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>

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.

Constructor & Destructor Documentation

◆ T_Molecular_primitive_internal_coordinates()

Builds an empty covalent structure.