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Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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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 |
Computes the internal coordinates from the covalent structure of a molecular conformation.
Computes the internal coordinates from the covalent structure of a molecular conformation.
ConformationType | Geometry of a molecule (coordinates of its particles). |
CovalentStructure | Graph representing the covalent structure of a conformation. |
typedef Covalent_structure::Bond_rep Bond_rep |
typedef ConformationType Conformation |
typedef CovalentStructure Covalent_structure |
typedef Conformation_traits::FT FT |
typedef CGAL::Sign Isomerism_type |
typedef T_Molecular_primitive_internal_coordinates<ConformationType, CovalentStructure> Self |
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Builds an empty covalent structure.
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