Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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_classifierget_classifier (void) const
 Const reference to the output structure classifier. More...
 
Molecular_structure_classifierget_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 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
ModuleTraitsTraits 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
ParticleWithSystemLabelTraitsmodel of ParticleTraits where particles have an attached system\'s label.
MolecularModelClassifierClassify 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.