Representation of a protein with its polypeptide chains. More...

#include <Protein_representation.hpp>

Public Types
typedef T_Protein_representation< PolypeptideChain >	Self
	The class itself.
typedef PolypeptideChain	Polypeptide_chain
	Representation of a single polypeptide chain within a Nucleic Acid representation.
typedef std::unordered_map< char, Polypeptide_chain >	Polypeptide_chains_map
	Map from chain identifiers to their representation.
typedef Polypeptide_chains_map::iterator	Polypeptide_chains_iterator
	Iterator over the map from chain identifiers to their representation.
typedef Polypeptide_chains_map::const_iterator	Polypeptide_chains_const_iterator
	Iterator over the map from chain identifiers to their representation (const)x.

Constructors
	T_Protein_representation ()
	Builds an empty protein.

Accessors
unsigned	get_number_of_particles () const
	Return the total number of particles in the protein.
unsigned	get_number_of_embedded_particles () const
	Return the number of particles in the protein with an associated geometric model.
bool	is_fully_embedded () const
	Return true iff all the chains are fully embedded.
unsigned	get_number_of_bonds () const
	Return the total number of bonds in the protein.
unsigned	get_number_of_embedded_bonds () const
	Return the number of bonds in the protein where both atoms have an associated geometric model.
unsigned	get_total_number_of_residues () const
	Return the total number of residues in the protein.
std::size_t	get_number_of_chains () const
	Return the number of polypeptide chains.
Polypeptide_chain &	get_chain (char c)
	Return the representation of the chain identified by the input character.
const Polypeptide_chain &	get_chain (char c) const
	Return a const representation of the chain identified by the input character.
const PolypeptideChain &	get_the_unique_chain () const
	Return a const representation of the unique chain of the protein.
PolypeptideChain &	get_the_unique_chain ()
	Return a const representation of the unique chain of the protein.
std::string &	get_name ()
	Return a reference to the name of this protein.
const std::string &	get_name () const
	Return the name of this protein.
void	statistics (std::ostream &out) const
	Return statistics on this protein.

Modifiers
void	create_chain (char c, Chain &chain, Molecular_covalent_structure &structure, const Conformation_type &C)
	Create a polypeptide chain in this protein.

Traversals
const Polypeptide_chains_map &	get_polypeptide_chain_representations () const
	Returns the polypeptide chain representations.
Polypeptide_chains_iterator	chains_begin ()
	Starts the container of chains.
Polypeptide_chains_iterator	chains_end ()
	Ends the container of chains.
Polypeptide_chains_const_iterator	chains_begin () const
	Starts the container of chains (const)
Polypeptide_chains_const_iterator	chains_end () const
	Ends the container of chains (const)

Detailed Description

template<class PolypeptideChain>
class SBL::CSB::T_Protein_representation< PolypeptideChain >

Representation of a protein with its polypeptide chains.

Template Parameters

PolypeptideChain Representation of a polypeptide chain (see SBL::CSB::T_Polypeptide_chain_representation)

Member Typedef Documentation

◆ Polypeptide_chain

template<class PolypeptideChain>

typedef PolypeptideChain Polypeptide_chain

Representation of a single polypeptide chain within a Nucleic Acid representation.

Template Parameters

ParticleTraits	Traits class providing the particle type, see package ParticleTraits
MolecularCovalentStructure	Graph representation of a covalent structure.
ConformationType	Representation of a conformation as a point in dimension D, where D is three times the number of particles in the conformation.

◆ Polypeptide_chains_const_iterator

template<class PolypeptideChain>

typedef Polypeptide_chains_map::const_iterator Polypeptide_chains_const_iterator

Iterator over the map from chain identifiers to their representation (const)x.

◆ Polypeptide_chains_iterator

template<class PolypeptideChain>

typedef Polypeptide_chains_map::iterator Polypeptide_chains_iterator

Iterator over the map from chain identifiers to their representation.

◆ Polypeptide_chains_map

template<class PolypeptideChain>

typedef std::unordered_map<char, Polypeptide_chain> Polypeptide_chains_map

Map from chain identifiers to their representation.

◆ Self

template<class PolypeptideChain>

typedef T_Protein_representation<PolypeptideChain> Self

The class itself.

Constructor & Destructor Documentation

◆ T_Protein_representation()

template<class PolypeptideChain>

T_Protein_representation ( )

inline

Builds an empty protein.

Member Function Documentation

◆ chains_begin() [1/2]

template<class PolypeptideChain>

T_Protein_representation< PolypeptideChain >::Polypeptide_chains_iterator chains_begin ( )

inline

Starts the container of chains.

Returns: Iterator at the start of the chain container.

◆ chains_begin() [2/2]

template<class PolypeptideChain>

T_Protein_representation< PolypeptideChain >::Polypeptide_chains_const_iterator chains_begin ( ) const

inline

Starts the container of chains (const)

Returns: Iterator at the start of the chain container.

◆ chains_end() [1/2]

template<class PolypeptideChain>

T_Protein_representation< PolypeptideChain >::Polypeptide_chains_iterator chains_end ( )

inline

Ends the container of chains.

Returns: Iterator at the end of the chain container.

◆ chains_end() [2/2]

template<class PolypeptideChain>

T_Protein_representation< PolypeptideChain >::Polypeptide_chains_const_iterator chains_end ( ) const

inline

Ends the container of chains (const)

Returns: Iterator at the end of the chain container.

◆ create_chain()

template<class PolypeptideChain>

void create_chain	(	char	c,
		Chain &	chain,
		Molecular_covalent_structure &	structure,
		const Conformation_type &	C )

inline

Create a polypeptide chain in this protein.

Parameters

c	Chain identifier
chain	from a Biophysical model
structure	Covalent structure of this protein
C	Geometric conformation of this protein

◆ get_chain() [1/2]

template<class PolypeptideChain>

PolypeptideChain & get_chain ( char c )

inline

Return the representation of the chain identified by the input character.

Parameters

c	Chain identifier

Returns: Polypeptide chain

◆ get_chain() [2/2]

template<class PolypeptideChain>

const PolypeptideChain & get_chain ( char c ) const

inline

Return a const representation of the chain identified by the input character.

Parameters

c	Chain identifier

Returns: Polypeptide chain (const)

◆ get_name() [1/2]

template<class PolypeptideChain>

std::string & get_name ( )

inline

Return a reference to the name of this protein.

Returns: Reference to the name.

◆ get_name() [2/2]

template<class PolypeptideChain>

const std::string & get_name ( ) const

inline

Return the name of this protein.

Returns: Name of this protein.

◆ get_number_of_bonds()

template<class PolypeptideChain>

unsigned get_number_of_bonds ( ) const

inline

Return the total number of bonds in the protein.

Returns: Total number of bonds in the protein.

◆ get_number_of_chains()

template<class PolypeptideChain>

std::size_t get_number_of_chains ( ) const

inline

Return the number of polypeptide chains.

Returns: Number of polypeptide chains

◆ get_number_of_embedded_bonds()

template<class PolypeptideChain>

unsigned get_number_of_embedded_bonds ( ) const

inline

Return the number of bonds in the protein where both atoms have an associated geometric model.

Returns: Number of embedded bonds in the protein.

◆ get_number_of_embedded_particles()

template<class PolypeptideChain>

unsigned get_number_of_embedded_particles ( ) const

inline

Return the number of particles in the protein with an associated geometric model.

Returns: Number of embedded particles in the protein.

◆ get_number_of_particles()

template<class PolypeptideChain>

unsigned get_number_of_particles ( ) const

inline

Return the total number of particles in the protein.

Returns: Total number of particles in the protein.

◆ get_polypeptide_chain_representations()

template<class PolypeptideChain>

const T_Protein_representation< PolypeptideChain >::Polypeptide_chains_map & get_polypeptide_chain_representations ( ) const

Returns the polypeptide chain representations.

Returns: Returns the polypeptide chain representations

◆ get_the_unique_chain() [1/2]

template<class PolypeptideChain>

PolypeptideChain & get_the_unique_chain ( )

inline

Return a const representation of the unique chain of the protein.

Returns: Polypeptide chain

◆ get_the_unique_chain() [2/2]

template<class PolypeptideChain>

const PolypeptideChain & get_the_unique_chain ( ) const

inline

Return a const representation of the unique chain of the protein.

Returns: Polypeptide chain

◆ get_total_number_of_residues()

template<class PolypeptideChain>

unsigned get_total_number_of_residues ( ) const

inline

Return the total number of residues in the protein.

Returns: Total number of residues in the protein.

◆ is_fully_embedded()

template<class PolypeptideChain>

bool is_fully_embedded ( ) const

inline

Return true iff all the chains are fully embedded.

Returns: Return true iff all the chains are fully embedded

◆ statistics()

template<typename PolypeptideChain>

void statistics ( std::ostream & out ) const

inline

Return statistics on this protein.

Returns: Statistics on this protein.

Public Types

Constructors

Accessors

Modifiers

Traversals

Detailed Description

Member Typedef Documentation

◆ Polypeptide_chain

◆ Polypeptide_chains_const_iterator

◆ Polypeptide_chains_iterator

◆ Polypeptide_chains_map

◆ Self

Constructor & Destructor Documentation

◆ T_Protein_representation()

Member Function Documentation

◆ chains_begin() [1/2]

◆ chains_begin() [2/2]

◆ chains_end() [1/2]

◆ chains_end() [2/2]

◆ create_chain()

◆ get_chain() [1/2]

◆ get_chain() [2/2]

◆ get_name() [1/2]

◆ get_name() [2/2]

◆ get_number_of_bonds()

◆ get_number_of_chains()

◆ get_number_of_embedded_bonds()

◆ get_number_of_embedded_particles()

◆ get_number_of_particles()

◆ get_polypeptide_chain_representations()

◆ get_the_unique_chain() [1/2]

◆ get_the_unique_chain() [2/2]

◆ get_total_number_of_residues()

◆ is_fully_embedded()

◆ statistics()