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  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 Molecular_conformation. More...
 
typedef T_Polypeptide_chain_representation< Particle_traits, Molecular_covalent_structure, Conformation_typeSelf
 The class itself. More...
 
typedef SBL::CSB::EPIC_kernel_with_atom::FT FT
 Representation of the number type. More...
 
typedef SBL::CSB::EPIC_kernel_with_atom::Point_3 Point_3
 Geometric representation of an atom, i.E a 3D point. More...
 
typedef ParticleTraits::Molecular_system Molecular_system
 Biophysical representation of a protein. More...
 
typedef Molecular_system::Model Molecular_model
 Biophysical representation of a model of the protein. More...
 
typedef Molecular_system::Chain Chain
 Biophysical representation of chain of a model of the protein. More...
 
typedef Molecular_system::Residue Residue
 Biophysical representation of a residue. More...
 
typedef Residue::Atom Atom
 Biophysical representation of an atom. More...
 
typedef Chain::Residues_iterator Residues_iterator
 Iterator through all residues within the polypetide chain. More...
 
typedef Chain::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_Heavy, Atoms_iteratorHeavy_iterator
 Iterator through all the c-alpha atoms within the polypeptide chain. More...
 
typedef boost::filter_iterator< Is_Heavy, Atoms_const_iteratorHeavy_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 (Chain &c, Molecular_covalent_structure &s, const Conformation_type &mc)
 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...
 
Heavy_iterator heavy_begin ()
 For iterating on the calphas of the protein. More...
 
Heavy_iterator heavy_end ()
 For iterating on the calphas of the protein. More...
 
Heavy_const_iterator heavy_begin () const
 For iterating on the calphas of the protein. More...
 
Heavy_const_iterator heavy_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<SBL::CSB::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

typedef Residue::Atom 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.

◆ Chain

typedef Molecular_system::Chain Chain

Biophysical representation of chain of a model of the protein.

◆ Conformation_type

typedef ConformationType Conformation_type

Representation of a conformation, see package Molecular_conformation.

◆ FT

typedef SBL::CSB::EPIC_kernel_with_atom::FT FT

Representation of the number type.

◆ Heavy_const_iterator

typedef boost::filter_iterator<Is_Heavy, Atoms_const_iterator> Heavy_const_iterator

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

◆ Heavy_iterator

typedef boost::filter_iterator<Is_Heavy, Atoms_iterator> Heavy_iterator

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

◆ 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.

◆ Molecular_system

typedef ParticleTraits::Molecular_system Molecular_system

Biophysical representation of a protein.

◆ Omega_const_iterator

typedef boost::filter_iterator<Is_Omega_angle, Dihedral_angle_const_iterator> 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

typedef boost::filter_iterator<Is_Phi_angle, Dihedral_angle_const_iterator> 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 SBL::CSB::EPIC_kernel_with_atom::Point_3 Point_3

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

◆ Psi_const_iterator

typedef boost::filter_iterator<Is_Psi_angle, Dihedral_angle_const_iterator> 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.

◆ Residues_const_iterator

typedef Chain::Residues_const_iterator Residues_const_iterator

Iterator through all residues within the polypetide chain (const)

◆ Residues_iterator

typedef Chain::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 chain from a biophysical model
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

◆ heavy_begin() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Heavy_iterator heavy_begin
inline

For iterating on the calphas of the protein.

Returns
Return the begin iterator for the calphas.

◆ heavy_begin() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Heavy_const_iterator heavy_begin
inline

For iterating on the calphas of the protein.

Returns
Return the begin iterator for the calphas.

◆ heavy_end() [1/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Heavy_iterator heavy_end
inline

For iterating on the calphas of the protein.

Returns
Return the end iterator for the calphas.

◆ heavy_end() [2/2]

T_Polypeptide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Heavy_const_iterator heavy_end
inline

For iterating on the calphas of the protein.

Returns
Return the end iterator for the calphas.

◆ 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.

◆ 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