Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Protein_representation< PolypeptideChain > Class Template Reference

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

#include <Protein_representation.hpp>

Public Types

typedef T_Protein_representation< PolypeptideChain > Self
 The class itself. More...
 
typedef PolypeptideChain Polypeptide_chain
 Reprenstation of a single polypeptidic chain within a protein representation. More...
 
typedef std::unordered_map< char, Polypeptide_chainPolypeptide_chains_map
 Map from chain identifiers to their representation. More...
 
typedef Polypeptide_chains_map::iterator Polypeptide_chains_iterator
 Iterator over the map from chain identifiers to their representation. More...
 
typedef Polypeptide_chains_map::const_iterator Polypeptide_chains_const_iterator
 Iterator over the map from chain identifiers to their representation (const)x. More...
 

Constructors

 T_Protein_representation ()
 Builds an empty protein. More...
 

Accessors

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

Modifiers

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

Traversals

Polypeptide_chains_iterator chains_begin ()
 Starts the container of chains. More...
 
Polypeptide_chains_iterator chains_end ()
 Ends the container of chains. More...
 
Polypeptide_chains_const_iterator chains_begin () const
 Starts the container of chains (const) More...
 
Polypeptide_chains_const_iterator chains_end () const
 Ends the container of chains (const) More...
 

Detailed Description

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

Representaiton of a protein with its polypeptide chains.

Representaiton of a protein with its polypeptide chains.

Template Parameters
PolypeptideChainRepresentation of a polypeptide chain (see SBL::CSB::T_Polypeptide_chain_representation)

Member Typedef Documentation

◆ Polypeptide_chain

typedef PolypeptideChain Polypeptide_chain

Reprenstation of a single polypeptidic chain within a protein representation.

Template Parameters
ParticleTraitsTraits class providing the particle type, see package ParticleTraits
MolecularCovalentStructureGraph representation of a covalent structure.
ConformationTypeRepresentation 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

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

typedef Polypeptide_chains_map::iterator Polypeptide_chains_iterator

Iterator over the map from chain identifiers to their representation.

◆ Polypeptide_chains_map

typedef std::unordered_map<char, Polypeptide_chain> Polypeptide_chains_map

Map from chain identifiers to their representation.

◆ Self

typedef T_Protein_representation<PolypeptideChain> Self

The class itself.

Constructor & Destructor Documentation

◆ T_Protein_representation()

Builds an empty protein.

Member Function Documentation

◆ chains_begin() [1/2]

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]

T_Protein_representation< PolypeptideChain >::Polypeptide_chains_const_iterator chains_begin
inline

Starts the container of chains (const)

Returns
Iterator at the start of the chain container.

◆ chains_end() [1/2]

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]

T_Protein_representation< PolypeptideChain >::Polypeptide_chains_const_iterator chains_end
inline

Ends the container of chains (const)

Returns
Iterator at the end of the chain container.

◆ create_chain()

void create_chain ( char  c,
Molecular_model &  model,
Molecular_covalent_structure &  structure,
const Conformation_type &  C 
)
inline

Create a polypeptide chain in this protein.

Parameters
cChain identifier
modelBiophysical model (ESBTL)
structureCovalent structure of this protein
CGeometric conformation of this protein

◆ get_chain() [1/2]

PolypeptideChain & get_chain ( char  c)
inline

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

Parameters
cChain identifier
Returns
Polypeptide chain

◆ get_chain() [2/2]

const PolypeptideChain & get_chain ( char  c) const
inline

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

Parameters
cChain identifier
Returns
Polypeptide chain (const)

◆ get_name() [1/2]

std::string & get_name ( void  )
inline

Return a reference to the name of this protein.

Returns
Reference to the name.

◆ get_name() [2/2]

const std::string & get_name ( void  ) const
inline

Return the name of this protein.

Returns
Name of this protein.

◆ get_number_of_bonds()

unsigned get_number_of_bonds
inline

Return the total number of bonds in the protein.

Returns
Total number of bonds in the protein.

◆ get_number_of_chains()

std::size_t get_number_of_chains
inline

Return the number of polypeptide chains.

Returns
Number of polypeptide chains

◆ get_number_of_embedded_bonds()

unsigned get_number_of_embedded_bonds
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()

unsigned get_number_of_embedded_particles
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()

unsigned get_number_of_particles
inline

Return the total number of particles in the protein.

Returns
Total number of particles in the protein.

◆ get_the_unique_chain() [1/2]

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]

const PolypeptideChain & get_the_unique_chain
inline

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

Returns
Polypeptide chain

◆ get_total_number_of_residues()

unsigned get_total_number_of_residues
inline

Return the total number of residues in the protein.

Returns
Total number of residues in the protein.

◆ is_fully_embedded()

bool is_fully_embedded
inline

Return true iff all the chains are fully embedded.

Returns
Return true iff all the chains are fully embedded

◆ statistics()

void statistics ( std::ostream &  out) const
inline

Return statistics on this protein.

Returns
Statistics on this protein.