Molecular_system< Items, Point > Class Template Reference

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.
bool	has_no_model () const
	Check if the Molecular_system has at least a model or none.
bool	has_model (int i) const
	Check if the Molecular_system has a model with the specified index.
size_t	number_of_models () const
	Get the number of models in the Molecular_system.
const std::string &	name () const
	Get the value of name *.
std::string &	name ()
	Set the value of name *.
const int &	index () const
	Get the value of index *.
int &	index ()
	Set the value of index *.
const char &	alternate_location () const
	Get the value of alternate_location *.
char &	alternate_location ()
	Set the value of alternate_location *.
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.
Model &	get_model (int i)
	Get the model with the specified index.
const Model &	get_model (int i) const
	Get the model with the specified index (const version).
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.
void	add_ss_bond (SS_bond ss_bond)
	Adds an SS_bond (Disulfide bond) to the system.
const Model_container &	models () const
	Returns a const reference to the model container.
Model_container &	models ()
	Returns a reference to the model container.
unsigned	number_of_ss_bonds (void) const
	Returns the number of SS_bond (Disulfide bond) in the system.
const std::list< SS_bond > &	get_ss_bonds (void) const
	Returns the container of SS_bond (Disulfide bond)
Chain &	get_chain_from_sheet_identifier (const std::string &id)
	Returns a reference to the Chain associated with the given sheet identifier.
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.
Models_iterator	models_begin ()
	Get an iterator pointing to the beginning of the models in the Molecular_system.
Models_iterator	models_end ()
	Get an iterator pointing to the end of the models in the Molecular_system.
Models_const_iterator	models_begin () const
	Get a const iterator pointing to the beginning of the models in the Molecular_system.
Models_const_iterator	models_end () const
	Get a const iterator pointing to the end of the models in the Molecular_system.

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()

template<class Items, class Point>

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()

template<class Items, class Point>

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()

template<class Items, class Point>

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]

template<class Items, class Point>

char & alternate_location ( )

inline

Set the value of alternate_location *.

*

Parameters

value

The new value of alternate_location

alternate_location() [2/2]

template<class Items, class Point>

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]

template<class Items, class Point>

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]

template<class Items, class Point>

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]

template<class Items, class Point>

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]

template<class Items, class Point>

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()

template<class Items, class Point>

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()

template<class Items, class Point>

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()

template<class Items, class Point>

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()

template<class Items, class Point>

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]

template<class Items, class Point>

int & index ( )

inline

Set the value of index *.

*

Parameters

value

The new value of index

index() [2/2]

template<class Items, class Point>

const int & index ( ) const

inline

Get the value of index *.

• Returns

  The value of index

models() [1/2]

template<class Items, class Point>

Model_container & models ( )

inline

Returns a reference to the model container.

Returns

The reference to the model container.

models() [2/2]

template<class Items, class Point>

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]

template<class Items, class Point>

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]

template<class Items, class Point>

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]

template<class Items, class Point>

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]

template<class Items, class Point>

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]

template<class Items, class Point>

std::string & name ( )

inline

Set the value of name *.

*

Parameters

value

The new value of name

name() [2/2]

template<class Items, class Point>

const std::string & name ( ) const

inline

Get the value of name *.

• Returns

  The value of name

number_of_models()

template<class Items, class Point>

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()

template<class Items, class Point>

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).