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

Bond_angle_rep	get_canonical_rep (Bond_angle_rep a) const
	Return the bond angle such that the smallest vertex index is first – out of the first and third vertices. More...

Torsion_angle_rep	get_canonical_rep (Torsion_angle_rep a) const
	If a proper angle: second and third vertices sorted; if improper angle: central atom first, remaining three sorted. 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_particle_linearPosition (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.

Template Parameters

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_canonical_rep() [1/3]

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

inline

Return the bond angle such that the smallest vertex index is first – out of the first and third vertices.

◆ get_canonical_rep() [2/3]

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

inline

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

◆ get_canonical_rep() [3/3]

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

inline

If a proper angle: second and third vertices sorted; if improper angle: central atom first, remaining three sorted.

◆ get_graph() [1/2]

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

inline

◆ get_graph() [2/2]

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

inline

◆ get_mirror_bond_rep()

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

int get_particle_linearPosition ( Particle_rep p ) const

inline

◆ get_particle_rep() [1/3]

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() [2/3]

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() [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]

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

inline

◆ get_x() [2/2]

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

inline

◆ get_y() [1/2]

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

inline

◆ get_y() [2/2]

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

inline

◆ get_z() [1/2]

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

inline

◆ get_z() [2/2]

const SBL::Models::T_Conformation_traits< Conformation >::FT & get_z	(	const 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_canonical_rep() [1/3]

◆ get_canonical_rep() [2/3]

◆ get_canonical_rep() [3/3]

◆ get_graph() [1/2]

◆ get_graph() [2/2]

◆ get_mirror_bond_rep()

◆ 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_linearPosition()

◆ 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 >