core::scoring::GenTorsionParams Class Reference

Parameter set for one torsion angle. More...

#include <GenericBondedPotential.hh>

Public Member Functions
	GenTorsionParams ()
	Default Constructor. More...
	GenTorsionParams (core::Real k1_in, core::Real k2_in, core::Real k3_in, core::Real k4_in, core::Real f1_in, core::Real f2_in, core::Real f3_in, core::Real f4_in, core::Size mult_in)
	Constructor with input params. More...
	GenTorsionParams (core::Real k1_in, core::Real k2_in, core::Real k3_in, core::Real k4_in, core::Real f1_in, core::Real f2_in, core::Real f3_in, core::Real f4_in, core::Size mult_in, std::string torsion_type_in)
	Constructor with input params and torsion tag. More...
Real	energy (core::Real value) const
	getters More...
Real	deriv (core::Real value) const
bool	is_null () const
Size	multiplicity () const
Real	get_params (std::string keyword) const
Real	k (core::Size idx) const
void	set_offset (core::Real value)
Real	offset () const
void	k6 (core::Real value)
std::string	torsion_type () const

Private Member Functions
void	calculate_offset ()
	calculate offset to given torsion param set that makes minimum 0 More...

Private Attributes
Real	k1_
Real	k2_
Real	k3_
Real	k4_
Real	f1_
Real	f2_
Real	f3_
Real	f4_
Real	k6_
Size	mult_
Real	offset_
std::string	torsion_type_

Detailed Description

Parameter set for one torsion angle.

Stores a set of constants required for enumerating a Karplus cosine function given torsion angle as variable. This set of parameters are required for regular torsion term (gen_bonded_torsion) scoring. More descriptions below:

E = sum_over_n { k_n * cos(n*x - f_n) } + offset

E: Energy value n: order of Karplus equation, from 1 to 4 x: variable of the function (torsion angle in this case) k1_ ~ k4_: coefficients k_n for each order of n f1_ ~ f4_: phases f_n for each order of n k6_: sixth order k; used only in special case (not included in default params) mult_: the specificity/generality of a constraint; when there is ambiguity in multiple parameter set, one with lower mult_ is selected offset: constant offset to E torsion_type: string tag (just for labeling)

Constructor & Destructor Documentation

core::scoring::GenTorsionParams::GenTorsionParams ( )

inline

Default Constructor.

References calculate_offset().

core::scoring::GenTorsionParams::GenTorsionParams ( core::Real  k1_in, core::Real  k2_in, core::Real  k3_in, core::Real  k4_in, core::Real  f1_in, core::Real  f2_in, core::Real  f3_in, core::Real  f4_in, core::Size  mult_in  )

inline

Constructor with input params.

References calculate_offset().

core::scoring::GenTorsionParams::GenTorsionParams ( core::Real  k1_in, core::Real  k2_in, core::Real  k3_in, core::Real  k4_in, core::Real  f1_in, core::Real  f2_in, core::Real  f3_in, core::Real  f4_in, core::Size  mult_in, std::string  torsion_type_in  )

inline

Constructor with input params and torsion tag.

References calculate_offset().

Member Function Documentation

void core::scoring::GenTorsionParams::calculate_offset ( )

private

calculate offset to given torsion param set that makes minimum 0

References protocols::buns::energy.

Referenced by GenTorsionParams().

Real core::scoring::GenTorsionParams::deriv

(

core::Real

value

)

const

Referenced by core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), and core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion().

Real core::scoring::GenTorsionParams::energy

(

core::Real

value

)

const

getters

Referenced by core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), and core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion().

Real core::scoring::GenTorsionParams::get_params

(

std::string

keyword

)

const

bool core::scoring::GenTorsionParams::is_null ( ) const

inline

References k1_, k2_, k3_, k4_, and k6_.

Referenced by core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), and core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion().

Real core::scoring::GenTorsionParams::k ( core::Size  idx ) const

inline

References k1_, k2_, k3_, k4_, and k6_.

Referenced by core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), and core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion().

void core::scoring::GenTorsionParams::k6 ( core::Real  value )

inline

References k6_.

Referenced by core::scoring::GenericBondedPotential::read_database().

Size core::scoring::GenTorsionParams::multiplicity ( ) const

inline

References mult_.

Real core::scoring::GenTorsionParams::offset ( ) const

inline

References offset_.

Referenced by core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion(), and core::scoring::GenericBondedPotential::eval_residue_pair_energy_and_derivative_torsion().

void core::scoring::GenTorsionParams::set_offset ( core::Real  value )

inline

References offset_.

Referenced by core::scoring::GenericBondedPotential::modify_tors_params(), and core::scoring::GenericBondedPotential::read_database().

std::string core::scoring::GenTorsionParams::torsion_type ( ) const

inline

References torsion_type_.

Referenced by core::scoring::GenericBondedPotential::eval_residue_energy_and_derivative_torsion().

Member Data Documentation

Real core::scoring::GenTorsionParams::f1_

private

Real core::scoring::GenTorsionParams::f2_

private

Real core::scoring::GenTorsionParams::f3_

private

Real core::scoring::GenTorsionParams::f4_

private

Real core::scoring::GenTorsionParams::k1_

private

Referenced by is_null(), and k().

Real core::scoring::GenTorsionParams::k2_

private

Referenced by is_null(), and k().

Real core::scoring::GenTorsionParams::k3_

private

Referenced by is_null(), and k().

Real core::scoring::GenTorsionParams::k4_

private

Referenced by is_null(), and k().

Real core::scoring::GenTorsionParams::k6_

private

Referenced by is_null(), k(), and k6().

Size core::scoring::GenTorsionParams::mult_

private

Referenced by multiplicity().

Real core::scoring::GenTorsionParams::offset_

private

Referenced by offset(), and set_offset().

std::string core::scoring::GenTorsionParams::torsion_type_

private

Referenced by torsion_type().

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The documentation for this class was generated from the following files:

• src/core/scoring/GenericBondedPotential.hh
• src/core/scoring/GenericBondedPotential.cc