Molecular_covalent_structure::Particle_info::Particle_traits::Molecular_system >, T_Molecular_covalent_structure_loader_from_MOL< MolecularCovalentStructure >, T_Molecular_covalent_structure_loader< Molecular_covalent_structure_builder_ >, T_Molecular_covalent_structure_loader< SBL::CSB::T_Molecular_covalent_structure_builder_for_proteins< typename Protein_representation_::Polypeptide_chain::Molecular_covalent_structure > >, T_Conformation_loader< Conformation_builder_ >, T_Archive_file_loader< InputArchive, SerializedData >, T_Name_annotator_for_pseudo_atoms< SetAnnotatedName >, T_Generic_annotator_without_file< AnnotationType, SetAnnotation, GetInstanceName >, T_Generic_annotator< KeyType, AnnotationType, MakeKey, SetAnnotation, GetOptionName, GetOptionHelp, GetOptionDisplayName >, T_Domain_annotator_for_particles< Annotations >, T_RMSD_comb_edge_weighted_module< ModuleTraits >, T_Morse_theory_based_analyzer_for_NNG_module< ModuleTraits >, T_Cluster_engine_module< ModuleTraits >, T_Alignment_structures_module< ModuleTraits, AlignmentEngineStructures >, and T_Alignment_sequences_module< ModuleTraits, AlignmentEngineSequences >.

check_filesystem_directory_exists()

void check_filesystem_directory_exists ( const std::string &  output_prefix )

inlineinherited

To avoid later crash: check filesystem / existence of directory / directory exists.

check_options()

bool check_options ( std::string &  message ) const

inlineoverridevirtual

Checks that the input options' values are coherent.

Reimplemented from T_Module_option_description< Dummy >.

clone()

Self_* clone ( const Self_ *  s ) const

inlineinherited

Clones the object using the copy constructor.

get_classifier() [1/2]

T_Molecular_structure_classifier_module< ModuleTraits >::Molecular_structure_classifier & get_classifier ( void  )

inline

Reference to the output structure classifier.

get_classifier() [2/2]

const T_Molecular_structure_classifier_module< ModuleTraits >::Molecular_structure_classifier & get_classifier ( void  ) const

inline

Const reference to the output structure classifier.

get_extra_classifier()

T_Molecular_structure_classifier_module< ModuleTraits >::Extra_label_classifier *& get_extra_classifier ( void  )

inline

Reference to a pointer over the input extra's labels classifier.

get_mediator_classifier()

T_Molecular_structure_classifier_module< ModuleTraits >::Mediator_label_classifier *& get_mediator_classifier ( void  )

inline

Reference to a pointer over the input mediator's labels classifier.

get_module_instance_name()

const std::string& get_module_instance_name ( void  ) const

inlineinherited

Get the name of this instance of this module.

get_molecular_model()

T_Molecular_structure_classifier_module< ModuleTraits >::Molecular_model *& get_molecular_model ( void  )

inline

Reference to a pointer over the input molecular model.

get_name()

std::string get_name ( void  ) const

inlineoverridevirtual

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()

std::string get_output_prefix ( void  ) const

inlineoverridevirtual

Returns a prefix that concatains the input line options used when running the module.

Reimplemented from T_Module_option_description< Dummy >.

get_partner_classifier()

T_Molecular_structure_classifier_module< ModuleTraits >::Partner_label_classifier *& get_partner_classifier ( void  )

inline

Reference to a pointer over the input partner's labels classifier.

get_report_mode()

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

inlineinherited

Get the report mode to be used when reporting.

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

inlineoverridevirtual

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 )

inlineoverridevirtual

Reports the output and statistics in output files.

Reimplemented from Module_base.

run()

void run ( unsigned  verbose, std::ostream &  out  )

inlineoverridevirtual

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 )

inlineoverridevirtual

Reports high-level statistics on the module.

Reimplemented from Module_base.