Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm > Class Template Reference

Contribution of all bonded energy terms to the potential energy function. More...

#include <Molecular_potential_energy_linear_structure.hpp>

Public Types

typedef T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm > Self
 
typedef EnergyBondedLengthsTerm::FT FT
 
typedef ConformationType Conformation
 
typedef PotentialEnergyParameters Potential_energy_parameters
 
typedef CovalentStructure Covalent_structure
 
typedef T_Molecular_potential_energy_contribution< T_Bonded_particles_visitor< CovalentStructure >, EnergyBondedLengthsTerm > Bond_lengths_contribution
 
typedef T_Molecular_potential_energy_contribution< T_Bond_angles_visitor< CovalentStructure >, EnergyBondAnglesTerm > Bond_angles_contribution
 
typedef T_Molecular_potential_energy_contribution< T_Dihedral_angles_visitor< CovalentStructure >, EnergyDihedralAnglesTerm > Dihedral_angles_contribution
 
typedef PotentialEnergyParameters::Unit_system_traits::Molar_energy_quantity Molar_energy_quantity
 

Public Member Functions

Molar_energy_quantity operator() (const Conformation &C, const Covalent_structure &S) const
 
Molar_energy_quantity get_bond_lengths_contribution (const Conformation &C, const Covalent_structure &S) const
 
Molar_energy_quantity get_bond_angles_contribution (const Conformation &C, const Covalent_structure &S) const
 
Molar_energy_quantity get_dihedral_angles_contribution (const Conformation &C, const Covalent_structure &S) const
 

Detailed Description

template<class ConformationType, class CovalentStructure, class PotentialEnergyParameters, class EnergyBondedLengthsTerm = T_Molecular_potential_energy_bond_length_term_harmonic<ConformationType, CovalentStructure, PotentialEnergyParameters>, class EnergyBondAnglesTerm = T_Molecular_potential_energy_bond_angle_term_harmonic<ConformationType, CovalentStructure, PotentialEnergyParameters>, class EnergyDihedralAnglesTerm = T_Molecular_potential_energy_torsion_angle_term_periodic<ConformationType, CovalentStructure, PotentialEnergyParameters>>
class SBL::CSB::T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm >

Contribution of all bonded energy terms to the potential energy function.

It combines the three contributions to the energy function related to bonded lengths, bonded angles and dihedral angles.

Template Parameters
ConformationTypeThe type of the input geometric conformation, as defined in the package ConformationTraits
CovalentStructureThe type of the input covalent structure, as defined in the package Molecular_covalent_structure
PotentialEnergyParametersClass defining the parameters of the associated force field as the class SBL::IO::T_Potential_energy_parameters
EnergyBondedLengthsTermmodel of term from bonded lengths.
EnergyBondAnglesTermmodel of term from bonded angles.
EnergyDihedralAnglesTermmodel of term from dihedral angles.
EnergyImproperAnglesTermmodel of term from improper angles.

It combines the three contributions to the energy function related to bonded lengths, bonded angles and torsion angles.

Template Parameters
CovalentStructureThe type of the input covalent structure, as defined in the package Molecular_covalent_structure.
PotentialEnergyParametersClass defining the parameters of the associated force field as the class SBL::IO::T_Potential_energy_parameters

Member Typedef Documentation

◆ Bond_angles_contribution

◆ Bond_lengths_contribution

◆ Conformation

typedef ConformationType Conformation

◆ Covalent_structure

typedef CovalentStructure Covalent_structure

◆ Dihedral_angles_contribution

◆ FT

typedef EnergyBondedLengthsTerm::FT FT

◆ Molar_energy_quantity

typedef PotentialEnergyParameters::Unit_system_traits::Molar_energy_quantity Molar_energy_quantity

◆ Potential_energy_parameters

typedef PotentialEnergyParameters Potential_energy_parameters

◆ Self

typedef T_Molecular_potential_energy_bonded_contribution<ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm> Self

Member Function Documentation

◆ get_bond_angles_contribution()

T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm >::Molar_energy_quantity get_bond_angles_contribution ( const Conformation C,
const Covalent_structure S 
) const
inline

◆ get_bond_lengths_contribution()

T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm >::Molar_energy_quantity get_bond_lengths_contribution ( const Conformation C,
const Covalent_structure S 
) const
inline

◆ get_dihedral_angles_contribution()

T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm >::Molar_energy_quantity get_dihedral_angles_contribution ( const Conformation C,
const Covalent_structure S 
) const
inline

◆ operator()()

T_Molecular_potential_energy_bonded_contribution< ConformationType, CovalentStructure, PotentialEnergyParameters, EnergyBondedLengthsTerm, EnergyBondAnglesTerm, EnergyDihedralAnglesTerm >::Molar_energy_quantity operator() ( const Conformation C,
const Covalent_structure S 
) const
inline