Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Molecular_primitive_internal_coordinates< ConformationType, CovalentStructure > Class Template Reference

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< ConformationConformation_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.

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

Template Parameters
ConformationTypeGeometry of a molecule (coordinates of its particles).
CovalentStructureGraph 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

◆ 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()

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