Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
List of all members | Public Types | Static Public Member Functions | Static Public Attributes
T_Potential_energy_parameters_optimal< CovalentStructure, UnitSystemTraits > Class Template Reference

#include <Potential_energy_parameters_optimal.hpp>

Public Types

typedef T_Potential_energy_parameters_optimal< CovalentStructure, UnitSystemTraits > Self
 
typedef UnitSystemTraits Unit_system_traits
 
typedef CovalentStructure::Particle_rep Particle_rep
 
typedef CovalentStructure::Bond_rep Bond_rep
 
typedef CovalentStructure::Bond_angle_rep Bond_angle_rep
 
typedef CovalentStructure::Torsion_angle_rep Torsion_angle_rep
 

Static Public Member Functions

static UnitSystemTraits::Length_quantity get_equilibrium_bond_length (const CovalentStructure &C, const Bond_rep &b)
 
static UnitSystemTraits::Bond_force_constant_quantity get_bond_length_force_constant (const CovalentStructure &C, const Bond_rep &b)
 
static UnitSystemTraits::Angle_quantity get_equilibrium_bond_angle (const CovalentStructure &C, const Bond_angle_rep &b)
 
static UnitSystemTraits::Angle_force_constant_quantity get_bond_angle_force_constant (const CovalentStructure &C, const Bond_angle_rep &b)
 
static UnitSystemTraits::Length_quantity get_equilibrium_Urey_Bradley (const CovalentStructure &C, const Bond_angle_rep &b)
 
static UnitSystemTraits::Bond_force_constant_quantity get_Urey_Bradley_force_constant (const CovalentStructure &C, const Bond_angle_rep &b)
 For bond angle potential energy calculations. More...
 
static unsigned int get_torsion_angle_number_of_periods (const CovalentStructure &C, const typename CovalentStructure::Torsion_angle_rep &b)
 
static std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Molar_energy_quantity > get_torsion_angle_parameters (const CovalentStructure &C, const typename CovalentStructure::Torsion_angle_rep &b, unsigned i)
 
static std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Angle_force_constant_quantity > get_improper_angle_parameters (const CovalentStructure &C, const typename CovalentStructure::Torsion_angle_rep &b)
 
static UnitSystemTraits::LJ_6_quantity get_Lennard_Jones_attractive_constant (const CovalentStructure &C, Particle_rep p, Particle_rep q)
 
static UnitSystemTraits::LJ_12_quantity get_Lennard_Jones_repulsive_constant (const CovalentStructure &C, Particle_rep p, Particle_rep q)
 
static UnitSystemTraits::Molar_energy_quantity get_Lennard_Jones_epsilon_constant (const CovalentStructure &C, const Particle_rep &p, const Particle_rep &q)
 
static UnitSystemTraits::Charge_quantity get_electrostatic_charge (const CovalentStructure &C, const Particle_rep &p)
 
static UnitSystemTraits::Dielectric_constant_quantity get_dielectric_constant (const CovalentStructure &C, const Particle_rep &p, const Particle_rep &q)
 
static UnitSystemTraits::Molar_energy_quantity get_dihedral_coefficient (const CovalentStructure &C, const Particle_rep &p, unsigned i)
 

Static Public Attributes

static std::vector< typename UnitSystemTraits::Length_quantity > s_equilibrium_bond_lengths
 
static std::vector< typename UnitSystemTraits::Bond_force_constant_quantity > s_bond_length_force_constants
 
static std::vector< typename UnitSystemTraits::Angle_quantity > s_equilibrium_bond_angles
 
static std::vector< typename UnitSystemTraits::Angle_force_constant_quantity > s_bond_angle_force_constants
 
static std::vector< typename UnitSystemTraits::Length_quantity > s_Urey_Bradley_equilibrium_constants
 
static std::vector< typename UnitSystemTraits::Bond_force_constant_quantity > s_Urey_Bradley_force_constants
 
static std::vector< unsigned > s_secondary_structure
 
static std::vector< typename UnitSystemTraits::Molar_energy_quantity > s_dihedral_coefficients
 
static std::vector< typename UnitSystemTraits::LJ_6_quantity > s_Lennard_Jones_attractive_constants
 
static std::vector< typename UnitSystemTraits::LJ_12_quantity > s_Lennard_Jones_repulsive_constants
 
static std::vector< std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Molar_energy_quantity > > s_torsion_angle_parameters
 
static std::vector< std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Angle_force_constant_quantity > > s_improper_angle_parameters
 
static std::vector< typename UnitSystemTraits::Length_quantity > s_sigma_constants
 
static std::vector< typename UnitSystemTraits::Molar_energy_quantity > s_Lennard_Jones_epsilon_constants
 
static double s_LJ_scale = 1
 
static double s_Coulomb_scale = 1
 
static double s_LJ14_scale = 1
 
static double s_Coulomb14_scale = 1
 
static bool s_ignore_1_3_interactions = false
 
static std::vector< typename UnitSystemTraits::Charge_quantity > s_electrostatic_charges
 

Member Typedef Documentation

◆ Bond_angle_rep

typedef CovalentStructure::Bond_angle_rep Bond_angle_rep

◆ Bond_rep

typedef CovalentStructure::Bond_rep Bond_rep

◆ Particle_rep

typedef CovalentStructure::Particle_rep Particle_rep

◆ Self

typedef T_Potential_energy_parameters_optimal<CovalentStructure, UnitSystemTraits> Self

◆ Torsion_angle_rep

typedef CovalentStructure::Torsion_angle_rep Torsion_angle_rep

◆ Unit_system_traits

typedef UnitSystemTraits Unit_system_traits

Member Function Documentation

◆ get_bond_angle_force_constant()

static UnitSystemTraits::Angle_force_constant_quantity get_bond_angle_force_constant ( const CovalentStructure &  C,
const Bond_angle_rep &  b 
)
inlinestatic

◆ get_bond_length_force_constant()

static UnitSystemTraits::Bond_force_constant_quantity get_bond_length_force_constant ( const CovalentStructure &  C,
const Bond_rep &  b 
)
inlinestatic

◆ get_dielectric_constant()

static UnitSystemTraits::Dielectric_constant_quantity get_dielectric_constant ( const CovalentStructure &  C,
const Particle_rep &  p,
const Particle_rep &  q 
)
inlinestatic

◆ get_dihedral_coefficient()

static UnitSystemTraits::Molar_energy_quantity get_dihedral_coefficient ( const CovalentStructure &  C,
const Particle_rep &  p,
unsigned  i 
)
inlinestatic

◆ get_electrostatic_charge()

static UnitSystemTraits::Charge_quantity get_electrostatic_charge ( const CovalentStructure &  C,
const Particle_rep &  p 
)
inlinestatic

◆ get_equilibrium_bond_angle()

static UnitSystemTraits::Angle_quantity get_equilibrium_bond_angle ( const CovalentStructure &  C,
const Bond_angle_rep &  b 
)
inlinestatic

◆ get_equilibrium_bond_length()

static UnitSystemTraits::Length_quantity get_equilibrium_bond_length ( const CovalentStructure &  C,
const Bond_rep &  b 
)
inlinestatic

◆ get_equilibrium_Urey_Bradley()

static UnitSystemTraits::Length_quantity get_equilibrium_Urey_Bradley ( const CovalentStructure &  C,
const Bond_angle_rep &  b 
)
inlinestatic

◆ get_improper_angle_parameters()

static std::tuple<unsigned,typename UnitSystemTraits::Angle_quantity,typename UnitSystemTraits::Angle_force_constant_quantity> get_improper_angle_parameters ( const CovalentStructure &  C,
const typename CovalentStructure::Torsion_angle_rep &  b 
)
inlinestatic

◆ get_Lennard_Jones_attractive_constant()

static UnitSystemTraits::LJ_6_quantity get_Lennard_Jones_attractive_constant ( const CovalentStructure &  C,
Particle_rep  p,
Particle_rep  q 
)
inlinestatic

◆ get_Lennard_Jones_epsilon_constant()

static UnitSystemTraits::Molar_energy_quantity get_Lennard_Jones_epsilon_constant ( const CovalentStructure &  C,
const Particle_rep &  p,
const Particle_rep &  q 
)
inlinestatic

◆ get_Lennard_Jones_repulsive_constant()

static UnitSystemTraits::LJ_12_quantity get_Lennard_Jones_repulsive_constant ( const CovalentStructure &  C,
Particle_rep  p,
Particle_rep  q 
)
inlinestatic

◆ get_torsion_angle_number_of_periods()

static unsigned int get_torsion_angle_number_of_periods ( const CovalentStructure &  C,
const typename CovalentStructure::Torsion_angle_rep &  b 
)
inlinestatic

◆ get_torsion_angle_parameters()

static std::tuple<unsigned,typename UnitSystemTraits::Angle_quantity,typename UnitSystemTraits::Molar_energy_quantity> get_torsion_angle_parameters ( const CovalentStructure &  C,
const typename CovalentStructure::Torsion_angle_rep &  b,
unsigned  i 
)
inlinestatic

◆ get_Urey_Bradley_force_constant()

static UnitSystemTraits::Bond_force_constant_quantity get_Urey_Bradley_force_constant ( const CovalentStructure &  C,
const Bond_angle_rep &  b 
)
inlinestatic

For bond angle potential energy calculations.

Member Data Documentation

◆ s_bond_angle_force_constants

std::vector< typename UnitSystemTraits::Angle_force_constant_quantity > s_bond_angle_force_constants
static

◆ s_bond_length_force_constants

std::vector< typename UnitSystemTraits::Bond_force_constant_quantity > s_bond_length_force_constants
static

◆ s_Coulomb14_scale

double s_Coulomb14_scale = 1
static

◆ s_Coulomb_scale

double s_Coulomb_scale = 1
static

◆ s_dihedral_coefficients

std::vector< typename UnitSystemTraits::Molar_energy_quantity > s_dihedral_coefficients
static

◆ s_electrostatic_charges

std::vector< typename UnitSystemTraits::Charge_quantity > s_electrostatic_charges
static

◆ s_equilibrium_bond_angles

std::vector< typename UnitSystemTraits::Angle_quantity > s_equilibrium_bond_angles
static

◆ s_equilibrium_bond_lengths

std::vector< typename UnitSystemTraits::Length_quantity > s_equilibrium_bond_lengths
static

◆ s_ignore_1_3_interactions

bool s_ignore_1_3_interactions = false
static

◆ s_improper_angle_parameters

std::vector< std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Angle_force_constant_quantity > > s_improper_angle_parameters
static

◆ s_Lennard_Jones_attractive_constants

std::vector< typename UnitSystemTraits::LJ_6_quantity > s_Lennard_Jones_attractive_constants
static

◆ s_Lennard_Jones_epsilon_constants

std::vector< typename UnitSystemTraits::Molar_energy_quantity > s_Lennard_Jones_epsilon_constants
static

◆ s_Lennard_Jones_repulsive_constants

std::vector< typename UnitSystemTraits::LJ_12_quantity > s_Lennard_Jones_repulsive_constants
static

◆ s_LJ14_scale

double s_LJ14_scale = 1
static

◆ s_LJ_scale

double s_LJ_scale = 1
static

◆ s_secondary_structure

std::vector< unsigned > s_secondary_structure
static

◆ s_sigma_constants

std::vector< typename UnitSystemTraits::Length_quantity > s_sigma_constants
static

◆ s_torsion_angle_parameters

std::vector< std::tuple< unsigned, typename UnitSystemTraits::Angle_quantity, typename UnitSystemTraits::Molar_energy_quantity > > s_torsion_angle_parameters
static

◆ s_Urey_Bradley_equilibrium_constants

std::vector< typename UnitSystemTraits::Length_quantity > s_Urey_Bradley_equilibrium_constants
static

◆ s_Urey_Bradley_force_constants

std::vector< typename UnitSystemTraits::Bond_force_constant_quantity > s_Urey_Bradley_force_constants
static