Computes the internal coordinates from the covalent structure of a molecular conformation. More...

#include <Molecular_primitive_internal_coordinates.hpp>

Public Types
typedef T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >	Self

typedef ConformationType	Conformation

typedef CovalentStructure	Covalent_structure

typedef SBL::Models::T_Conformation_traits< Conformation >	Conformation_traits

typedef Conformation_traits::FT	FT

typedef Covalent_structure::Particle_rep	Particle_rep

typedef Covalent_structure::Bond_rep	Bond_rep

typedef Covalent_structure::Bond_angle_rep	Bond_angle_rep

typedef Covalent_structure::Torsion_angle_rep	Torsion_angle_rep

typedef Covalent_structure::Particles_iterator	Particles_iterator

typedef Covalent_structure::Bonds_iterator	Bonds_iterator

typedef Covalent_structure::Bond_angles_iterator	Bond_angles_iterator

typedef Covalent_structure::Dihedral_angles_iterator	Dihedral_angles_iterator

typedef Covalent_structure::Improper_angles_iterator	Improper_angles_iterator

typedef Covalent_structure::Incident_bonds_iterator	Incident_bonds_iterator

typedef CGAL::Sign	Isomerism_type

Attributes
static Isomerism_type	ISOMERISM_CIS = CGAL::POSITIVE

static Isomerism_type	ISOMERISM_TRANS = CGAL::NEGATIVE

static Isomerism_type	ISOMERISM_UNDEF = CGAL::ZERO

Constructors
	T_Molecular_primitive_internal_coordinates (void)
	Builds an empty covalent structure. More...

Internal coordinates
FT	get_squared_distance (const Conformation &C, const CovalentStructure &S, Particle_rep p, Particle_rep q) const

FT	get_distance (const Conformation &C, const CovalentStructure &S, Particle_rep p, Particle_rep q) const

FT	get_signed_squared_cosine_of_bond_angle (const Conformation &C, const CovalentStructure &S, const Bond_angle_rep &b) const

FT	get_bond_angle (const Conformation &C, const CovalentStructure &S, const Bond_angle_rep &b) const

FT	get_valence_angle (const Conformation &C, const CovalentStructure &S, const Bond_angle_rep &b) const

FT	get_signed_squared_cosine_of_torsion_angle (const Conformation &C, const CovalentStructure &S, const Torsion_angle_rep &b) const

CGAL::Sign	get_sign_of_torsion_angle (const Conformation &C, const CovalentStructure &S, const Torsion_angle_rep &b) const

Isomerism_type	get_cis_trans_orientation (const Conformation &C, const CovalentStructure &S, const Torsion_angle_rep &b) const

FT	get_torsion_angle (const Conformation &C, const CovalentStructure &S, const Torsion_angle_rep &b) const

FT	get_dihedral_angle (const Conformation &C, const CovalentStructure &S, const Torsion_angle_rep &b) const

Approximate internal coordinates
template<class OutputIterator >
OutputIterator	get_bond_distances (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

template<class OutputIterator >
OutputIterator	get_bond_angles (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

template<class OutputIterator >
OutputIterator	get_valence_angles (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

template<class OutputIterator >
OutputIterator	get_dihedral_angles (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

template<class OutputIterator >
OutputIterator	get_improper_angles (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

Exact internal coordinates
template<class OutputIterator >
OutputIterator	get_squared_bond_distances (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

template<class OutputIterator >
OutputIterator	get_signed_squared_cosine_of_bond_angles (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

template<class OutputIterator >
OutputIterator	get_signed_squared_cosine_of_dihedral_angles (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

template<class OutputIterator >
OutputIterator	get_signed_squared_cosine_of_improper_angles (const Conformation &C, const CovalentStructure &S, OutputIterator out) const

Detailed Description

template<class ConformationType, class CovalentStructure>
class SBL::CSB::T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >

Computes the internal coordinates from the covalent structure of a molecular conformation.

Template Parameters

ConformationType	Geometry of a molecule (coordinates of its particles).
CovalentStructure	Graph representing the covalent structure of a conformation.

Member Typedef Documentation

◆ Bond_angle_rep

typedef Covalent_structure::Bond_angle_rep Bond_angle_rep

◆ Bond_angles_iterator

typedef Covalent_structure::Bond_angles_iterator Bond_angles_iterator

◆ Bond_rep

typedef Covalent_structure::Bond_rep Bond_rep

◆ Bonds_iterator

typedef Covalent_structure::Bonds_iterator Bonds_iterator

◆ Conformation

typedef ConformationType Conformation

◆ Conformation_traits

typedef SBL::Models::T_Conformation_traits<Conformation> Conformation_traits

◆ Covalent_structure

typedef CovalentStructure Covalent_structure

◆ Dihedral_angles_iterator

typedef Covalent_structure::Dihedral_angles_iterator Dihedral_angles_iterator

◆ FT

typedef Conformation_traits::FT FT

◆ Improper_angles_iterator

typedef Covalent_structure::Improper_angles_iterator Improper_angles_iterator

◆ Incident_bonds_iterator

typedef Covalent_structure::Incident_bonds_iterator Incident_bonds_iterator

◆ Isomerism_type

typedef CGAL::Sign Isomerism_type

◆ Particle_rep

typedef Covalent_structure::Particle_rep Particle_rep

◆ Particles_iterator

typedef Covalent_structure::Particles_iterator Particles_iterator

◆ Self

typedef T_Molecular_primitive_internal_coordinates<ConformationType, CovalentStructure> Self

◆ Torsion_angle_rep

typedef Covalent_structure::Torsion_angle_rep Torsion_angle_rep

Constructor & Destructor Documentation

◆ T_Molecular_primitive_internal_coordinates()

T_Molecular_primitive_internal_coordinates ( void )

inline

Builds an empty covalent structure.

Member Function Documentation

◆ get_bond_angle()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_bond_angle	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Bond_angle_rep &	b
	)		const

inline

◆ get_bond_angles()

OutputIterator get_bond_angles	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_bond_distances()

OutputIterator get_bond_distances	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_cis_trans_orientation()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::Isomerism_type get_cis_trans_orientation	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Torsion_angle_rep &	b
	)		const

inline

◆ get_dihedral_angle()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_dihedral_angle	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Torsion_angle_rep &	b
	)		const

inline

◆ get_dihedral_angles()

OutputIterator get_dihedral_angles	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_distance()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_distance	(	const Conformation &	C,
		const CovalentStructure &	S,
		Particle_rep	p,
		Particle_rep	q
	)		const

inline

◆ get_improper_angles()

OutputIterator get_improper_angles	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_sign_of_torsion_angle()

CGAL::Sign get_sign_of_torsion_angle	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Torsion_angle_rep &	b
	)		const

inline

◆ get_signed_squared_cosine_of_bond_angle()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_signed_squared_cosine_of_bond_angle	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Bond_angle_rep &	b
	)		const

inline

◆ get_signed_squared_cosine_of_bond_angles()

OutputIterator get_signed_squared_cosine_of_bond_angles	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_signed_squared_cosine_of_dihedral_angles()

OutputIterator get_signed_squared_cosine_of_dihedral_angles	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_signed_squared_cosine_of_improper_angles()

OutputIterator get_signed_squared_cosine_of_improper_angles	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_signed_squared_cosine_of_torsion_angle()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_signed_squared_cosine_of_torsion_angle	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Torsion_angle_rep &	b
	)		const

inline

◆ get_squared_bond_distances()

OutputIterator get_squared_bond_distances	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

◆ get_squared_distance()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_squared_distance	(	const Conformation &	C,
		const CovalentStructure &	S,
		Particle_rep	p,
		Particle_rep	q
	)		const

inline

◆ get_torsion_angle()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_torsion_angle	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Torsion_angle_rep &	b
	)		const

inline

◆ get_valence_angle()

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::FT get_valence_angle	(	const Conformation &	C,
		const CovalentStructure &	S,
		const Bond_angle_rep &	b
	)		const

inline

◆ get_valence_angles()

OutputIterator get_valence_angles	(	const Conformation &	C,
		const CovalentStructure &	S,
		OutputIterator	out
	)		const

inline

Member Data Documentation

◆ ISOMERISM_CIS

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::Isomerism_type ISOMERISM_CIS = CGAL::POSITIVE

static

◆ ISOMERISM_TRANS

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::Isomerism_type ISOMERISM_TRANS = CGAL::NEGATIVE

static

◆ ISOMERISM_UNDEF

T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >::Isomerism_type ISOMERISM_UNDEF = CGAL::ZERO

static

Public Types

Attributes

Constructors

Internal coordinates

Approximate internal coordinates

Exact internal coordinates

Detailed Description

template<class ConformationType, class CovalentStructure> class SBL::CSB::T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >

Member Typedef Documentation

◆ Bond_angle_rep

◆ Bond_angles_iterator

◆ Bond_rep

◆ Bonds_iterator

◆ Conformation

◆ Conformation_traits

◆ Covalent_structure

◆ Dihedral_angles_iterator

◆ FT

◆ Improper_angles_iterator

◆ Incident_bonds_iterator

◆ Isomerism_type

◆ Particle_rep

◆ Particles_iterator

◆ Self

◆ Torsion_angle_rep

Constructor & Destructor Documentation

◆ T_Molecular_primitive_internal_coordinates()

Member Function Documentation

◆ get_bond_angle()

◆ get_bond_angles()

◆ get_bond_distances()

◆ get_cis_trans_orientation()

◆ get_dihedral_angle()

◆ get_dihedral_angles()

◆ get_distance()

◆ get_improper_angles()

◆ get_sign_of_torsion_angle()

◆ get_signed_squared_cosine_of_bond_angle()

◆ get_signed_squared_cosine_of_bond_angles()

◆ get_signed_squared_cosine_of_dihedral_angles()

◆ get_signed_squared_cosine_of_improper_angles()

◆ get_signed_squared_cosine_of_torsion_angle()

◆ get_squared_bond_distances()

◆ get_squared_distance()

◆ get_torsion_angle()

◆ get_valence_angle()

◆ get_valence_angles()

Member Data Documentation

◆ ISOMERISM_CIS

◆ ISOMERISM_TRANS

◆ ISOMERISM_UNDEF

template<class ConformationType, class CovalentStructure>
class SBL::CSB::T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure >