Representation of the covalent structure of a molecular conformation. More...

#include <Molecular_covalent_structure.hpp>

Classes
class	Bond_angles_iterator_base

class	Dihedral_angles_iterator_base

class	Is_embedded

class	Is_valid

class	Label_writer

class	Make_valid

Public Types
enum	Bond_type { SIMPLE_BOND = 1, DOUBLE_BOND = 2, TRIPLE_BOND = 3 }

typedef T_Molecular_covalent_structure< ParticleInfo >	Self

typedef T_Particle_info_traits< ParticleInfo >	Particle_info_traits

typedef Particle_info_traits::Particle_info	Particle_info

typedef boost::subgraph< boost::adjacency_list< boost::vecS, boost::vecS, boost::undirectedS, Particle_info, boost::property< boost::edge_index_t, int, Bond_type > > >	Covalent_structure_graph

typedef boost::graph_traits< Covalent_structure_graph >	Covalent_structure_graph_traits

typedef Covalent_structure_graph_traits::vertex_descriptor	Particle_rep

typedef Covalent_structure_graph_traits::edge_descriptor	Bond_rep

typedef boost::tuple< Bond_rep, Bond_rep >	Bond_angle_rep

typedef boost::tuple< Bond_rep, Bond_rep, Bond_rep >	Torsion_angle_rep

typedef Covalent_structure_graph_traits::vertex_iterator	Particles_iterator_base

typedef boost::filter_iterator< Is_embedded, Particles_iterator_base >	Particles_iterator

typedef Covalent_structure_graph_traits::edge_iterator	Bonds_iterator_base

typedef boost::filter_iterator< Is_embedded, Bonds_iterator_base >	Bonds_iterator_filtered

typedef boost::transform_iterator< Make_valid, Bonds_iterator_filtered >	Bonds_iterator

typedef Covalent_structure_graph_traits::out_edge_iterator	Incident_bonds_iterator_base

typedef boost::filter_iterator< Is_embedded, Incident_bonds_iterator_base >	Incident_bonds_iterator

typedef boost::filter_iterator< Is_valid, Bond_angles_iterator_base >	Bond_angles_iterator

typedef boost::filter_iterator< Is_valid, Dihedral_angles_iterator_base >	Dihedral_angles_iterator

typedef std::vector< Torsion_angle_rep >::const_iterator	Improper_angles_iterator_base

typedef boost::filter_iterator< Is_valid, Improper_angles_iterator_base >	Improper_angles_iterator

Public Member Functions
template<class InputIterator >
T_Molecular_covalent_structure< ParticleInfo > &	get_sub_structure (InputIterator begin, InputIterator end, Self &S)

Predicates
bool	are_1_2 (Particle_rep p, Particle_rep q) const
	check that p and q share a bond More...

bool	are_1_3 (Particle_rep p, Particle_rep q) const
	check that p and q share an incident particle More...

bool	are_1_4 (Particle_rep p, Particle_rep q) const

Accessors
const Covalent_structure_graph &	get_graph (void) const

Covalent_structure_graph &	get_graph (void)

unsigned	get_number_of_particles (void) const

unsigned	get_number_of_modeled_particles (void) const

unsigned	get_number_of_embedded_particles (void) const

bool	is_fully_embedded (void) const

unsigned	get_number_of_bonds (void) const

unsigned	get_number_of_modeled_bonds (void) const

unsigned	get_number_of_embedded_bonds (void) const

std::pair< Particle_rep, Particle_rep >	get_particles (Bond_rep b) const

Bond_rep	get_bond (Bond_angle_rep b, unsigned i) const
	Get the (i+1)-th bond from a bond angle, with i = 0 or 1. More...

Bond_rep	get_bond (Torsion_angle_rep b, unsigned i) const
	Get the (i+1)-th bond from a torsion angle, with i = 0,1 or 2. More...

Particle_rep	get_particle_rep (Bond_rep b, unsigned i) const
	Get the (i+1)-th particle from a bond, with i = 0 or 1. More...

Particle_rep	get_particle_rep (Bond_angle_rep b, unsigned i) const
	Get the (i+1)-th particle from a bond angle, with i = 0,1 or 2. More...

Particle_rep	get_particle_rep (Torsion_angle_rep b, unsigned i) const
	Get the (i+1)-th particle from a torsion angle, with i = 0, 1, 2 or 3. More...

std::pair< bool, Bond_rep >	get_bond_rep (Particle_rep p, Particle_rep q) const
	Get the bond represented by the two input particles, if any. More...

Bond_rep	get_mirror_bond_rep (Bond_rep u) const

std::pair< bool, Bond_angle_rep >	get_bond_angle_rep (Bond_rep b_1, Bond_rep b_2) const

std::pair< bool, Torsion_angle_rep >	get_torsion_angle_rep (Bond_rep b_1, Bond_rep b_2, Bond_rep b_3) const

Bond_rep	get_cannonized_rep (Bond_rep b) const
	Return the bond such that the smallest vertex index is first. More...

Bond_angle_rep	get_cannonized_rep (Bond_angle_rep a) const
	Return the bond angle such that the smallest vertex index is first. More...

Torsion_angle_rep	get_cannonized_rep (Torsion_angle_rep a) const
	If a proper angle, return it with the samellest vertex index first, otherwise return the improper angle itself. More...

std::pair< bool, Particle_rep >	find_particle (const Particle_info &info) const

bool	has_model (Particle_rep p) const

bool	is_embedded (Particle_rep p) const

int	get_model_position (Particle_rep p) const

template<class Conformation >
const SBL::Models::T_Conformation_traits< Conformation >::FT &	get_x (const Conformation &C, Particle_rep p) const

template<class Conformation >
SBL::Models::T_Conformation_traits< Conformation >::FT &	get_x (Conformation &C, Particle_rep p) const

template<class Conformation >
const SBL::Models::T_Conformation_traits< Conformation >::FT &	get_y (const Conformation &C, Particle_rep p) const

template<class Conformation >
SBL::Models::T_Conformation_traits< Conformation >::FT &	get_y (Conformation &C, Particle_rep p) const

template<class Conformation >
const SBL::Models::T_Conformation_traits< Conformation >::FT &	get_z (const Conformation &C, Particle_rep p) const

template<class Conformation >
SBL::Models::T_Conformation_traits< Conformation >::FT &	get_z (Conformation &C, Particle_rep p) const

Modifiers
Particle_rep	add_particle (const Particle_info &info)
	Add a new particle in the covalent structure corresponding to the ith particle in a given conformation of the molecule. More...

std::pair< Bond_rep, bool >	add_bond (Particle_rep p, Particle_rep q, Bond_type bond_type=SIMPLE_BOND)

std::pair< bool, Torsion_angle_rep >	add_improper_constraint (Particle_rep p, Particle_rep q, Particle_rep r, Particle_rep s)

void	set_particle_position (Particle_rep p, int position)

Traversal
Particles_iterator	particles_begin (bool is_embedded=true) const

Particles_iterator	particles_end (bool is_embedded=true) const

Bonds_iterator	bonds_begin (bool is_embedded=true) const

Bonds_iterator	bonds_end (bool is_embedded=true) const

Incident_bonds_iterator	incident_bonds_begin (Particle_rep p, bool is_embedded=true) const

Incident_bonds_iterator	incident_bonds_end (Particle_rep p, bool is_embedded=true) const

Bond_angles_iterator	bond_angles_begin (bool is_embedded=true) const
	Iterate over the bond angles (u, v, w) so that u and v are the largest indices lower than w such that (u, v) and (v, w) are bonds. More...

Bond_angles_iterator	bond_angles_end (bool is_embedded=true) const
	Iterate over the bond angles (u, v, w) so that u and v are the largest indices lower than w such that (u, v) and (v, w) are bonds. More...

Dihedral_angles_iterator	dihedral_angles_begin (bool is_embedded=true) const
	Iterate over the torsion angles (u, v, w, t) so that u, v and w are the largest indices lower than t such that (u, v), (v, w) and (w, t) are bonds. More...

Dihedral_angles_iterator	dihedral_angles_end (bool is_embedded=true) const
	Iterate over the torsion angles (u, v, w, t) so that u, v and w are the largest indices lower than t such that (u, v), (v, w) and (w, t) are bonds. More...

Improper_angles_iterator	improper_angles_begin (bool is_embedded=true) const
	Iterate over the torsion angles (u, v, w, t) so that (u, v), (u, w) and (u, t) are bonds. More...

Improper_angles_iterator	improper_angles_end (bool is_embedded=true) const
	Iterate over the torsion angles (u, v, w, t) so that (u, v), (u, w) and (u, t) are bonds. More...

Subgraphs
template<class OutputIterator >
OutputIterator	get_molecules (OutputIterator out) const
	Computes the connected components of this graph and returns one vertex for each connected component. More...

template<class OutputIterator >
OutputIterator	get_particles_in_molecule (Particle_rep p, OutputIterator out) const
	Returns the ensemble of particles in the same molecule (i.e connected component) as p. More...

template<class InputIterator >
Self &	get_sub_structure (InputIterator begin, InputIterator end, Self &S)
	Builds a new covalent structure containing only the particles in the input range; note that no new copy of the information is created, and modifying the underlying graph of one covalent structure affects the other one. More...

Self &	get_molecule (Particle_rep p, Self &S)
	Builds a new covalent structure containing only the particles of the molecule containing p;. More...

Print
std::ostream &	print (std::ostream &out) const

Detailed Description

template<class ParticleInfo = std::string>
class SBL::CSB::T_Molecular_covalent_structure< ParticleInfo >

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.

  \tparam ParticleInfo Information to attached to the particle (default is a simple string). It should be comparable (less operator) and streamable.

Member Typedef Documentation

◆ Bond_angle_rep

typedef boost::tuple<Bond_rep, Bond_rep> Bond_angle_rep

◆ Bond_angles_iterator

typedef boost::filter_iterator<Is_valid, Bond_angles_iterator_base> Bond_angles_iterator

◆ Bond_rep

typedef Covalent_structure_graph_traits::edge_descriptor Bond_rep

◆ Bonds_iterator

typedef boost::transform_iterator<Make_valid, Bonds_iterator_filtered> Bonds_iterator

◆ Bonds_iterator_base

typedef Covalent_structure_graph_traits::edge_iterator Bonds_iterator_base

◆ Bonds_iterator_filtered

typedef boost::filter_iterator<Is_embedded, Bonds_iterator_base> Bonds_iterator_filtered

◆ Covalent_structure_graph

typedef boost::subgraph<boost::adjacency_list<boost::vecS, boost::vecS, boost::undirectedS, Particle_info, boost::property< boost::edge_index_t, int, Bond_type> > > Covalent_structure_graph

Graph representation of the covalent structure : it can be subdivided in subgraphs with the following hierarchy : chains, residues, (backbone, sidechain)

◆ Covalent_structure_graph_traits

typedef boost::graph_traits<Covalent_structure_graph> Covalent_structure_graph_traits

◆ Dihedral_angles_iterator

typedef boost::filter_iterator<Is_valid, Dihedral_angles_iterator_base> Dihedral_angles_iterator

◆ Improper_angles_iterator

typedef boost::filter_iterator<Is_valid, Improper_angles_iterator_base> Improper_angles_iterator

◆ Improper_angles_iterator_base

typedef std::vector<Torsion_angle_rep>::const_iterator Improper_angles_iterator_base

◆ Incident_bonds_iterator

typedef boost::filter_iterator<Is_embedded, Incident_bonds_iterator_base> Incident_bonds_iterator

◆ Incident_bonds_iterator_base

typedef Covalent_structure_graph_traits::out_edge_iterator Incident_bonds_iterator_base

◆ Particle_info

typedef Particle_info_traits::Particle_info Particle_info

◆ Particle_info_traits

typedef T_Particle_info_traits<ParticleInfo> Particle_info_traits

◆ Particle_rep

typedef Covalent_structure_graph_traits::vertex_descriptor Particle_rep

◆ Particles_iterator

typedef boost::filter_iterator<Is_embedded, Particles_iterator_base> Particles_iterator

◆ Particles_iterator_base

typedef Covalent_structure_graph_traits::vertex_iterator Particles_iterator_base

◆ Self

typedef T_Molecular_covalent_structure<ParticleInfo> Self

◆ Torsion_angle_rep

typedef boost::tuple<Bond_rep, Bond_rep, Bond_rep> Torsion_angle_rep

Member Enumeration Documentation

◆ Bond_type

enum Bond_type

Enumerator
SIMPLE_BOND
DOUBLE_BOND
TRIPLE_BOND

Member Function Documentation

◆ add_bond()

std::pair< typename T_Molecular_covalent_structure< ParticleInfo >::Bond_rep, bool > add_bond	(	Particle_rep	p,
		Particle_rep	q,
		Bond_type	bond_type = `SIMPLE_BOND`
	)

inline

◆ add_improper_constraint()

std::pair< bool, typename T_Molecular_covalent_structure< ParticleInfo >::Torsion_angle_rep > add_improper_constraint	(	Particle_rep	p,
		Particle_rep	q,
		Particle_rep	r,
		Particle_rep	s
	)

inline

◆ add_particle()

T_Molecular_covalent_structure< ParticleInfo >::Particle_rep add_particle ( const Particle_info & info )

inline

Add a new particle in the covalent structure corresponding to the ith particle in a given conformation of the molecule.

◆ are_1_2()

bool are_1_2	(	Particle_rep	p,
		Particle_rep	q
	)		const

inline

check that p and q share a bond

◆ are_1_3()

bool are_1_3	(	Particle_rep	p,
		Particle_rep	q
	)		const

inline

check that p and q share an incident particle

◆ are_1_4()

bool are_1_4	(	Particle_rep	p,
		Particle_rep	q
	)		const

inline

check that there are incident bonds to p and q that share a common incident bond

◆ bond_angles_begin()

T_Molecular_covalent_structure< ParticleInfo >::Bond_angles_iterator bond_angles_begin ( bool is_embedded = true ) const

inline

Iterate over the bond angles (u, v, w) so that u and v are the largest indices lower than w such that (u, v) and (v, w) are bonds.

◆ bond_angles_end()

T_Molecular_covalent_structure< ParticleInfo >::Bond_angles_iterator bond_angles_end ( bool is_embedded = true ) const

inline

Iterate over the bond angles (u, v, w) so that u and v are the largest indices lower than w such that (u, v) and (v, w) are bonds.

◆ bonds_begin()

T_Molecular_covalent_structure< ParticleInfo >::Bonds_iterator bonds_begin ( bool is_embedded = true ) const

inline

◆ bonds_end()

T_Molecular_covalent_structure< ParticleInfo >::Bonds_iterator bonds_end ( bool is_embedded = true ) const

inline

◆ dihedral_angles_begin()

T_Molecular_covalent_structure< ParticleInfo >::Dihedral_angles_iterator dihedral_angles_begin ( bool is_embedded = true ) const

inline

Iterate over the torsion angles (u, v, w, t) so that u, v and w are the largest indices lower than t such that (u, v), (v, w) and (w, t) are bonds.

◆ dihedral_angles_end()

T_Molecular_covalent_structure< ParticleInfo >::Dihedral_angles_iterator dihedral_angles_end ( bool is_embedded = true ) const

inline

Iterate over the torsion angles (u, v, w, t) so that u, v and w are the largest indices lower than t such that (u, v), (v, w) and (w, t) are bonds.

◆ find_particle()

std::pair< bool, typename T_Molecular_covalent_structure< ParticleInfo >::Particle_rep > find_particle ( const Particle_info & info ) const

inline

◆ get_bond() [1/2]

T_Molecular_covalent_structure< ParticleInfo >::Bond_rep get_bond	(	Bond_angle_rep	b,
		unsigned	i
	)		const

inline

Get the (i+1)-th bond from a bond angle, with i = 0 or 1.

◆ get_bond() [2/2]

T_Molecular_covalent_structure< ParticleInfo >::Bond_rep get_bond	(	Torsion_angle_rep	b,
		unsigned	i
	)		const

inline

Get the (i+1)-th bond from a torsion angle, with i = 0,1 or 2.

◆ get_bond_angle_rep()

std::pair< bool, typename T_Molecular_covalent_structure< ParticleInfo >::Bond_angle_rep > get_bond_angle_rep	(	Bond_rep	b_1,
		Bond_rep	b_2
	)		const

inline

◆ get_bond_rep()

std::pair< bool,typename T_Molecular_covalent_structure< ParticleInfo >::Bond_rep > get_bond_rep	(	Particle_rep	p,
		Particle_rep	q
	)		const

inline

Get the bond represented by the two input particles, if any.

◆ get_cannonized_rep() [1/3]

T_Molecular_covalent_structure< ParticleInfo >::Bond_rep get_cannonized_rep ( Bond_rep b ) const

inline

Return the bond such that the smallest vertex index is first.

◆ get_cannonized_rep() [2/3]

T_Molecular_covalent_structure< ParticleInfo >::Bond_angle_rep get_cannonized_rep ( Bond_angle_rep a ) const

inline

Return the bond angle such that the smallest vertex index is first.

◆ get_cannonized_rep() [3/3]

T_Molecular_covalent_structure< ParticleInfo >::Torsion_angle_rep get_cannonized_rep ( Torsion_angle_rep a ) const

inline

If a proper angle, return it with the samellest vertex index first, otherwise return the improper angle itself.

◆ get_graph() [1/2]

const T_Molecular_covalent_structure< ParticleInfo >::Covalent_structure_graph & get_graph ( void ) const

inline

◆ get_graph() [2/2]

T_Molecular_covalent_structure< ParticleInfo >::Covalent_structure_graph & get_graph ( void )

inline

◆ get_mirror_bond_rep()

T_Molecular_covalent_structure< ParticleInfo >::Bond_rep get_mirror_bond_rep ( Bond_rep u ) const

inline

◆ get_model_position()

int get_model_position ( Particle_rep p ) const

inline

◆ get_molecule()

T_Molecular_covalent_structure< ParticleInfo > & get_molecule	(	Particle_rep	p,
		Self &	S
	)

inline

Builds a new covalent structure containing only the particles of the molecule containing p;.

◆ get_molecules()

OutputIterator get_molecules ( OutputIterator out ) const

inline

Computes the connected components of this graph and returns one vertex for each connected component.

◆ get_number_of_bonds()

unsigned get_number_of_bonds ( void ) const

inline

◆ get_number_of_embedded_bonds()

unsigned get_number_of_embedded_bonds ( void ) const

inline

◆ get_number_of_embedded_particles()

unsigned get_number_of_embedded_particles ( void ) const

inline

◆ get_number_of_modeled_bonds()

unsigned get_number_of_modeled_bonds ( void ) const

inline

◆ get_number_of_modeled_particles()

unsigned get_number_of_modeled_particles ( void ) const

inline

◆ get_number_of_particles()

unsigned get_number_of_particles ( void ) const

inline

◆ get_particle_rep() [1/3]

T_Molecular_covalent_structure< ParticleInfo >::Particle_rep get_particle_rep	(	Bond_rep	b,
		unsigned	i
	)		const

inline

Get the (i+1)-th particle from a bond, with i = 0 or 1.

◆ get_particle_rep() [2/3]

T_Molecular_covalent_structure< ParticleInfo >::Particle_rep get_particle_rep	(	Bond_angle_rep	b,
		unsigned	i
	)		const

inline

Get the (i+1)-th particle from a bond angle, with i = 0,1 or 2.

◆ get_particle_rep() [3/3]

T_Molecular_covalent_structure< ParticleInfo >::Particle_rep get_particle_rep	(	Torsion_angle_rep	b,
		unsigned	i
	)		const

inline

Get the (i+1)-th particle from a torsion angle, with i = 0, 1, 2 or 3.

◆ get_particles()

std::pair< typename T_Molecular_covalent_structure< ParticleInfo >::Particle_rep, typename T_Molecular_covalent_structure< ParticleInfo >::Particle_rep > get_particles ( Bond_rep b ) const

inline

◆ get_particles_in_molecule()

OutputIterator get_particles_in_molecule	(	Particle_rep	p,
		OutputIterator	out
	)		const

inline

Returns the ensemble of particles in the same molecule (i.e connected component) as p.

◆ get_sub_structure() [1/2]

Self& get_sub_structure	(	InputIterator	begin,
		InputIterator	end,
		Self &	S
	)

inline

Builds a new covalent structure containing only the particles in the input range; note that no new copy of the information is created, and modifying the underlying graph of one covalent structure affects the other one.

◆ get_sub_structure() [2/2]

T_Molecular_covalent_structure<ParticleInfo>& get_sub_structure	(	InputIterator	begin,
		InputIterator	end,
		Self &	S
	)

◆ get_torsion_angle_rep()

std::pair< bool, typename T_Molecular_covalent_structure< ParticleInfo >::Torsion_angle_rep > get_torsion_angle_rep	(	Bond_rep	b_1,
		Bond_rep	b_2,
		Bond_rep	b_3
	)		const

inline

◆ get_x() [1/2]

const SBL::Models::T_Conformation_traits< Conformation >::FT & get_x	(	const Conformation &	C,
		Particle_rep	p
	)		const

inline

◆ get_x() [2/2]

SBL::Models::T_Conformation_traits< Conformation >::FT & get_x	(	Conformation &	C,
		Particle_rep	p
	)		const

inline

◆ get_y() [1/2]

const SBL::Models::T_Conformation_traits< Conformation >::FT & get_y	(	const Conformation &	C,
		Particle_rep	p
	)		const

inline

◆ get_y() [2/2]

SBL::Models::T_Conformation_traits< Conformation >::FT & get_y	(	Conformation &	C,
		Particle_rep	p
	)		const

inline

◆ get_z() [1/2]

const SBL::Models::T_Conformation_traits< Conformation >::FT & get_z	(	const Conformation &	C,
		Particle_rep	p
	)		const

inline

◆ get_z() [2/2]

SBL::Models::T_Conformation_traits< Conformation >::FT & get_z	(	Conformation &	C,
		Particle_rep	p
	)		const

inline

◆ has_model()

bool has_model ( Particle_rep p ) const

inline

◆ improper_angles_begin()

T_Molecular_covalent_structure< ParticleInfo >::Improper_angles_iterator improper_angles_begin ( bool is_embedded = true ) const

inline

Iterate over the torsion angles (u, v, w, t) so that (u, v), (u, w) and (u, t) are bonds.

◆ improper_angles_end()

T_Molecular_covalent_structure< ParticleInfo >::Improper_angles_iterator improper_angles_end ( bool is_embedded = true ) const

inline

Iterate over the torsion angles (u, v, w, t) so that (u, v), (u, w) and (u, t) are bonds.

◆ incident_bonds_begin()

T_Molecular_covalent_structure< ParticleInfo >::Incident_bonds_iterator incident_bonds_begin	(	Particle_rep	p,
		bool	is_embedded = `true`
	)		const

inline

◆ incident_bonds_end()

T_Molecular_covalent_structure< ParticleInfo >::Incident_bonds_iterator incident_bonds_end	(	Particle_rep	p,
		bool	is_embedded = `true`
	)		const

inline

◆ is_embedded()

bool is_embedded ( Particle_rep p ) const

inline

◆ is_fully_embedded()

bool is_fully_embedded ( void ) const

inline

◆ particles_begin()

T_Molecular_covalent_structure< ParticleInfo >::Particles_iterator particles_begin ( bool is_embedded = true ) const

inline

◆ particles_end()

T_Molecular_covalent_structure< ParticleInfo >::Particles_iterator particles_end ( bool is_embedded = true ) const

inline

◆ print()

std::ostream & print ( std::ostream & out ) const

◆ set_particle_position()

void set_particle_position	(	Particle_rep	p,
		int	position
	)

inline

Classes

Public Types

Public Member Functions

Predicates

Accessors

Modifiers

Traversal

Subgraphs

Print

Detailed Description

template<class ParticleInfo = std::string> class SBL::CSB::T_Molecular_covalent_structure< ParticleInfo >

Member Typedef Documentation

◆ Bond_angle_rep

◆ Bond_angles_iterator

◆ Bond_rep

◆ Bonds_iterator

◆ Bonds_iterator_base

◆ Bonds_iterator_filtered

◆ Covalent_structure_graph

◆ Covalent_structure_graph_traits

◆ Dihedral_angles_iterator

◆ Improper_angles_iterator

◆ Improper_angles_iterator_base

◆ Incident_bonds_iterator

◆ Incident_bonds_iterator_base

◆ Particle_info

◆ Particle_info_traits

◆ Particle_rep

◆ Particles_iterator

◆ Particles_iterator_base

◆ Self

◆ Torsion_angle_rep

Member Enumeration Documentation

◆ Bond_type

Member Function Documentation

◆ add_bond()

◆ add_improper_constraint()

◆ add_particle()

◆ are_1_2()

◆ are_1_3()

◆ are_1_4()

◆ bond_angles_begin()

◆ bond_angles_end()

◆ bonds_begin()

◆ bonds_end()

◆ dihedral_angles_begin()

◆ dihedral_angles_end()

◆ find_particle()

◆ get_bond() [1/2]

◆ get_bond() [2/2]

◆ get_bond_angle_rep()

◆ get_bond_rep()

◆ get_cannonized_rep() [1/3]

◆ get_cannonized_rep() [2/3]

◆ get_cannonized_rep() [3/3]

◆ get_graph() [1/2]

◆ get_graph() [2/2]

◆ get_mirror_bond_rep()

◆ get_model_position()

◆ get_molecule()

◆ get_molecules()

◆ get_number_of_bonds()

◆ get_number_of_embedded_bonds()

◆ get_number_of_embedded_particles()

◆ get_number_of_modeled_bonds()

◆ get_number_of_modeled_particles()

◆ get_number_of_particles()

◆ get_particle_rep() [1/3]

◆ get_particle_rep() [2/3]

◆ get_particle_rep() [3/3]

◆ get_particles()

◆ get_particles_in_molecule()

◆ get_sub_structure() [1/2]

◆ get_sub_structure() [2/2]

◆ get_torsion_angle_rep()

◆ get_x() [1/2]

◆ get_x() [2/2]

◆ get_y() [1/2]

◆ get_y() [2/2]

◆ get_z() [1/2]

template<class ParticleInfo = std::string>
class SBL::CSB::T_Molecular_covalent_structure< ParticleInfo >