Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType > Class Template Reference

Reprenstation of a single polypeptidic chain within a protein representation. More...

#include <Polypeptide_chain_representation.hpp>

Classes

class  Backbone_const_iterator
 Iterator through the atoms of the polypeptide chain backbone (const). More...
 
class  Backbone_iterator
 Iterator through the atoms of the polypeptide chain backbone. More...
 
class  Bond
 Representation of a bond between two atoms. More...
 
class  Bond_angle
 Representation of a valence angle between three atoms. More...
 
class  Bond_angle_const_iterator
 Iterator through all the valence angles in the polypeptide chain (const). More...
 
class  Bond_angle_iterator
 Iterator through all the valence angles in the polypeptide chain. More...
 
class  Bond_const_iterator
 Iterator through all the bonds in the polypeptide chain (const). More...
 
class  Bond_iterator
 Iterator through all the bonds in the polypeptide chain. More...
 
class  Dihedral_angle
 Representation of a proper dihedral angle between four atoms. More...
 
class  Dihedral_angle_const_iterator
 Iterator through all the proper dihedral angles in the polypeptide chain (const). More...
 
class  Dihedral_angle_iterator
 Iterator through all the proper dihedral angles in the polypeptide chain. More...
 
class  Incident_atoms_const_iterator
 Iterator through bonded atoms to an input atom (const). More...
 
class  Incident_atoms_iterator
 Iterator through bonded atoms to an input atom. More...
 
class  Is_Calpha
 
class  Is_Omega_angle
 
class  Is_Phi_angle
 
class  Is_Psi_angle
 
class  Residue_atoms_const_iterator
 Iterator through all the atoms of an input residue (const). More...
 
class  Residue_atoms_iterator
 Iterator through all the atoms of an input residue. More...
 

Public Types

typedef ParticleTraits Particle_traits
 Traits class defining types related to a particle, see ParticleTraits. More...
 
typedef MolecularCovalentStructure Molecular_covalent_structure
 Representation of the covalent structure of a molecular conformation. More...
 
typedef ConformationType Conformation_type
 Representation of a conformation, see package ConformationTraits. More...
 
typedef T_Polypeptide_chain_representation< Particle_traits, Molecular_covalent_structure, Conformation_typeSelf
 The class itself. More...
 
typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT FT
 Representation of the number type. More...
 
typedef ESBTL::CGAL::EPIC_kernel_with_atom::Point_3 Point_3
 Geometric representation of an atom, i.E a 3D point. More...
 
typedef Particle_traits::Particle_type Atom
 Biophysical representation of an atom. More...
 
typedef ParticleTraits::Molecular_system Molecular_system
 Biophysical representation of a protein, from ESBTL More...
 
typedef Molecular_system::Model Molecular_model
 Biophysical representation of a model of the protein, from ESBTL More...
 
typedef Molecular_system::Residue Residue
 Biophysical representation of a residue, from ESBTL More...
 
typedef Molecular_model::Residues_iterator Residues_iterator
 Iterator through all residues within the polypetide chain. More...
 
typedef Molecular_model::Residues_const_iterator Residues_const_iterator
 Iterator through all residues within the polypetide chain (const) More...
 
typedef Molecular_model::Chain::Atoms_iterator Atoms_iterator
 Iterator through all atoms within the polypeptide chain. More...
 
typedef Molecular_model::Chain::Atoms_const_iterator Atoms_const_iterator
 Iterator through all atoms within the polypeptide chain (const) More...
 
typedef boost::filter_iterator< Is_Calpha, Atoms_iteratorCalpha_iterator
 Iterator through all the c-alpha atoms within the polypeptide chain. More...
 
typedef boost::filter_iterator< Is_Calpha, Atoms_const_iteratorCalpha_const_iterator
 Iterator through all the c-alpha atoms within the polypeptide chain (const) More...
 
typedef boost::filter_iterator< Is_Phi_angle, Dihedral_angle_iteratorPhi_iterator
 Iterator through all the phi dihedral angles within the polypeptide chain. More...
 
typedef boost::filter_iterator< Is_Phi_angle, Dihedral_angle_const_iteratorPhi_const_iterator
 Iterator through all the phi dihedral angles within the polypeptide chain (const) More...
 
typedef boost::filter_iterator< Is_Psi_angle, Dihedral_angle_iteratorPsi_iterator
 Iterator through all the psi dihedral angles within the polypeptide chain. More...
 
typedef boost::filter_iterator< Is_Psi_angle, Dihedral_angle_const_iteratorPsi_const_iterator
 Iterator through all the psi dihedral angles within the polypeptide chain (const) More...
 
typedef boost::filter_iterator< Is_Omega_angle, Dihedral_angle_iteratorOmega_iterator
 Iterator through all the omega dihedral angles within the polypeptide chain. More...
 
typedef boost::filter_iterator< Is_Omega_angle, Dihedral_angle_const_iteratorOmega_const_iterator
 Iterator through all the omega dihedral angles within the polypeptide chain (const) More...
 

Constructors

 T_Polypeptide_chain_representation ()
 Builds an empty polypeptide chain. More...
 
 T_Polypeptide_chain_representation (Molecular_model &m, Molecular_covalent_structure &s, const Conformation_type &c)
 Builds a polypeptide chain based on the biophysical information from the input model, the topology from the input covalent structure, and the geometry from the input conformation. More...
 

Operators

T_Polypeptide_chain_representationoperator= (const T_Polypeptide_chain_representation &other)
 

Accessors

char get_chain_id () const
 
FT get_x (const Atom &a) const
 Operator for allowing access to the x coordinate of a particle in the current conformation. More...
 
FT get_y (const Atom &a) const
 Operator for allowing access to the y coordinate of a particle in the current conformation. More...
 
FT get_z (const Atom &a) const
 Operator for allowing access to the z coordinate of a particle in the current conformation. More...
 
FTget_x (const Atom &a)
 Operator for allowing access to the x coordinate of a particle in the current conformation. More...
 
FTget_y (const Atom &a)
 Operator for allowing access to the y coordinate of a particle in the current conformation. More...
 
FTget_z (const Atom &a)
 Operator for allowing access to the z coordinate of a particle in the current conformation. More...
 
Point_3 get_coordinates (const Atom &a) const
 Operator for allowing access to the coordinates of a particle in the current conformation. More...
 
unsigned get_number_of_residues () const
 Return the number of residues in the chain or in a component. More...
 
Point_3 compute_heavy_atoms_center_of_mass (int cc=-1) const
 Compute the center of mass of heavy atoms of the whole chain or of a connected component. More...
 
unsigned get_number_of_embedded_particles (int cc=-1) const
 Return the number of embedded particles in the chain or in one component. More...
 
bool is_fully_embedded (int cc=-1) const
 Return true iff all particles in the chain or in a component are embedded. More...
 
FT get_phi_angle (const Residue &res) const
 Return the phi angle associated to a residue. More...
 
FT get_psi_angle (const Residue &res) const
 Return the psi angle associated to a residue. More...
 
FT get_omega_angle (const Residue &res) const
 Return the omega angle associated to a residue. More...
 
FT get_phi_angle (unsigned resn) const
 Return the phi angle associated to a residue. More...
 
FT get_psi_angle (unsigned resn) const
 Return the psi angle associated to a residue. More...
 
FT get_omega_angle (unsigned resn) const
 Return the omega angle associated to a residue. More...
 
unsigned get_number_of_bonds (int cc=-1) const
 Return the number of bonds in the chain or in a component. More...
 
unsigned get_number_of_embedded_bonds (int cc=-1) const
 Return the number of embedded bonds in the chain or in a component. More...
 
unsigned get_number_of_particles (int cc=-1) const
 Return the total number of particles. More...
 
unsigned get_number_of_components () const
 Return the number of connected components. More...
 
const Residueget_first_residue (int cc=-1) const
 Return the first residue of the chain or of the component. More...
 
const Residueget_last_residue (int cc=-1) const
 Return the last residue of the chain or of the component. More...
 
Particle_rep get_particle_rep (const Atom &a) const
 (deprecated) Return the atom representation of the input within the covalent structure More...
 
const Molecular_covalent_structureget_covalent_structure () const
 Return the underlying covalent structure. More...
 
const Conformation_typeget_conformation () const
 Return the underlying geometrical conformation. More...
 

Modifiers

void set_conformation (Conformation_type &C)
 Modify the conformation. More...
 

Iterators

Incident_atoms_iterator incident_atoms_begin (const Atom &a)
 Function to initialize incident atoms iterator. More...
 
Incident_atoms_iterator incident_atoms_end (const Atom &a)
 Function to initialize incident atoms iterator. More...
 
Incident_atoms_const_iterator incident_atoms_begin (const Atom &a) const
 Function to initialize incident atoms iterator. More...
 
Incident_atoms_const_iterator incident_atoms_end (const Atom &a) const
 Function to initialize incident atoms iterator. More...
 
Residues_iterator residues_begin ()
 Function to initialize residues iterator. More...
 
Residues_iterator residues_end ()
 Function to initialize residues iterator. More...
 
Residues_const_iterator residues_begin () const
 Function to initialize residues iterator. More...
 
Residues_const_iterator residues_end () const
 Function to initialize residues iterator. More...
 
Atoms_iterator atoms_begin ()
 For iterating on atoms. More...
 
Atoms_iterator atoms_end ()
 For iterating on atoms. More...
 
Atoms_const_iterator atoms_begin () const
 For iterating on atoms. More...
 
Atoms_const_iterator atoms_end () const
 For iterating on atoms. More...
 
Residue_atoms_iterator atoms_begin (Residue &res)
 For iterating on atoms of a residue. More...
 
Residue_atoms_iterator atoms_end (Residue &res)
 For iterating on atoms of a residue. More...
 
Residue_atoms_const_iterator atoms_begin (const Residue &res) const
 For iterating on atoms of a residue. More...
 
Residue_atoms_const_iterator atoms_end (const Residue &res) const
 For iterating on atoms of a residue. More...
 
Backbone_iterator backbone_begin (int cc=-1)
 For iterating on the back bone of the chain or its component. More...
 
Backbone_iterator backbone_end (int cc=-1)
 For iterating on the back bonee of the chain or its component. More...
 
Backbone_const_iterator backbone_begin (int cc=-1) const
 For iterating on the back bonee of the chain or its component. More...
 
Backbone_const_iterator backbone_end (int cc=-1) const
 For iterating on the back bonee of the chain or its component. More...
 
Calpha_iterator calphas_begin ()
 For iterating on the calphas of the protein. More...
 
Calpha_iterator calphas_end ()
 For iterating on the calphas of the protein. More...
 
Calpha_const_iterator calphas_begin () const
 For iterating on the calphas of the protein. More...
 
Calpha_const_iterator calphas_end () const
 For iterating on the calphas of the protein. More...
 
Bond_iterator bonds_begin ()
 For iterating on the bonds of the protein. More...
 
Bond_iterator bonds_end ()
 For iterating on the bonds of the protein. More...
 
Bond_const_iterator bonds_begin () const
 For iterating on the bonds of the protein. More...
 
Bond_const_iterator bonds_end () const
 For iterating on the bonds of the protein. More...
 
Bond_angle_iterator bond_angles_begin ()
 For iterating on the bond angles of the protein. More...
 
Bond_angle_iterator bond_angles_end ()
 For iterating on the bond angles of the protein. More...
 
Bond_angle_const_iterator bond_angles_begin () const
 For iterating on the bond angles of the protein. More...
 
Bond_angle_const_iterator bond_angles_end () const
 For iterating on the bond angles of the protein. More...
 
Dihedral_angle_iterator dihedral_angles_begin ()
 For iterating on the dihedral angles of the protein. More...
 
Dihedral_angle_iterator dihedral_angles_end ()
 For iterating on the dihedral angles of the protein. More...
 
Dihedral_angle_const_iterator dihedral_angles_begin () const
 For iterating on the dihedral angles of the protein. More...
 
Dihedral_angle_const_iterator dihedral_angles_end () const
 For iterating on the dihedral angles of the protein. More...
 
Phi_iterator phi_angles_begin ()
 For iterating on the phi angles of the protein. More...
 
Phi_iterator phi_angles_end ()
 For iterating on the phi angles of the protein. More...
 
Phi_const_iterator phi_angles_begin () const
 For iterating on the phi angles of the protein. More...
 
Phi_const_iterator phi_angles_end () const
 For iterating on the phi angles of the protein. More...
 
Psi_iterator psi_angles_begin ()
 For iterating on the psi angles of the protein. More...
 
Psi_iterator psi_angles_end ()
 For iterating on the psi angles of the protein. More...
 
Psi_const_iterator psi_angles_begin () const
 For iterating on the psi angles of the protein. More...
 
Psi_const_iterator psi_angles_end () const
 For iterating on the psi angles of the protein. More...
 
Omega_iterator omega_angles_begin ()
 For iterating on the omega angles of the protein. More...
 
Omega_iterator omega_angles_end ()
 For iterating on the omega angles of the protein. More...
 
Omega_const_iterator omega_angles_begin () const
 For iterating on the omega angles of the protein. More...
 
Omega_const_iterator omega_angles_end () const
 For iterating on the omega angles of the protein. More...
 

Detailed Description

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_for_proteins<ParticleTraits> >, class ConformationType = std::vector<ESBTL::CGAL::EPIC_kernel_with_atom::FT>>
class SBL::CSB::T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >

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.

Member Typedef Documentation

◆ Atom

Biophysical representation of an atom.

◆ Atoms_const_iterator

typedef Molecular_model::Chain::Atoms_const_iterator Atoms_const_iterator

Iterator through all atoms within the polypeptide chain (const)

◆ Atoms_iterator

typedef Molecular_model::Chain::Atoms_iterator Atoms_iterator

Iterator through all atoms within the polypeptide chain.

◆ Calpha_const_iterator

typedef boost::filter_iterator<Is_Calpha, Atoms_const_iterator> Calpha_const_iterator

Iterator through all the c-alpha atoms within the polypeptide chain (const)

◆ Calpha_iterator

typedef boost::filter_iterator<Is_Calpha, Atoms_iterator> Calpha_iterator

Iterator through all the c-alpha atoms within the polypeptide chain.

◆ Conformation_type

typedef ConformationType Conformation_type

Representation of a conformation, see package ConformationTraits.

◆ FT

typedef ESBTL::CGAL::EPIC_kernel_with_atom::FT FT

Representation of the number type.

◆ Molecular_covalent_structure

typedef MolecularCovalentStructure Molecular_covalent_structure

Representation of the covalent structure of a molecular conformation.

It uses a boost graph for encoding that covalent structure and offers the possibility to access internal and cartesian coordinates of the structure.

Template Parameters
ParticleInfoInformation to attached to the particle (default is a simple string). It should be comparable (less operator) and streamable.

◆ Molecular_model

typedef Molecular_system::Model Molecular_model

Biophysical representation of a model of the protein, from ESBTL

◆ Molecular_system

typedef ParticleTraits::Molecular_system Molecular_system

Biophysical representation of a protein, from ESBTL

◆ Omega_const_iterator

Iterator through all the omega dihedral angles within the polypeptide chain (const)

◆ Omega_iterator

typedef boost::filter_iterator<Is_Omega_angle, Dihedral_angle_iterator> Omega_iterator

Iterator through all the omega dihedral angles within the polypeptide chain.

◆ Particle_traits

typedef ParticleTraits Particle_traits

Traits class defining types related to a particle, see ParticleTraits.

◆ Phi_const_iterator

Iterator through all the phi dihedral angles within the polypeptide chain (const)

◆ Phi_iterator

typedef boost::filter_iterator<Is_Phi_angle, Dihedral_angle_iterator> Phi_iterator

Iterator through all the phi dihedral angles within the polypeptide chain.

◆ Point_3

typedef ESBTL::CGAL::EPIC_kernel_with_atom::Point_3 Point_3

Geometric representation of an atom, i.E a 3D point.

◆ Psi_const_iterator

Iterator through all the psi dihedral angles within the polypeptide chain (const)

◆ Psi_iterator

typedef boost::filter_iterator<Is_Psi_angle, Dihedral_angle_iterator> Psi_iterator

Iterator through all the psi dihedral angles within the polypeptide chain.

◆ Residue

typedef Molecular_system::Residue Residue

Biophysical representation of a residue, from ESBTL

◆ Residues_const_iterator

typedef Molecular_model::Residues_const_iterator Residues_const_iterator

Iterator through all residues within the polypetide chain (const)

◆ Residues_iterator

typedef Molecular_model::Residues_iterator Residues_iterator

Iterator through all residues within the polypetide chain.

◆ Self

Constructor & Destructor Documentation

◆ T_Polypeptide_chain_representation() [1/2]

Builds an empty polypeptide chain.

◆ T_Polypeptide_chain_representation() [2/2]

Builds a polypeptide chain based on the biophysical information from the input model, the topology from the input covalent structure, and the geometry from the input conformation.

Parameters
minput biophysical model from the ESBTL
sinput covalent structure
cinput geometrical conformation

Member Function Documentation

◆ atoms_begin() [1/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Atoms_iterator atoms_begin
inline

For iterating on atoms.

Returns
Return the begin iterator for atoms.

◆ atoms_begin() [2/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Atoms_const_iterator atoms_begin
inline

For iterating on atoms.

Returns
Return the begin iterator for atoms.

◆ atoms_begin() [3/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residue_atoms_const_iterator atoms_begin ( const Residue res) const
inline

For iterating on atoms of a residue.

Returns
Return the begin iterator for atoms.

◆ atoms_begin() [4/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residue_atoms_iterator atoms_begin ( Residue res)
inline

For iterating on atoms of a residue.

Returns
Return the begin iterator for atoms.

◆ atoms_end() [1/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Atoms_iterator atoms_end
inline

For iterating on atoms.

Returns
Return the end iterator for atoms.

◆ atoms_end() [2/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Atoms_const_iterator atoms_end
inline

For iterating on atoms.

Returns
Return the end iterator for atoms.

◆ atoms_end() [3/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residue_atoms_const_iterator atoms_end ( const Residue res) const
inline

For iterating on atoms of a residue.

Returns
Return the end iterator for atoms.

◆ atoms_end() [4/4]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residue_atoms_iterator atoms_end ( Residue res)
inline

For iterating on atoms of a residue.

Returns
Return the end iterator for atoms.

◆ backbone_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Backbone_iterator backbone_begin ( int  cc = -1)
inline

For iterating on the back bone of the chain or its component.

Returns
Return the begin iterator for the back bone.

◆ backbone_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Backbone_const_iterator backbone_begin ( int  cc = -1) const
inline

For iterating on the back bonee of the chain or its component.

Returns
Return the begin iterator for the back bone.

◆ backbone_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Backbone_iterator backbone_end ( int  cc = -1)
inline

For iterating on the back bonee of the chain or its component.

Returns
Return the end iterator for the back bone.

◆ backbone_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Backbone_const_iterator backbone_end ( int  cc = -1) const
inline

For iterating on the back bonee of the chain or its component.

Returns
Return the end iterator for the back bone.

◆ bond_angles_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_angle_iterator bond_angles_begin
inline

For iterating on the bond angles of the protein.

Returns
Return the begin iterator for the bond angles.

◆ bond_angles_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_angle_const_iterator bond_angles_begin
inline

For iterating on the bond angles of the protein.

Returns
Return the begin iterator for the bond angles.

◆ bond_angles_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_angle_iterator bond_angles_end
inline

For iterating on the bond angles of the protein.

Returns
Return the end iterator for the bond angles.

◆ bond_angles_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_angle_const_iterator bond_angles_end
inline

For iterating on the bond angles of the protein.

Returns
Return the end iterator for the bond angles.

◆ bonds_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_iterator bonds_begin
inline

For iterating on the bonds of the protein.

Returns
Return the begin iterator for the bonds.

◆ bonds_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_const_iterator bonds_begin
inline

For iterating on the bonds of the protein.

Returns
Return the begin iterator for the bonds.

◆ bonds_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_iterator bonds_end
inline

For iterating on the bonds of the protein.

Returns
Return the end iterator for the bonds.

◆ bonds_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Bond_const_iterator bonds_end
inline

For iterating on the bonds of the protein.

Returns
Return the end iterator for the bonds.

◆ calphas_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Calpha_iterator calphas_begin
inline

For iterating on the calphas of the protein.

Returns
Return the begin iterator for the calphas.

◆ calphas_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Calpha_const_iterator calphas_begin
inline

For iterating on the calphas of the protein.

Returns
Return the begin iterator for the calphas.

◆ calphas_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Calpha_iterator calphas_end
inline

For iterating on the calphas of the protein.

Returns
Return the end iterator for the calphas.

◆ calphas_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Calpha_const_iterator calphas_end
inline

For iterating on the calphas of the protein.

Returns
Return the end iterator for the calphas.

◆ compute_heavy_atoms_center_of_mass()

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Point_3 compute_heavy_atoms_center_of_mass ( int  cc = -1) const
inline

Compute the center of mass of heavy atoms of the whole chain or of a connected component.

Returns
Return the COM as a CGAL::Point_3

◆ dihedral_angles_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Dihedral_angle_iterator dihedral_angles_begin
inline

For iterating on the dihedral angles of the protein.

Returns
Return the begin iterator for the dihedral angles.

◆ dihedral_angles_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Dihedral_angle_const_iterator dihedral_angles_begin
inline

For iterating on the dihedral angles of the protein.

Returns
Return the begin iterator for the dihedral angles.

◆ dihedral_angles_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Dihedral_angle_iterator dihedral_angles_end
inline

For iterating on the dihedral angles of the protein.

Returns
Return the end iterator for the dihedral angles.

◆ dihedral_angles_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Dihedral_angle_const_iterator dihedral_angles_end
inline

For iterating on the dihedral angles of the protein.

Returns
Return the end iterator for the dihedral angles.

◆ get_chain_id()

char get_chain_id
Returns
Return the polypeptide chain ID

◆ get_conformation()

const T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Conformation_type & get_conformation
inline

Return the underlying geometrical conformation.

Returns
Underlying conformation

◆ get_coordinates()

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Point_3 get_coordinates ( const Atom a) const
inline

Operator for allowing access to the coordinates of a particle in the current conformation.

Parameters
aReference to the particle in question
Returns
Return it's coordinates as a CGAL::Point_3

◆ get_covalent_structure()

const T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Molecular_covalent_structure & get_covalent_structure
inline

Return the underlying covalent structure.

Returns
Underlying covalent structure

◆ get_first_residue()

const T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residue & get_first_residue ( int  cc = -1) const
inline

Return the first residue of the chain or of the component.

Returns
Return the first residue

◆ get_last_residue()

const T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residue & get_last_residue ( int  cc = -1) const
inline

Return the last residue of the chain or of the component.

Returns
Return the last residue

◆ get_number_of_bonds()

unsigned get_number_of_bonds ( int  cc = -1) const
inline

Return the number of bonds in the chain or in a component.

Returns
Return the bond count as an unsigned

◆ get_number_of_components()

unsigned get_number_of_components
inline

Return the number of connected components.

Returns
Return the number of connected components

◆ get_number_of_embedded_bonds()

unsigned get_number_of_embedded_bonds ( int  cc = -1) const
inline

Return the number of embedded bonds in the chain or in a component.

Returns
Return the bond count as an unsigned

◆ get_number_of_embedded_particles()

unsigned get_number_of_embedded_particles ( int  cc = -1) const
inline

Return the number of embedded particles in the chain or in one component.

Returns
Return the particle count as an unsigned

◆ get_number_of_particles()

unsigned get_number_of_particles ( int  cc = -1) const
inline

Return the total number of particles.

Returns
Return the particle count as an unsigned

◆ get_number_of_residues()

unsigned get_number_of_residues ( ) const
inline

Return the number of residues in the chain or in a component.

Returns
Return the residue count as an unsigned

◆ get_omega_angle() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_omega_angle ( const Residue res) const
inline

Return the omega angle associated to a residue.

Parameters
resA const ref to the residue in question.
Returns
Return omega value as float type

◆ get_omega_angle() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_omega_angle ( unsigned  resn) const
inline

Return the omega angle associated to a residue.

Parameters
resnThe residue sequence number of the residue in question
Returns
Return omega value as float type

◆ get_particle_rep()

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Particle_rep get_particle_rep ( const Atom a) const
inline

(deprecated) Return the atom representation of the input within the covalent structure

Parameters
aInput atom
Returns
Atom representation within the covalent structure

◆ get_phi_angle() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_phi_angle ( const Residue res) const
inline

Return the phi angle associated to a residue.

Parameters
resA const ref to the residue in question.
Returns
Return phi value as float type

◆ get_phi_angle() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_phi_angle ( unsigned  resn) const
inline

Return the phi angle associated to a residue.

Parameters
resnThe residue sequence number of the residue in question
Returns
Return phi value as float type

◆ get_psi_angle() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_psi_angle ( const Residue res) const
inline

Return the psi angle associated to a residue.

Parameters
resA const ref to the residue in question.
Returns
Return psi value as float type

◆ get_psi_angle() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_psi_angle ( unsigned  resn) const
inline

Return the psi angle associated to a residue.

Parameters
resnThe residue sequence number of the residue in question
Returns
Return psi value as float type

◆ get_x() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT & get_x ( const Atom a)
inline

Operator for allowing access to the x coordinate of a particle in the current conformation.

Parameters
aReference to the particle in question
Returns
Return it's x coordinate as float type

◆ get_x() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_x ( const Atom a) const
inline

Operator for allowing access to the x coordinate of a particle in the current conformation.

Parameters
aReference to the particle in question
Returns
Return it's x coordinate as float type

◆ get_y() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT & get_y ( const Atom a)
inline

Operator for allowing access to the y coordinate of a particle in the current conformation.

Parameters
aReference to the particle in question
Returns
Return it's y coordinate as float type

◆ get_y() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_y ( const Atom a) const
inline

Operator for allowing access to the y coordinate of a particle in the current conformation.

Parameters
aReference to the particle in question
Returns
Return it's y coordinate as float type

◆ get_z() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT & get_z ( const Atom a)
inline

Operator for allowing access to the z coordinate of a particle in the current conformation.

Parameters
aReference to the particle in question
Returns
Return it's z coordinate as float type

◆ get_z() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT get_z ( const Atom a) const
inline

Operator for allowing access to the z coordinate of a particle in the current conformation.

Parameters
aReference to the particle in question
Returns
Return it's z coordinate as float type

◆ incident_atoms_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Incident_atoms_iterator incident_atoms_begin ( const Atom a)
inline

Function to initialize incident atoms iterator.

Parameters
aReference to the atom in question.
Returns
Return the begin iterator for the incident atoms of a

◆ incident_atoms_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Incident_atoms_const_iterator incident_atoms_begin ( const Atom a) const
inline

Function to initialize incident atoms iterator.

Parameters
aReference to the atom in question.
Returns
Return the begin iterator for the incident atoms of a

◆ incident_atoms_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Incident_atoms_iterator incident_atoms_end ( const Atom a)
inline

Function to initialize incident atoms iterator.

Parameters
aReference to the atom in question.
Returns
Return the end iterator for the incident atoms of a

◆ incident_atoms_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Incident_atoms_const_iterator incident_atoms_end ( const Atom a) const
inline

Function to initialize incident atoms iterator.

Parameters
aReference to the atom in question.
Returns
Return the end iterator for the incident atoms of a

◆ is_fully_embedded()

bool is_fully_embedded ( int  cc = -1) const
inline

Return true iff all particles in the chain or in a component are embedded.

Returns
Return true iff all particles are embedded

◆ omega_angles_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Omega_iterator omega_angles_begin
inline

For iterating on the omega angles of the protein.

Returns
Return the begin iterator for the omega angles.

◆ omega_angles_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Omega_const_iterator omega_angles_begin
inline

For iterating on the omega angles of the protein.

Returns
Return the begin iterator for the omega angles.

◆ omega_angles_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Omega_iterator omega_angles_end
inline

For iterating on the omega angles of the protein.

Returns
Return the end iterator for the omega angles.

◆ omega_angles_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Omega_const_iterator omega_angles_end
inline

For iterating on the omega angles of the protein.

Returns
Return the end iterator for the omega angles.

◆ operator=()

T_Polypeptide_chain_representation& operator= ( const T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType > &  other)
inline

◆ phi_angles_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Phi_iterator phi_angles_begin
inline

For iterating on the phi angles of the protein.

Returns
Return the begin iterator for the phi angles.

◆ phi_angles_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Phi_const_iterator phi_angles_begin
inline

For iterating on the phi angles of the protein.

Returns
Return the begin iterator for the phi angles.

◆ phi_angles_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Phi_iterator phi_angles_end
inline

For iterating on the phi angles of the protein.

Returns
Return the end iterator for the phi angles.

◆ phi_angles_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Phi_const_iterator phi_angles_end
inline

For iterating on the phi angles of the protein.

Returns
Return the end iterator for the phi angles.

◆ psi_angles_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Psi_iterator psi_angles_begin
inline

For iterating on the psi angles of the protein.

Returns
Return the begin iterator for the psi angles.

◆ psi_angles_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Psi_const_iterator psi_angles_begin
inline

For iterating on the psi angles of the protein.

Returns
Return the begin iterator for the psi angles.

◆ psi_angles_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Psi_iterator psi_angles_end
inline

For iterating on the psi angles of the protein.

Returns
Return the end iterator for the phi angles.

◆ psi_angles_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Psi_const_iterator psi_angles_end
inline

For iterating on the psi angles of the protein.

Returns
Return the end iterator for the phi angles.

◆ residues_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residues_iterator residues_begin
inline

Function to initialize residues iterator.

Returns
Return the begin iterator for the residues from the molecular chain.

◆ residues_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residues_const_iterator residues_begin
inline

Function to initialize residues iterator.

Returns
Return the begin iterator for the residues from the molecular chain.

◆ residues_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residues_iterator residues_end
inline

Function to initialize residues iterator.

Returns
Return the end iterator for the residues from the molecular chain.

◆ residues_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Residues_const_iterator residues_end
inline

Function to initialize residues iterator.

Returns
Return the end iterator for the residues from the molecular chain.

◆ set_conformation()

void set_conformation ( Conformation_type C)
inline

Modify the conformation.

Parameters
CReference to the new conformation