A class representing a molecular system. More...

#include <Molecular_system.h>

Public Member Functions
	Molecular_system (int index, std::string name="no_name")
	Constructs a Molecular_system object. More...

bool	has_no_model () const
	Check if the Molecular_system has at least a model or none. More...

bool	has_model (int i) const
	Check if the Molecular_system has a model with the specified index. More...

size_t	number_of_models () const
	Get the number of models in the Molecular_system. More...

const std::string &	name () const
	Get the value of name *. More...

std::string &	name ()
	Set the value of name *. More...

const int &	index () const
	Get the value of index *. More...

int &	index ()
	Set the value of index *. More...

const char &	alternate_location () const
	Get the value of alternate_location *. More...

char &	alternate_location ()
	Set the value of alternate_location *. More...

Model &	get_or_create_model (int i)
	Get or create a model with the specified index. If the model does not exist, it will be created empty and added to the Molecular_system. More...

Model &	get_model (int i)
	Get the model with the specified index. More...

const Model &	get_model (int i) const
	Get the model with the specified index (const version). More...

Secondary_structure_element &	add_secondary_structure_element (const Secondary_structure_element &sse)
	Add a Secondary_structure_element to the Molecular_system. The Secondary_structure_element can be a helix or a sheet. SSE are added per system since they are independent from the NMR model. However, it should be accessible from the Molecular_chain. More...

void	add_ss_bond (SS_bond ss_bond)
	Adds an SS_bond (Disulfide bond) to the system. More...

const Model_container &	models () const
	Returns a const reference to the model container. More...

Model_container &	models ()
	Returns a reference to the model container. More...

unsigned	number_of_ss_bonds (void) const
	Returns the number of SS_bond (Disulfide bond) in the system. More...

const std::list< SS_bond > &	get_ss_bonds (void) const
	Returns the container of SS_bond (Disulfide bond) More...

Chain &	get_chain_from_sheet_identifier (const std::string &id)
	Returns a reference to the Chain associated with the given sheet identifier. More...

const Chain &	get_chain_from_sheet_identifier (const std::string &id) const
	Returns a const reference to the Chain associated with the given sheet identifier. More...

Models_iterator	models_begin ()
	Get an iterator pointing to the beginning of the models in the Molecular_system. More...

Models_iterator	models_end ()
	Get an iterator pointing to the end of the models in the Molecular_system. More...

Models_const_iterator	models_begin () const
	Get a const iterator pointing to the beginning of the models in the Molecular_system. More...

Models_const_iterator	models_end () const
	Get a const iterator pointing to the end of the models in the Molecular_system. More...

Detailed Description

template<class Items, class Point>
class SBL::CSB::Molecular_system< Items, Point >

A class representing a molecular system.

Template Parameters

Items	The class that provides the type definitions for different components of the molecular system
Point	A point type with coordinates and const access methods x(), y(), and z()

Constructor & Destructor Documentation

◆ Molecular_system()

Molecular_system	(	int	index,
		std::string	name = `"no_name"`
	)

inline

Constructs a Molecular_system object.

Parameters

index	The index of the molecular system.
name	(Optional) The name of the molecular system. Defaults to "no_name" if not provided.

Returns: A Molecular_system object.

Member Function Documentation

◆ add_secondary_structure_element()

Secondary_structure_element& add_secondary_structure_element ( const Secondary_structure_element & sse )

inline

Add a Secondary_structure_element to the Molecular_system. The Secondary_structure_element can be a helix or a sheet. SSE are added per system since they are independent from the NMR model. However, it should be accessible from the Molecular_chain.

Parameters

sse	The Secondary_structure_element to add.

Returns: A reference to the added Secondary_structure_element.

◆ add_ss_bond()

void add_ss_bond ( SS_bond ss_bond )

inline

Adds an SS_bond (Disulfide bond) to the system.

Parameters

ss_bond The SS_bond (Disulfide bond) to add.

◆ alternate_location() [1/2]

char& alternate_location ( )

inline

Set the value of alternate_location *.

*

Parameters

value The new value of alternate_location

◆ alternate_location() [2/2]

const char& alternate_location ( ) const

inline

Get the value of alternate_location *.

Returns
The value of alternate_location

◆ get_chain_from_sheet_identifier() [1/2]

Chain& get_chain_from_sheet_identifier ( const std::string & id )

inline

Returns a reference to the Chain associated with the given sheet identifier.

Parameters

id	The identifier of the sheet.

Returns: A reference to the Chain associated with the sheet identifier.

Note: This function assumes that the sheet identifier exists in the Molecular_system, or triggers an assertion.

◆ get_chain_from_sheet_identifier() [2/2]

const Chain& get_chain_from_sheet_identifier ( const std::string & id ) const

inline

Returns a const reference to the Chain associated with the given sheet identifier.

Parameters

id	The identifier of the sheet.

Returns: A const reference to the Chain associated with the sheet identifier.

Note: This function assumes that the sheet identifier exists in the Molecular_system, or triggers an assertion.

◆ get_model() [1/2]

Model& get_model ( int i )

inline

Get the model with the specified index.

Parameters

i	The index of the model to retrieve.

Returns: A reference to the model with the specified index.

Exceptions

std::runtime_error If the model with the specified index does not exist.

◆ get_model() [2/2]

const Model& get_model ( int i ) const

inline

Get the model with the specified index (const version).

Parameters

i	The index of the model to retrieve.

Returns: A const reference to the model with the specified index.

Exceptions

std::runtime_error If the model with the specified index does not exist.

◆ get_or_create_model()

Model& get_or_create_model ( int i )

inline

Get or create a model with the specified index. If the model does not exist, it will be created empty and added to the Molecular_system.

Parameters

i	The index of the model.

Returns: A reference to the model with the specified index.

◆ get_ss_bonds()

const std::list<SS_bond>& get_ss_bonds ( void ) const

inline

Returns the container of SS_bond (Disulfide bond)

Returns: A const reference to the container of SS_bond (Disulfide bond)

◆ has_model()

bool has_model ( int i ) const

inline

Check if the Molecular_system has a model with the specified index.

Parameters

i	The index of the model to check.

Returns: True if the Molecular_system has a model with the specified index, false otherwise.

◆ has_no_model()

bool has_no_model ( ) const

inline

Check if the Molecular_system has at least a model or none.

Returns: True if the Molecular_system has none, false if it has at least one model.

◆ index() [1/2]

int& index ( )

inline

Set the value of index *.

*

Parameters

value The new value of index

◆ index() [2/2]

const int& index ( ) const

inline

Get the value of index *.

Returns
The value of index

◆ models() [1/2]

Model_container& models ( )

inline

Returns a reference to the model container.

Returns: The reference to the model container.

◆ models() [2/2]

const Model_container& models ( ) const

inline

Returns a const reference to the model container.

To retrieve the Molecular_model with smallest id of a Molecular_system object auto& model = (molecular_system->models().begin())->second;

Returns: The const reference to the model container.

◆ models_begin() [1/2]

Models_iterator models_begin ( )

inline

Get an iterator pointing to the beginning of the models in the Molecular_system.

Returns: An iterator pointing to the beginning of the models.

◆ models_begin() [2/2]

Models_const_iterator models_begin ( ) const

inline

Get a const iterator pointing to the beginning of the models in the Molecular_system.

Returns: A const iterator pointing to the beginning of the models.

◆ models_end() [1/2]

Models_iterator models_end ( )

inline

Get an iterator pointing to the end of the models in the Molecular_system.

Returns: An iterator pointing to the end of the models.

◆ models_end() [2/2]

Models_const_iterator models_end ( ) const

inline

Get a const iterator pointing to the end of the models in the Molecular_system.

Returns: A const iterator pointing to the end of the models.

◆ name() [1/2]

std::string& name ( )

inline

Set the value of name *.

*

Parameters

value The new value of name

◆ name() [2/2]

const std::string& name ( ) const

inline

Get the value of name *.

Returns
The value of name

◆ number_of_models()

size_t number_of_models ( ) const

inline

Get the number of models in the Molecular_system.

Returns: The number of models in the Molecular_system.

◆ number_of_ss_bonds()

unsigned number_of_ss_bonds ( void ) const

inline

Returns the number of SS_bond (Disulfide bond) in the system.

Returns: The number of SS_bond (Disulfide bond).

Public Member Functions

Detailed Description

template<class Items, class Point> class SBL::CSB::Molecular_system< Items, Point >

Constructor & Destructor Documentation

◆ Molecular_system()

Member Function Documentation

◆ add_secondary_structure_element()

◆ add_ss_bond()

◆ alternate_location() [1/2]

◆ alternate_location() [2/2]

◆ get_chain_from_sheet_identifier() [1/2]

◆ get_chain_from_sheet_identifier() [2/2]

◆ get_model() [1/2]

◆ get_model() [2/2]

◆ get_or_create_model()

◆ get_ss_bonds()

◆ has_model()

◆ has_no_model()

◆ index() [1/2]

◆ index() [2/2]

◆ models() [1/2]

◆ models() [2/2]

◆ models_begin() [1/2]

◆ models_begin() [2/2]

◆ models_end() [1/2]

◆ models_end() [2/2]

◆ name() [1/2]

◆ name() [2/2]

◆ number_of_models()

◆ number_of_ss_bonds()

template<class Items, class Point>
class SBL::CSB::Molecular_system< Items, Point >