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_type >	Self
	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_iterator >	Calpha_iterator
	Iterator through all the c-alpha atoms within the polypeptide chain. More...

typedef boost::filter_iterator< Is_Calpha, Atoms_const_iterator >	Calpha_const_iterator
	Iterator through all the c-alpha atoms within the polypeptide chain (const) More...

typedef boost::filter_iterator< Is_Heavy, Atoms_iterator >	Heavy_iterator
	Iterator through all the c-alpha atoms within the polypeptide chain. More...

typedef boost::filter_iterator< Is_Heavy, Atoms_const_iterator >	Heavy_const_iterator
	Iterator through all the c-alpha atoms within the polypeptide chain (const) More...

typedef boost::filter_iterator< Is_Phi_angle, Dihedral_angle_iterator >	Phi_iterator
	Iterator through all the phi dihedral angles within the polypeptide chain. More...

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) More...

typedef boost::filter_iterator< Is_Psi_angle, Dihedral_angle_iterator >	Psi_iterator
	Iterator through all the psi dihedral angles within the polypeptide chain. More...

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) More...

typedef boost::filter_iterator< Is_Omega_angle, Dihedral_angle_iterator >	Omega_iterator
	Iterator through all the omega dihedral angles within the polypeptide chain. More...

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) 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_representation &	operator= (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...

FT &	get_x (const Atom &a)
	Operator for allowing access to the x coordinate of a particle in the current conformation. More...

FT &	get_y (const Atom &a)
	Operator for allowing access to the y coordinate of a particle in the current conformation. More...

FT &	get_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 Residue &	get_first_residue (int cc=-1) const
	Return the first residue of the chain or of the component. More...

const Residue &	get_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_structure &	get_covalent_structure () const
	Return the underlying covalent structure. More...

const Conformation_type &	get_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

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.

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

ParticleInfo Information 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

typedef T_Polypeptide_chain_representation<Particle_traits, Molecular_covalent_structure, Conformation_type> Self

The class itself.

Constructor & Destructor Documentation

◆ T_Polypeptide_chain_representation() [1/2]

T_Polypeptide_chain_representation

Builds an empty polypeptide chain.

◆ T_Polypeptide_chain_representation() [2/2]

T_Polypeptide_chain_representation	(	Chain &	c,
		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.

Parameters

m	input chain from a biophysical model
s	input covalent structure
c	input 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

a	Reference 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

res	A 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

resn	The 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

a	Input 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

res	A 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

resn	The 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

res	A 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

resn	The 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

a	Reference 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

a	Reference 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

a	Reference 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

a	Reference 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

a	Reference 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

a	Reference 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

a	Reference 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

a	Reference 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

a	Reference 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

a	Reference 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

C	Reference to the new conformation

Classes

Public Types

Constructors

Operators

Accessors

Modifiers

Iterators

Detailed Description

Member Typedef Documentation

◆ Atom

◆ Atoms_const_iterator

◆ Atoms_iterator

◆ Calpha_const_iterator

◆ Calpha_iterator

◆ Chain

◆ Conformation_type

◆ FT

◆ Heavy_const_iterator

◆ Heavy_iterator

◆ Molecular_covalent_structure

◆ Molecular_model

◆ Molecular_system

◆ Omega_const_iterator

◆ Omega_iterator

◆ Particle_traits

◆ Phi_const_iterator

◆ Phi_iterator

◆ Point_3

◆ Psi_const_iterator

◆ Psi_iterator

◆ Residue

◆ Residues_const_iterator

◆ Residues_iterator

◆ Self

Constructor & Destructor Documentation

◆ T_Polypeptide_chain_representation() [1/2]

◆ T_Polypeptide_chain_representation() [2/2]

Member Function Documentation

◆ atoms_begin() [1/4]

◆ atoms_begin() [2/4]

◆ atoms_begin() [3/4]

◆ atoms_begin() [4/4]

◆ atoms_end() [1/4]

◆ atoms_end() [2/4]

◆ atoms_end() [3/4]

◆ atoms_end() [4/4]

◆ backbone_begin() [1/2]

◆ backbone_begin() [2/2]

◆ backbone_end() [1/2]

◆ backbone_end() [2/2]

◆ bond_angles_begin() [1/2]

◆ bond_angles_begin() [2/2]

◆ bond_angles_end() [1/2]

◆ bond_angles_end() [2/2]

◆ bonds_begin() [1/2]

◆ bonds_begin() [2/2]

◆ bonds_end() [1/2]

◆ bonds_end() [2/2]

◆ calphas_begin() [1/2]

◆ calphas_begin() [2/2]

◆ calphas_end() [1/2]

◆ calphas_end() [2/2]

◆ compute_heavy_atoms_center_of_mass()

◆ dihedral_angles_begin() [1/2]

◆ dihedral_angles_begin() [2/2]

◆ dihedral_angles_end() [1/2]

◆ dihedral_angles_end() [2/2]

◆ get_chain_id()

◆ get_conformation()

◆ get_coordinates()

◆ get_covalent_structure()

◆ get_first_residue()

◆ get_last_residue()

◆ get_number_of_bonds()

◆ get_number_of_components()

◆ get_number_of_embedded_bonds()

◆ get_number_of_embedded_particles()

◆ get_number_of_particles()

◆ get_number_of_residues()

◆ get_omega_angle() [1/2]