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

#include <Molecular_covalent_structure.hpp>

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 an incident particle. More...

bool	are_1_4 (Particle_rep p, Particle_rep q) const
	Check that p and q share a common incident bond. More...

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

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

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

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

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

template<class Conformation >
SBL::CSB::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...

void	remove_particle (Particle_rep rep)

std::pair< Bond_rep, bool >	add_bond (Particle_rep p, Particle_rep q, Bond_type bond_type=SIMPLE_BOND)
	Add a new bond to the covalent structure. More...

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
	Provides an iterator (on embedded or not particles. More...

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)
	Creates a new covalent structure containing only the particles of the molecule (connected component) containing p. More...

void	get_chain (char chain_id, Self &S)
	Creates a new covalent structure in S, containing only the particles of the chain with chain_id. More...

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

Detailed Description

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

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 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 a new bond to the covalent structure.

◆ 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.

Check a particle indentified by the Particle_rep p and a particle identified by the Particle_rep q share a bond.

◆ are_1_3()

bool are_1_3	(	Particle_rep	p,
		Particle_rep	q
	)		const

inline

Check that p and q an incident particle.

Check a particle indentified by the Particle_rep p and a particle identified by the Particle_rep q share an incident particle.

◆ are_1_4()

bool are_1_4	(	Particle_rep	p,
		Particle_rep	q
	)		const

inline

Check that p and q share a common incident bond.

Check a particle indentified by the Particle_rep p and a particle identified by the Particle_rep q 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.

◆ 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.

◆ 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_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_chain()

void get_chain	(	char	chain_id,
		Self &	S
	)

Creates a new covalent structure in S, containing only the particles of the chain with chain_id.

◆ get_molecule()

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

inline

Creates a new covalent structure containing only the particles of the molecule (connected component) 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_modeled_particles()

unsigned get_number_of_modeled_particles ( void ) const

inline

◆ get_number_of_particles()

unsigned get_number_of_particles ( void ) const

inline

/brief Provides the total number of particles /details Returns the total number of particles in the graph (its number of vertices) /returns an unsigned in counting the total number of particles in the graph

◆ 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_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()

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.

◆ 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.

◆ particles_begin()

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

inline

Provides an iterator (on embedded or not particles.

If embedded is set to true, only the particleRep of embedded particles are

◆ print()

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

/brief Writes to "out" the Molecular_covalent_structure in the graphviz format

Predicates

Accessors

Modifiers

Traversal

Subgraphs

Print

Detailed Description

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

Member Function Documentation

◆ add_bond()

◆ add_particle()

◆ are_1_2()

◆ are_1_3()

◆ are_1_4()

◆ bond_angles_begin()

◆ bond_angles_end()

◆ dihedral_angles_begin()

◆ dihedral_angles_end()

◆ get_bond() [1/2]

◆ get_bond() [2/2]

◆ get_bond_rep()

◆ get_canonical_rep() [1/3]

◆ get_canonical_rep() [2/3]

◆ get_canonical_rep() [3/3]

◆ get_chain()

◆ get_molecule()

◆ get_molecules()

◆ 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_in_molecule()

◆ get_sub_structure()

◆ improper_angles_begin()

◆ improper_angles_end()

◆ particles_begin()

◆ print()

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