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

#include <Molecular_primitive_internal_coordinates.hpp>

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

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.

Constructor & Destructor Documentation

T_Molecular_primitive_internal_coordinates ( void )

inline

Builds an empty covalent structure.