T_Nucleic_acid_representation< PolynucleotideChain > Class Template Reference

#include <Nucleic_acid_representation.hpp>

Public Types
typedef T_Nucleic_acid_representation< PolynucleotideChain >	Self
	The class itself.
typedef PolynucleotideChain	Polynucleotide_chain
	Representation of a single polynucleotide chain within a Nucleic Acid representation.
typedef std::unordered_map< char, Polynucleotide_chain >	Polynucleotide_chains_map
	Map from chain identifiers to their representation.
typedef Polynucleotide_chains_map::iterator	Polynucleotide_chains_iterator
	Iterator over the map from chain identifiers to their representation.
typedef Polynucleotide_chains_map::const_iterator	Polynucleotide_chains_const_iterator
	Iterator over the map from chain identifiers to their representation (const)x.

Constructors
	T_Nucleic_acid_representation ()
	Builds an empty nucleic acid.

Accessors
unsigned	get_number_of_particles () const
	Return the total number of particles in the nucleic acid.
unsigned	get_number_of_embedded_particles () const
	Return the number of particles in the nucleic acid 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 nucleic acid.
unsigned	get_number_of_embedded_bonds () const
	Return the number of bonds in the nucleic acid where both atoms have an associated geometric model.
unsigned	get_total_number_of_residues () const
	Return the total number of residues in the nucleic acid.
std::size_t	get_number_of_chains () const
	Return the number of polynucleotide chains.
Polynucleotide_chain &	get_chain (char c)
	Return the representation of the chain identified by the input character.
const Polynucleotide_chain &	get_chain (char c) const
	Return a const representation of the chain identified by the input character.
const PolynucleotideChain &	get_the_unique_chain () const
	Return a const representation of the unique chain of the nucleic acid.
PolynucleotideChain &	get_the_unique_chain ()
	Return a const representation of the unique chain of the nucleic acid.
std::string &	get_name ()
	Return a reference to the name of this nucleic acid.
const std::string &	get_name () const
	Return the name of this nucleic acid.
void	statistics (std::ostream &out) const
	Return statistics on this nucleic acid.

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

Traversals
Polynucleotide_chains_iterator	chains_begin ()
	Starts the container of chains.
Polynucleotide_chains_iterator	chains_end ()
	Ends the container of chains.
Polynucleotide_chains_const_iterator	chains_begin () const
	Starts the container of chains (const)
Polynucleotide_chains_const_iterator	chains_end () const
	Ends the container of chains (const)

Detailed Description

template<class PolynucleotideChain>
class SBL::CSB::T_Nucleic_acid_representation< PolynucleotideChain >

\sbl_add_package_main_class{Nucleic_acid_representation, T_Nucleic_acid_representation, Representation of a nucleic acid with its polynucleotide chains. \details Representation of a nucleic acid with its polynucleotide chains.

Template Parameters

PolynucleotideChain

Representation of a polynucleotide chain (see SBL::CSB::T_Polynucleotide_chain_representation)

}

Member Typedef Documentation

Polynucleotide_chain

template<class PolynucleotideChain>

typedef PolynucleotideChain Polynucleotide_chain

Representation of a single polynucleotide 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.

Polynucleotide_chains_const_iterator

template<class PolynucleotideChain>

typedef Polynucleotide_chains_map::const_iterator Polynucleotide_chains_const_iterator

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

Polynucleotide_chains_iterator

template<class PolynucleotideChain>

typedef Polynucleotide_chains_map::iterator Polynucleotide_chains_iterator

Iterator over the map from chain identifiers to their representation.

Polynucleotide_chains_map

template<class PolynucleotideChain>

typedef std::unordered_map<char, Polynucleotide_chain> Polynucleotide_chains_map

Map from chain identifiers to their representation.

Self

template<class PolynucleotideChain>

typedef T_Nucleic_acid_representation<PolynucleotideChain> Self

The class itself.

Constructor & Destructor Documentation

T_Nucleic_acid_representation()

template<class PolynucleotideChain>

T_Nucleic_acid_representation ( )

inline

Builds an empty nucleic acid.

Member Function Documentation

chains_begin() [1/2]

template<class PolynucleotideChain>

T_Nucleic_acid_representation< PolynucleotideChain >::Polynucleotide_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 PolynucleotideChain>

T_Nucleic_acid_representation< PolynucleotideChain >::Polynucleotide_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 PolynucleotideChain>

T_Nucleic_acid_representation< PolynucleotideChain >::Polynucleotide_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 PolynucleotideChain>

T_Nucleic_acid_representation< PolynucleotideChain >::Polynucleotide_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 PolynucleotideChain>

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

inline

Create a polynucleotide chain in this nucleic acid.

Parameters

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

get_chain() [1/2]

template<class PolynucleotideChain>

PolynucleotideChain & get_chain ( char c )

inline

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

Parameters

c	Chain identifier

Returns

Polynucleotide chain

get_chain() [2/2]

template<class PolynucleotideChain>

const PolynucleotideChain & get_chain ( char c ) const

inline

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

Parameters

c	Chain identifier

Returns

Polynucleotide chain (const)

get_name() [1/2]

template<class PolynucleotideChain>

std::string & get_name ( )

inline

Return a reference to the name of this nucleic acid.

Returns

Reference to the name.

get_name() [2/2]

template<class PolynucleotideChain>

const std::string & get_name ( ) const

inline

Return the name of this nucleic acid.

Returns

Name of this nucleic acid.

get_number_of_bonds()

template<class PolynucleotideChain>

unsigned get_number_of_bonds ( ) const

inline

Return the total number of bonds in the nucleic acid.

Returns

Total number of bonds in the nucleic acid.

get_number_of_chains()

template<class PolynucleotideChain>

std::size_t get_number_of_chains ( ) const

inline

Return the number of polynucleotide chains.

Returns

Number of polynucleotide chains

get_number_of_embedded_bonds()

template<class PolynucleotideChain>

unsigned get_number_of_embedded_bonds ( ) const

inline

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

Returns

Number of embedded bonds in the nucleic acid.

get_number_of_embedded_particles()

template<class PolynucleotideChain>

unsigned get_number_of_embedded_particles ( ) const

inline

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

Returns

Number of embedded particles in the nucleic acid.

get_number_of_particles()

template<class PolynucleotideChain>

unsigned get_number_of_particles ( ) const

inline

Return the total number of particles in the nucleic acid.

Returns

Total number of particles in the nucleic acid.

get_the_unique_chain() [1/2]

template<class PolynucleotideChain>

PolynucleotideChain & get_the_unique_chain ( )

inline

Return a const representation of the unique chain of the nucleic acid.

Returns

Polynucleotide chain

get_the_unique_chain() [2/2]

template<class PolynucleotideChain>

const PolynucleotideChain & get_the_unique_chain ( ) const

inline

Return a const representation of the unique chain of the nucleic acid.

Returns

Polynucleotide chain

get_total_number_of_residues()

template<class PolynucleotideChain>

unsigned get_total_number_of_residues ( ) const

inline

Return the total number of residues in the nucleic acid.

Returns

Total number of residues in the nucleic acid.

is_fully_embedded()

template<class PolynucleotideChain>

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 PolynucleotideChain>

void statistics ( std::ostream & out ) const

inline

Return statistics on this nucleic acid.

Returns

Statistics on this nucleic acid.