Representation of a single polynucleotide chain within a Nucleic Acid representation. More...

#include <Polynucleotide_chain_representation.hpp>

Public Types
typedef ParticleTraits	Particle_traits
	Traits class defining types related to a particle, see ParticleTraits.
typedef MolecularCovalentStructure	Molecular_covalent_structure
	Representation of the covalent structure of a molecular conformation.
typedef ConformationType	Conformation_type
	Representation of a conformation, see package Molecular_conformation.
typedef T_Polynucleotide_chain_representation< Particle_traits, Molecular_covalent_structure, Conformation_type >	Self
	The class itself.
typedef Base::FT	FT
	Representation of the number type.
typedef Base::Chain	Chain
	Biophysical representation of chain of a model of the nucleic acid.
typedef Base::Residue	Residue
	Biophysical representation of a residue.
typedef Base::Atom	Atom
	Biophysical representation of an atom.
typedef Base::Residues_iterator	Residues_iterator
	Iterator through all residues within the polynucleotide chain.
typedef Base::Residues_const_iterator	Residues_const_iterator
	Iterator through all residues within the polynucleotide chain (const)
typedef Base::Atoms_iterator	Atoms_iterator
	Iterator through all atoms within the chain.
typedef Base::Atoms_const_iterator	Atoms_const_iterator
	Iterator through all atoms within the chain (const)
typedef Base::Residue_atoms_iterator	Residue_atoms_iterator
	Iterator through all atoms within a residue.
typedef Base::Residue_atoms_const_iterator	Residue_atoms_const_iterator
	Iterator through all atoms within a residue (const)
typedef Base::Is_Heavy	Is_Heavy
	Checks whether an atom is a heavy atom.
typedef boost::filter_iterator< Is_P, Atoms_iterator >	P_iterator
	Iterators through selected atoms within the polynucleotide chain (5' ==> 3')
typedef Base::Dihedral_angle	Dihedral_angle
	Dihedral angle.
typedef Base::Dihedral_angle_iterator	Dihedral_angle_iterator
	Iterator through all atoms within the chain (const)
typedef Base::Dihedral_angle_const_iterator	Dihedral_angle_const_iterator
	Iterator through all atoms within the chain (const)
typedef Base::Chosen_angle_iterator	Chosen_angle_iterator
	To iterate on dihedral angles of a certain type.
typedef Base::Chosen_angle_const_iterator	Chosen_angle_const_iterator
	To iterate on dihedral angles of a certain type (const)
typedef boost::filter_iterator< Is_Alpha_angle, Dihedral_angle_iterator >	Alpha_iterator
	Iterator(s) through named backbone dihedral angles within the polypeptide chain (here alpha)
typedef boost::filter_iterator< Is_Alpha_angle, Dihedral_angle_const_iterator >	Alpha_const_iterator
	Iterator(s) through named backbone dihedral angles within the polypeptide chain (here alpha) (const)
typedef SBL::CSB::EPIC_kernel_with_atom::Point_3	Point_3
	Geometric representation of an atom, i.E a 3D point.
typedef ParticleTraits::Molecular_system	Molecular_system
	Biophysical representation of a linear polymer.
typedef Molecular_system::Model	Molecular_model
	Biophysical representation of a model of the linear polymer.
typedef boost::filter_iterator< Is_Heavy, Atoms_iterator >	Heavy_iterator
	Iterator through all the c-alpha atoms within the chain.
typedef boost::filter_iterator< Is_Heavy, Atoms_const_iterator >	Heavy_const_iterator
	Iterator through all the c-alpha atoms within the chain (const)

Constructors
	T_Polynucleotide_chain_representation ()
	Builds an empty chain.
	T_Polynucleotide_chain_representation (Chain &c, Molecular_covalent_structure &s, const Conformation_type &mc)
	Builds a chain based on the biophysical information from the input model, the topology from the input covalent structure, and the geometry from the input conformation.

Operators
std::pair< bool, FT >	get_alpha_angle (const Residue &res) const
	Return the alpha angle associated to a residue.
std::pair< bool, FT >	get_alpha_angle (unsigned resn) const
	Return the alpha angle associated to a residue.
std::pair< bool, FT >	get_beta_angle (const Residue &res) const
	Return the beta angle associated to a residue.
std::pair< bool, FT >	get_beta_angle (unsigned resn) const
	Return the beta angle associated to a residue.
bool	is_residue_heavy_atoms_embedded (const Residue &res) const
	Returns whether a residue's heavy atoms are all embedded.

Iterators
C4p_iterator	c4ps_begin ()
	For iterating on the c4ps of the NA chain.
C4p_iterator	c4ps_end ()
	For iterating on the c4ps of the NA chain.
C4p_const_iterator	c4ps_begin () const
	For iterating on the c4ps of the NA chain.
C4p_const_iterator	c4ps_end () const
	For iterating on the c4ps of the NA chain.
Alpha_iterator	alpha_angles_begin ()
	For iterating on the alpha angles of the NA chain.
Alpha_iterator	alpha_angles_end ()
	For iterating on the alpha angles of the NA chain.
Alpha_const_iterator	alpha_angles_begin () const
	For iterating on the alpha angles of the NA chain.
Alpha_const_iterator	alpha_angles_end () const
	For iterating on the alpha angles of the NA chain.

Operators
const Atom *	operator[] (const Particle_rep &p) const
	Operator for allowing access to a particle given it's index in the covalent structure.
Bond_pair	get_particles (const Bond_rep &b) const
	Function to get the particle representations from a bond.
std::pair< bool, const Atom * >	get_atom (const std::string &atom_name, const Residue &res) const
	Function to get the specified atom from the specified residue.
std::pair< bool, FT >	get_backbone_torsion_angle (int offset_starting_atom, const Residue &res) const
	Function to get the backbone torsion angle specificied with an offset from a residue.

Accessors
char	get_chain_id () const
std::string	get_chain_type ()
	Set the linear chain type specifier m_chain_type.
int	get_res_backbone_size () const
FT	get_x (const Atom &a) const
	Operator for allowing access to the x coordinate of a particle in the current conformation.
FT &	get_x (const Atom &a)
	Operator for allowing access to the x coordinate of a particle in the current conformation.
FT	get_y (const Atom &a) const
	Operator for allowing access to the y coordinate of a particle in the current conformation.
FT &	get_y (const Atom &a)
	Operator for allowing access to the y coordinate of a particle in the current conformation.
FT	get_z (const Atom &a) const
	Operator for allowing access to the z coordinate of a particle in the current conformation.
FT &	get_z (const Atom &a)
	Operator for allowing access to the z coordinate of a particle in the current conformation.
Point_3	get_coordinates (const Atom &a) const
	Operator for allowing access to the coordinates of a particle in the current conformation.
unsigned	get_number_of_residues () const
	Return the number of residues in the chain or in a component.
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.
unsigned	get_number_of_embedded_particles (int cc=-1) const
	Return the number of embedded particles in the chain or in one component.
bool	is_fully_embedded (int cc=-1) const
	Return true iff all particles in the chain or in a component are embedded.
unsigned	get_number_of_bonds (int cc=-1) const
	Return the number of bonds in the chain or in a component.
unsigned	get_number_of_embedded_bonds (int cc=-1) const
	Return the number of embedded bonds in the chain or in a component.
unsigned	get_number_of_particles (int cc=-1) const
	Return the total number of particles.
unsigned	get_number_of_components () const
	Return the number of connected components.
const Residue &	get_first_residue (int cc=-1) const
	Return the first residue of the chain or of the component.
const Residue &	get_last_residue (int cc=-1) const
	Return the last residue of the chain or of the component.
Particle_rep	get_particle_rep (const Atom &a) const
	(deprecated) Return the atom representation of the input within the covalent structure
const Molecular_covalent_structure &	get_covalent_structure () const
	Return the underlying covalent structure.
const Conformation_type &	get_conformation () const
	Return the underlying geometrical conformation.

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

Iterators
Incident_atoms_iterator	incident_atoms_begin (const Atom &a)
	Function to initialize incident atoms iterator.
Incident_atoms_const_iterator	incident_atoms_begin (const Atom &a) const
	Function to initialize incident atoms iterator.
Incident_atoms_iterator	incident_atoms_end (const Atom &a)
	Function to initialize incident atoms iterator.
Incident_atoms_const_iterator	incident_atoms_end (const Atom &a) const
	Function to initialize incident atoms iterator.
Residues_iterator	residues_begin ()
	Function to initialize residues iterator.
Residues_const_iterator	residues_begin () const
	Function to initialize residues iterator.
Residues_iterator	residues_end ()
	Function to initialize residues iterator.
Residues_const_iterator	residues_end () const
	Function to initialize residues iterator.
Atoms_iterator	atoms_begin ()
	For iterating on atoms.
Atoms_const_iterator	atoms_begin () const
	For iterating on atoms.
Residue_atoms_iterator	atoms_begin (Residue &res)
	For iterating on atoms of a residue.
Residue_atoms_const_iterator	atoms_begin (const Residue &res) const
	For iterating on atoms of a residue.
Atoms_iterator	atoms_end ()
	For iterating on atoms.
Atoms_const_iterator	atoms_end () const
	For iterating on atoms.
Residue_atoms_iterator	atoms_end (Residue &res)
	For iterating on atoms of a residue.
Residue_atoms_const_iterator	atoms_end (const Residue &res) const
	For iterating on atoms of a residue.
Backbone_iterator	backbone_begin (int cc=-1)
	For iterating on the back bone of the chain or its component.
Backbone_const_iterator	backbone_begin (int cc=-1) const
	For iterating on the back bonee of the chain or its component.
Backbone_iterator	backbone_end (int cc=-1)
	For iterating on the back bonee of the chain or its component.
Backbone_const_iterator	backbone_end (int cc=-1) const
	For iterating on the back bonee of the chain or its component.
Heavy_iterator	heavy_begin ()
	For iterating on the heavy atoms of the polymer.
Heavy_const_iterator	heavy_begin () const
	For iterating on the heavy atoms of the polymer.
Heavy_iterator	heavy_end ()
	For iterating on the heavy atoms of the polymer.
Heavy_const_iterator	heavy_end () const
	For iterating on the heavy atoms of the polymer.
Bond_iterator	bonds_begin ()
	For iterating on the bonds of the polymer.
Bond_const_iterator	bonds_begin () const
	For iterating on the bonds of the polymer.
Bond_iterator	bonds_end ()
	For iterating on the bonds of the polymer.
Bond_const_iterator	bonds_end () const
	For iterating on the bonds of the polymer.
Bond_angle_iterator	bond_angles_begin ()
	For iterating on the bond angles of the polymer.
Bond_angle_const_iterator	bond_angles_begin () const
	For iterating on the bond angles of the polymer.
Bond_angle_iterator	bond_angles_end ()
	For iterating on the bond angles of the polymer.
Bond_angle_const_iterator	bond_angles_end () const
	For iterating on the bond angles of the polymer.
Dihedral_angle_iterator	dihedral_angles_begin ()
	For iterating on the dihedral angles of the polymer.
Dihedral_angle_const_iterator	dihedral_angles_begin () const
	For iterating on the dihedral angles of the polymer.
Dihedral_angle_iterator	dihedral_angles_end ()
	For iterating on the dihedral angles of the polymer.
Dihedral_angle_const_iterator	dihedral_angles_end () const
	For iterating on the dihedral angles of the polymer.

Attributes
const Residue *	m_first_residue
	The N-terminal residue of the chain.
const Residue *	m_last_residue
	The C-terminal residue of the chain.
Chain &	m_chain
	Contains the hierarchical info for polymers (Residues, Atoms) but not the SSE.
Molecular_covalent_structure &	m_covalent_structure
	The covalent structure of the chain.
Conformation_type	m_conformation
	The conformation of the chain.
AtomId_to_particleRep_map_type	m_atomId_to_particleRep
	The mapping from an atom serial number to its vertex id in the graph of the covalent structure.
char	m_chain_id
	The chain ID.
std::string	m_chain_type
	The chain type.
std::vector< Molecular_covalent_structure >	m_components
	The components of this chain, when there are multiple connected components.
std::vector< std::pair< std::pair< int, char >, std::pair< int, char > > >	m_components_resids
	The bounding residue ids for each component.

Detailed Description

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>
class SBL::CSB::T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >

Representation of a single polynucleotide chain within a Nucleic Acid representation.

Template Parameters

ParticleTraits	Traits class providing the particle type, see package ParticleTraits
MolecularCovalentStructure	Graph representation of a covalent structure.
ConformationType	Representation of a conformation as a point in dimension D, where D is three times the number of particles in the conformation.

Member Typedef Documentation

◆ Alpha_const_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef boost::filter_iterator<Is_Alpha_angle, Dihedral_angle_const_iterator> Alpha_const_iterator

Iterator(s) through named backbone dihedral angles within the polypeptide chain (here alpha) (const)

◆ Alpha_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef boost::filter_iterator<Is_Alpha_angle, Dihedral_angle_iterator> Alpha_iterator

Iterator(s) through named backbone dihedral angles within the polypeptide chain (here alpha)

◆ Atom

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Atom Atom

Biophysical representation of an atom.

◆ Atoms_const_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Atoms_const_iterator Atoms_const_iterator

Iterator through all atoms within the chain (const)

◆ Atoms_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Atoms_iterator Atoms_iterator

Iterator through all atoms within the chain.

◆ Chain

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Chain Chain

Biophysical representation of chain of a model of the nucleic acid.

◆ Chosen_angle_const_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Chosen_angle_const_iterator Chosen_angle_const_iterator

To iterate on dihedral angles of a certain type (const)

◆ Chosen_angle_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Chosen_angle_iterator Chosen_angle_iterator

To iterate on dihedral angles of a certain type.

◆ Conformation_type

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef ConformationType Conformation_type

Representation of a conformation, see package Molecular_conformation.

◆ Dihedral_angle

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Dihedral_angle Dihedral_angle

Dihedral angle.

◆ Dihedral_angle_const_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Dihedral_angle_const_iterator Dihedral_angle_const_iterator

Iterator through all atoms within the chain (const)

◆ Dihedral_angle_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Dihedral_angle_iterator Dihedral_angle_iterator

Iterator through all atoms within the chain (const)

◆ FT

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::FT FT

Representation of the number type.

◆ Heavy_const_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

typedef boost::filter_iterator<Is_Heavy, Atoms_const_iterator> Heavy_const_iterator

inherited

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

◆ Heavy_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

typedef boost::filter_iterator<Is_Heavy, Atoms_iterator> Heavy_iterator

inherited

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

◆ Is_Heavy

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Is_Heavy Is_Heavy

Checks whether an atom is a heavy atom.

◆ Molecular_covalent_structure

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

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

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

typedef Molecular_system::Model Molecular_model

inherited

Biophysical representation of a model of the linear polymer.

◆ Molecular_system

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

typedef ParticleTraits::Molecular_system Molecular_system

inherited

Biophysical representation of a linear polymer.

◆ P_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef boost::filter_iterator<Is_P, Atoms_iterator> P_iterator

Iterators through selected atoms within the polynucleotide chain (5' ==> 3')

◆ Particle_traits

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef ParticleTraits Particle_traits

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

◆ Point_3

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

typedef SBL::CSB::EPIC_kernel_with_atom::Point_3 Point_3

inherited

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

◆ Residue

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Residue Residue

Biophysical representation of a residue.

◆ Residue_atoms_const_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Residue_atoms_const_iterator Residue_atoms_const_iterator

Iterator through all atoms within a residue (const)

◆ Residue_atoms_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Residue_atoms_iterator Residue_atoms_iterator

Iterator through all atoms within a residue.

◆ Residues_const_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Residues_const_iterator Residues_const_iterator

Iterator through all residues within the polynucleotide chain (const)

◆ Residues_iterator

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef Base::Residues_iterator Residues_iterator

Iterator through all residues within the polynucleotide chain.

◆ Self

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

typedef T_Polynucleotide_chain_representation<Particle_traits, Molecular_covalent_structure, Conformation_type> Self

The class itself.

Constructor & Destructor Documentation

◆ T_Polynucleotide_chain_representation() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

T_Polynucleotide_chain_representation ( )

inline

Builds an empty chain.

◆ T_Polynucleotide_chain_representation() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>>

T_Polynucleotide_chain_representation	(	Chain &	c,
		Molecular_covalent_structure &	s,
		const Conformation_type &	c )

inline

Builds a 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

◆ alpha_angles_begin() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Alpha_iterator alpha_angles_begin ( )

inline

For iterating on the alpha angles of the NA chain.

Returns: Return the begin iterator for the alpha angles.

◆ alpha_angles_begin() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Alpha_const_iterator alpha_angles_begin ( ) const

inline

For iterating on the alpha angles of the NA chain.

Returns: Return the begin iterator for the alpha angles.

◆ alpha_angles_end() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Alpha_iterator alpha_angles_end ( )

inline

For iterating on the alpha angles of the NA chain.

Returns: Return the end iterator for the alpha angles.

◆ alpha_angles_end() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::Alpha_const_iterator alpha_angles_end ( ) const

inline

For iterating on the alpha angles of the NA chain.

Returns: Return the end iterator for the alpha angles.

◆ atoms_begin() [1/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Atoms_iterator atoms_begin ( )

inlineinherited

For iterating on atoms.

Returns: Return the begin iterator for atoms.

◆ atoms_begin() [2/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Atoms_const_iterator atoms_begin ( ) const

inlineinherited

For iterating on atoms.

Returns: Return the begin iterator for atoms.

◆ atoms_begin() [3/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residue_atoms_const_iterator atoms_begin ( const Residue & res ) const

inlineinherited

For iterating on atoms of a residue.

Returns: Return the begin iterator for atoms.

◆ atoms_begin() [4/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residue_atoms_iterator atoms_begin ( Residue & res )

inlineinherited

For iterating on atoms of a residue.

Returns: Return the begin iterator for atoms.

◆ atoms_end() [1/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Atoms_iterator atoms_end ( )

inlineinherited

For iterating on atoms.

Returns: Return the end iterator for atoms.

◆ atoms_end() [2/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Atoms_const_iterator atoms_end ( ) const

inlineinherited

For iterating on atoms.

Returns: Return the end iterator for atoms.

◆ atoms_end() [3/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residue_atoms_const_iterator atoms_end ( const Residue & res ) const

inlineinherited

For iterating on atoms of a residue.

Returns: Return the end iterator for atoms.

◆ atoms_end() [4/4]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residue_atoms_iterator atoms_end ( Residue & res )

inlineinherited

For iterating on atoms of a residue.

Returns: Return the end iterator for atoms.

◆ backbone_begin() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

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

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

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

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

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

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

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

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle_iterator bond_angles_begin ( )

inlineinherited

For iterating on the bond angles of the polymer.

Returns: Return the begin iterator for the bond angles.

◆ bond_angles_begin() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle_const_iterator bond_angles_begin ( ) const

inlineinherited

For iterating on the bond angles of the polymer.

Returns: Return the begin iterator for the bond angles.

◆ bond_angles_end() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle_iterator bond_angles_end ( )

inlineinherited

For iterating on the bond angles of the polymer.

Returns: Return the end iterator for the bond angles.

◆ bond_angles_end() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_angle_const_iterator bond_angles_end ( ) const

inlineinherited

For iterating on the bond angles of the polymer.

Returns: Return the end iterator for the bond angles.

◆ bonds_begin() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_iterator bonds_begin ( )

inlineinherited

For iterating on the bonds of the polymer.

Returns: Return the begin iterator for the bonds.

◆ bonds_begin() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_const_iterator bonds_begin ( ) const

inlineinherited

For iterating on the bonds of the polymer.

Returns: Return the begin iterator for the bonds.

◆ bonds_end() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_iterator bonds_end ( )

inlineinherited

For iterating on the bonds of the polymer.

Returns: Return the end iterator for the bonds.

◆ bonds_end() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_const_iterator bonds_end ( ) const

inlineinherited

For iterating on the bonds of the polymer.

Returns: Return the end iterator for the bonds.

◆ c4ps_begin() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::C4p_iterator c4ps_begin ( )

inline

For iterating on the c4ps of the NA chain.

Returns: Return the begin iterator for the c4ps.

◆ c4ps_begin() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::C4p_const_iterator c4ps_begin ( ) const

inline

For iterating on the c4ps of the NA chain.

Returns: Return the begin iterator for the c4ps.

◆ c4ps_end() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::C4p_iterator c4ps_end ( )

inline

For iterating on the c4ps of the NA chain.

Returns: Return the end iterator for the c4ps.

◆ c4ps_end() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::C4p_const_iterator c4ps_end ( ) const

inline

For iterating on the c4ps of the NA chain.

Returns: Return the end iterator for the c4ps.

◆ compute_heavy_atoms_center_of_mass()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

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

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle_iterator dihedral_angles_begin ( )

inherited

For iterating on the dihedral angles of the polymer.

Returns: Return the begin iterator for the dihedral angles.

◆ dihedral_angles_begin() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle_const_iterator dihedral_angles_begin ( ) const

inlineinherited

For iterating on the dihedral angles of the polymer.

Returns: Return the begin iterator for the dihedral angles.

◆ dihedral_angles_end() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle_iterator dihedral_angles_end ( )

inlineinherited

For iterating on the dihedral angles of the polymer.

Returns: Return the end iterator for the dihedral angles.

◆ dihedral_angles_end() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Dihedral_angle_const_iterator dihedral_angles_end ( ) const

inlineinherited

For iterating on the dihedral angles of the polymer.

Returns: Return the end iterator for the dihedral angles.

◆ get_alpha_angle() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

std::pair< bool, typename T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT > get_alpha_angle ( const Residue & res ) const

inline

Return the alpha angle associated to a residue.

Parameters

res	A const ref to the residue in question.

Returns: Return alpha value as float type

◆ get_alpha_angle() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

std::pair< bool, typename T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT > get_alpha_angle ( unsigned resn ) const

inline

Return the alpha angle associated to a residue.

Parameters

resn	The residue sequence number of the residue in question

Returns: Return alpha value as float type

◆ get_atom()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

std::pair< bool, const typename T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Atom * > get_atom	(	const std::string &	atom_name,
		const Residue &	res ) const

inlineinherited

Function to get the specified atom from the specified residue.

Parameters

atom_name	The name of the atom
res	The residue containing wanted atom

Returns: Return a pair with (false, nullptr) if the atom is not present or (true, atom) if it is

◆ get_backbone_torsion_angle()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

std::pair< bool, typename T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::FT > get_backbone_torsion_angle	(	int	offset_starting_atom,
		const Residue &	res ) const

inlineinherited

Function to get the backbone torsion angle specificied with an offset from a residue.

Parameters

offset_starting_atom	offset describing the torsion angle
res	The residue from which the offset is applied to find the torsion angle

Returns: Return a pair with (false, min_FT) if the torsion angle is not present or (true, angle) if it is

◆ get_beta_angle() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

std::pair< bool, typename T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT > get_beta_angle ( const Residue & res ) const

inline

Return the beta angle associated to a residue.

Parameters

res	A const ref to the residue in question.

Returns: Return beta value as float type

◆ get_beta_angle() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

std::pair< bool, typename T_Polynucleotide_chain_representation< ParticleTraits, MolecularCovalentStructure, ConformationType >::FT > get_beta_angle ( unsigned resn ) const

inline

Return the beta angle associated to a residue.

Parameters

resn	The residue sequence number of the residue in question

Returns: Return beta value as float type

◆ get_chain_id()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

char get_chain_id ( ) const

inherited

Returns: Return the chain ID

◆ get_chain_type()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

std::string get_chain_type ( )

inherited

Set the linear chain type specifier m_chain_type.

Parameters

(none).

Returns: (none)

◆ get_conformation()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

const T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Conformation_type & get_conformation ( ) const

inlineinherited

Return the underlying geometrical conformation.

Returns: Underlying conformation

◆ get_coordinates()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Point_3 get_coordinates ( const Atom & a ) const

inlineinherited

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()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

const T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Molecular_covalent_structure & get_covalent_structure ( ) const

inlineinherited

Return the underlying covalent structure.

Returns: Underlying covalent structure

◆ get_first_residue()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

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

inlineinherited

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

Returns: Return the first residue

◆ get_last_residue()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

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

inlineinherited

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

Returns: Return the last residue

◆ get_number_of_bonds()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

unsigned get_number_of_bonds ( int cc = -1 ) const

inlineinherited

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

Returns: Return the bond count as an unsigned

◆ get_number_of_components()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

unsigned get_number_of_components ( ) const

inlineinherited

Return the number of connected components.

Returns: Return the number of connected components

◆ get_number_of_embedded_bonds()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

unsigned get_number_of_embedded_bonds ( int cc = -1 ) const

inlineinherited

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()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

unsigned get_number_of_embedded_particles ( int cc = -1 ) const

inlineinherited

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()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

unsigned get_number_of_particles ( int cc = -1 ) const

inlineinherited

Return the total number of particles.

Returns: Return the particle count as an unsigned

◆ get_number_of_residues()

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

unsigned get_number_of_residues ( ) const

inlineinherited

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

Returns: Return the residue count as an unsigned

◆ get_particle_rep()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Particle_rep get_particle_rep ( const Atom & a ) const

inlineinherited

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

Parameters

a	Input atom

Returns: Atom representation within the covalent structure

◆ get_particles()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Bond_pair get_particles ( const Bond_rep & b ) const

inlineinherited

Function to get the particle representations from a bond.

Parameters

b	Reference to the representation of a bond in the covalent structure.

Returns: Return a pair of particle representations (which are ment to be handled internally)

◆ get_res_backbone_size()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

int get_res_backbone_size ( ) const

inherited

Returns: Return the chain ID

◆ get_x() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::FT & get_x ( const Atom & a )

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::FT get_x ( const Atom & a ) const

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::FT & get_y ( const Atom & a )

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::FT get_y ( const Atom & a ) const

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::FT & get_z ( const Atom & a )

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::FT get_z ( const Atom & a ) const

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Heavy_iterator heavy_begin ( )

inlineinherited

For iterating on the heavy atoms of the polymer.

Returns: Return the begin iterator for the heavy atoms.

◆ heavy_begin() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Heavy_const_iterator heavy_begin ( ) const

inlineinherited

For iterating on the heavy atoms of the polymer.

Returns: Return the begin iterator for the heavy atoms.

◆ heavy_end() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Heavy_iterator heavy_end ( )

inlineinherited

For iterating on the heavy atoms of the polymer.

Returns: Return the end iterator for the heavy atoms.

◆ heavy_end() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Heavy_const_iterator heavy_end ( ) const

inlineinherited

For iterating on the heavy atoms of the polymer.

Returns: Return the end iterator for the heavy atoms.

◆ incident_atoms_begin() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Incident_atoms_iterator incident_atoms_begin ( const Atom & a )

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Incident_atoms_const_iterator incident_atoms_begin ( const Atom & a ) const

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Incident_atoms_iterator incident_atoms_end ( const Atom & a )

inlineinherited

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]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Incident_atoms_const_iterator incident_atoms_end ( const Atom & a ) const

inlineinherited

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()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

bool is_fully_embedded ( int cc = -1 ) const

inlineinherited

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

Returns: Return true iff all particles are embedded

◆ is_residue_heavy_atoms_embedded()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType>

bool is_residue_heavy_atoms_embedded ( const Residue & res ) const

inline

Returns whether a residue's heavy atoms are all embedded.

Parameters

res	A const ref to the residue in question.

Returns: Return true if all heavy atoms of the residue are embedded, false otherwise

◆ operator[]()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

const T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Atom * operator[] ( const Particle_rep & p ) const

inlineinherited

Operator for allowing access to a particle given it's index in the covalent structure.

Parameters

p	Reference to the representation of the particle (or index) in the covalent structure.

Returns: Return a pointer to the particle in question. This in terms allows access to all the particle information through its dedicated accessors.

◆ residues_begin() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residues_iterator residues_begin ( )

inlineinherited

Function to initialize residues iterator.

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

◆ residues_begin() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residues_const_iterator residues_begin ( ) const

inlineinherited

Function to initialize residues iterator.

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

◆ residues_end() [1/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residues_iterator residues_end ( )

inlineinherited

Function to initialize residues iterator.

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

◆ residues_end() [2/2]

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

T_Linear_polymer_representation< ParticleTraits, MolecularCovalentStructure, ConformationType, DAMT >::Residues_const_iterator residues_end ( ) const

inlineinherited

Function to initialize residues iterator.

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

◆ set_conformation()

template<class ParticleTraits, class MolecularCovalentStructure, class ConformationType, class DAMT>

void set_conformation ( Conformation_type & C )

inlineinherited

Modify the conformation.

Parameters

C	Reference to the new conformation

Member Data Documentation

◆ m_atomId_to_particleRep

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

AtomId_to_particleRep_map_type m_atomId_to_particleRep

protectedinherited

The mapping from an atom serial number to its vertex id in the graph of the covalent structure.

◆ m_chain

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

Chain& m_chain

protectedinherited

Contains the hierarchical info for polymers (Residues, Atoms) but not the SSE.

◆ m_chain_id

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

char m_chain_id

protectedinherited

The chain ID.

◆ m_chain_type

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

std::string m_chain_type

protectedinherited

The chain type.

◆ m_components

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

std::vector<Molecular_covalent_structure> m_components

protectedinherited

The components of this chain, when there are multiple connected components.

◆ m_components_resids

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

std::vector<std::pair<std::pair<int, char>, std::pair<int, char> > > m_components_resids

protectedinherited

The bounding residue ids for each component.

◆ m_conformation

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

Conformation_type m_conformation

protectedinherited

The conformation of the chain.

◆ m_covalent_structure

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

Molecular_covalent_structure& m_covalent_structure

protectedinherited

The covalent structure of the chain.

◆ m_first_residue

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

const Residue* m_first_residue

protectedinherited

The N-terminal residue of the chain.

◆ m_last_residue

template<class ParticleTraits, class MolecularCovalentStructure = SBL::CSB::T_Molecular_covalent_structure<SBL::CSB::T_Particle_info_biomolecules<ParticleTraits> >, class ConformationType = std::vector<SBL::CSB::EPIC_kernel_with_atom::FT>, class DAMT = std::map<void, boost::tuple<std::string, std::string, std::string, std::string>>>

const Residue* m_last_residue

protectedinherited

The C-terminal residue of the chain.

Public Types

Constructors

Operators

Iterators

Operators

Accessors

Modifiers

Iterators

Attributes

Detailed Description

Member Typedef Documentation

◆ Alpha_const_iterator

◆ Alpha_iterator

◆ Atom

◆ Atoms_const_iterator

◆ Atoms_iterator

◆ Chain

◆ Chosen_angle_const_iterator

◆ Chosen_angle_iterator

◆ Conformation_type

◆ Dihedral_angle

◆ Dihedral_angle_const_iterator

◆ Dihedral_angle_iterator

◆ FT

◆ Heavy_const_iterator

◆ Heavy_iterator

◆ Is_Heavy

◆ Molecular_covalent_structure

◆ Molecular_model

◆ Molecular_system

◆ P_iterator

◆ Particle_traits

◆ Point_3

◆ Residue

◆ Residue_atoms_const_iterator

◆ Residue_atoms_iterator

◆ Residues_const_iterator

◆ Residues_iterator

◆ Self

Constructor & Destructor Documentation

◆ T_Polynucleotide_chain_representation() [1/2]

◆ T_Polynucleotide_chain_representation() [2/2]

Member Function Documentation

◆ alpha_angles_begin() [1/2]

◆ alpha_angles_begin() [2/2]

◆ alpha_angles_end() [1/2]

◆ alpha_angles_end() [2/2]

◆ 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]

◆ c4ps_begin() [1/2]

◆ c4ps_begin() [2/2]

◆ c4ps_end() [1/2]

◆ c4ps_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_alpha_angle() [1/2]

◆ get_alpha_angle() [2/2]

◆ get_atom()

◆ get_backbone_torsion_angle()