Module building the bicolor, mediated and tricolor interfaces of a molecular structure. Module building the bicolor, mediated and tricolor interfaces of a molecular structure. More...

#include "Molecular_interfaces_module.hpp"

Public Types
typedef T_Molecular_interfaces_module< ModuleTraits >	Self

typedef SBL::Modules::Module_base	Base

Static Public Member Functions
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)

Traits Requirements
typedef ModuleTraits::Molecular_interfaces_builder	Molecular_interfaces_builder
	Construct all the primitive and hierarchical interfaces associated to a molecular model represented by an alpha-complex. More...

Other Types
typedef Molecular_interfaces_builder::Molecular_structure_classifier	Molecular_structure_classifier
	Classify the particles of molecular systems that are at a given interface. More...

typedef Molecular_interfaces_builder::Bicolor_interface	Bicolor_interface
	Wrapper for a bicolor interface. It provides iterators and queries. More...

typedef Molecular_interfaces_builder::Mediated_interface	Mediated_interface
	Wrapper for a mediated interface. It provides iterators and queries. More...

typedef Molecular_interfaces_builder::Tricolor_interface	Tricolor_interface
	Wrapper for a tricolor interface. It provides iterators and queries. More...

Input Accessors
Molecular_structure_classifier *&	get_structure_classifier (void)
	Reference to a pointer to the input structure classifier. More...

Output Accessors
const Molecular_interfaces_builder &	get_interfaces_builder (void) const
	Const reference to the output interface builder. More...

Molecular_interfaces_builder &	get_interfaces_builder (void)
	Reference to the output interface builder. More...

const Bicolor_interface &	get_bicolor_interface (Partner_label partner_1, Partner_label partner_2) const
	Const reference to the output bicolor interface between the given partners. More...

Bicolor_interface &	get_bicolor_interface (Partner_label partner_1, Partner_label partner_2)
	Reference to the output bicolor interface between the given partners. More...

const Mediated_interface &	get_mediated_interface (Partner_label partner_1, Partner_label partner_2, Mediator_label mediator) const
	Const reference to the output mediated interface between the given partners and mediator. More...

Mediated_interface &	get_mediated_interface (Partner_label partner_1, Partner_label partner_2, Mediator_label mediator)
	Reference to the output mediated interface between the given partners and mediator. More...

const Tricolor_interface &	get_tricolor_interface (Partner_label partner_1, Partner_label partner_2, Mediator_label mediator) const
	Const reference to the output tricolor interface between the given partners and mediator. More...

Tricolor_interface &	get_tricolor_interface (Partner_label partner_1, Partner_label partner_2, Mediator_label mediator)
	Reference to the output tricolor interface between the given partners and mediator. More...

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...

std::string	get_name (void) const
	Returns the name of the package. More...

Optional Requirements
boost::program_options::options_description	add_options (void) 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...

std::string	get_output_prefix (void) const
	Returns a prefix that concatains the input line options used when running the module. 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...

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_interfaces_module< ModuleTraits >

Module building the bicolor, mediated and tricolor interfaces of a molecular structure. Module building the bicolor, mediated and tricolor interfaces of a molecular structure.

It builds from a given structure classifier an object SBL::Modules::T_Molecular_interfaces_module::Molecular_interfaces_builder that groups into data structures the contacts between two given partners, and possibly contacts mediated by a mediator:

SBL::Modules::T_Molecular_interfaces_module::Bicolor_interface accessible from SBL::Modules::T_Molecular_interfaces_module::get_bicolor_interface,

SBL::Modules::T_Molecular_interfaces_module::Mediated_interface accessible from SBL::Modules::T_Molecular_interfaces_module::get_mediated_interface,

SBL::Modules::T_Molecular_interfaces_module::Tricolor_interface accessible from SBL::Modules::T_Molecular_interfaces_module::get_tricolor_interface.

These data structures offer iterators over the different components of the interfaces (particles of a partner or a mediator, contacts between two given partners, or mediated contacts, connected components of adjacent contacts, etc...). Note that while the primitive interfaces are computed at the construction of the SBL::Modules::T_Molecular_interfaces_module::Molecular_interfaces_builder object, the hierarchical interfaces are computed when one wants to access them.

Various statistics on the interfaces are dumped:

the particles: number of connected components, number of particles per connected component,

the contacts: number of contacts per connected component, surface area, perimeter and curvature of the interface,

the interface shelling (optional): integer representing how much a contact is buried in the interface.

When reporting the results into files, three files are created for each pair of partners:

an XML file containing the full description of all the interfaces involving the two given partners,

a VMD file for visualizing the interfaces involving the two given partners; note that when the interface shelling is computed, the interfaces are colored following the burying of the contacts,

when computing the interface shelling, a XML file describing the shelling of the interfaces of the two given partners with all possible mediators.

Template Parameters

ModuleTraits Traits class defining the type SBL::Modules::T_Molecular_interfaces_module::Molecular_interfaces_builder.

Member Typedef Documentation

◆ Base

typedef SBL::Modules::Module_base Base

◆ Bicolor_interface

typedef Molecular_interfaces_builder::Bicolor_interface Bicolor_interface

Wrapper for a bicolor interface. It provides iterators and queries.

◆ Mediated_interface

typedef Molecular_interfaces_builder::Mediated_interface Mediated_interface

Wrapper for a mediated interface. It provides iterators and queries.

◆ Molecular_interfaces_builder

typedef ModuleTraits::Molecular_interfaces_builder Molecular_interfaces_builder

Construct all the primitive and hierarchical interfaces associated to a molecular model represented by an alpha-complex.

Initialized with the alpha-complex of a molecular model, it first classify all the contacts of the primitive interfaces using the classifier. Then, it computes the primitive interfaces. Finally, accessors are provided for getting any kind of interfaces (primitive or hierarchical).

Template Parameters

MolecularStructureTraits	Traits class defining the alpha complex and molecular interfaces.
MolecularStructureClassifier	Traits Traits class defining the alpha complex and molecular interfaces.

◆ Molecular_structure_classifier

typedef Molecular_interfaces_builder::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.

◆ Self

typedef T_Molecular_interfaces_module<ModuleTraits> Self

◆ Tricolor_interface

typedef Molecular_interfaces_builder::Tricolor_interface Tricolor_interface

Wrapper for a tricolor interface. It provides iterators and queries.

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_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

inlinevirtual

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.

◆ delete_options()

static void delete_options ( void )

inlinestaticinherited

◆ get_bicolor_interface() [1/2]

T_Molecular_interfaces_module< ModuleTraits >::Bicolor_interface & get_bicolor_interface	(	Partner_label	partner_1,
		Partner_label	partner_2
	)

inline

Reference to the output bicolor interface between the given partners.

◆ get_bicolor_interface() [2/2]

const T_Molecular_interfaces_module< ModuleTraits >::Bicolor_interface & get_bicolor_interface	(	Partner_label	partner_1,
		Partner_label	partner_2
	)		const

inline

Const reference to the output bicolor interface between the given partners.

◆ get_interfaces_builder() [1/2]

T_Molecular_interfaces_module< ModuleTraits >::Molecular_interfaces_builder & get_interfaces_builder ( void )

inline

Reference to the output interface builder.

◆ get_interfaces_builder() [2/2]

const T_Molecular_interfaces_module< ModuleTraits >::Molecular_interfaces_builder & get_interfaces_builder ( void ) const

inline

Const reference to the output interface builder.

◆ get_mediated_interface() [1/2]

T_Molecular_interfaces_module< ModuleTraits >::Mediated_interface & get_mediated_interface	(	Partner_label	partner_1,
		Partner_label	partner_2,
		Mediator_label	mediator
	)

inline

Reference to the output mediated interface between the given partners and mediator.

◆ get_mediated_interface() [2/2]

const T_Molecular_interfaces_module< ModuleTraits >::Mediated_interface & get_mediated_interface	(	Partner_label	partner_1,
		Partner_label	partner_2,
		Mediator_label	mediator
	)		const

inline

Const reference to the output mediated interface between the given partners and mediator.

◆ 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()

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

inlinevirtual

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

Reimplemented from T_Module_option_description< Dummy >.

◆ get_report_mode()

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

inlineinherited

Get the report mode to be used when reporting.

◆ get_structure_classifier()

T_Molecular_interfaces_module< ModuleTraits >::Molecular_structure_classifier *& get_structure_classifier ( void )

inline

Reference to a pointer to the input structure classifier.

◆ get_tricolor_interface() [1/2]

T_Molecular_interfaces_module< ModuleTraits >::Tricolor_interface & get_tricolor_interface	(	Partner_label	partner_1,
		Partner_label	partner_2,
		Mediator_label	mediator
	)

inline

Reference to the output tricolor interface between the given partners and mediator.

◆ get_tricolor_interface() [2/2]

const T_Molecular_interfaces_module< ModuleTraits >::Tricolor_interface & get_tricolor_interface	(	Partner_label	partner_1,
		Partner_label	partner_2,
		Mediator_label	mediator
	)		const

inline

Const reference to the output tricolor interface between the given partners and mediator.

◆ has_options()

static bool has_options ( void )

inlinestaticinherited

◆ 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

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_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.

Public Types

Static Public Member Functions

Traits Requirements

Other Types

Input Accessors

Output Accessors

Mandatory Requirements

Optional Requirements

Modules Management

Optional Requirements

Others

Detailed Description

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

Member Typedef Documentation

◆ Base

◆ Bicolor_interface

◆ Mediated_interface

◆ Molecular_interfaces_builder

◆ Molecular_structure_classifier

◆ Self

◆ Tricolor_interface

Member Function Documentation

◆ add_options()

◆ check_filesystem_directory_exists()

◆ check_options()

◆ clone()

◆ delete_options()

◆ get_bicolor_interface() [1/2]

◆ get_bicolor_interface() [2/2]

◆ get_interfaces_builder() [1/2]

◆ get_interfaces_builder() [2/2]

◆ get_mediated_interface() [1/2]

◆ get_mediated_interface() [2/2]

◆ get_module_instance_name()

◆ get_name()

◆ get_options()

◆ get_output_prefix()

◆ get_report_mode()

◆ get_structure_classifier()

◆ get_tricolor_interface() [1/2]

◆ get_tricolor_interface() [2/2]

◆ has_options()

◆ initialize_options()

◆ is_condition_module()

◆ is_logical_module()

◆ is_modules_collection()

◆ is_runnable()

◆ operator()()

◆ report()

◆ run()

◆ set_module_instance_name()

◆ set_report_mode() [1/2]

◆ set_report_mode() [2/2]

◆ statistics()

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