#include <CHIEnergyFunction.hh>

Inheritance diagram for core::scoring::carbohydrates::CHIEnergyFunction:

Public Member Functions
	CHIEnergyFunction ()
	Default constructor. More...

virtual	~CHIEnergyFunction ()

Energy	operator() (LinkageType type, Angle x) const

Real	evaluate_derivative (LinkageType type, Angle x) const

Private Member Functions
Energy	evaluate_term (LinkageType type, uint i, Angle x) const

Energy	evaluate_function (LinkageType type, Angle x) const

void	init ()

Private Attributes
utility::vector1 < utility::vector1< Real > >	a_

utility::vector1 < utility::vector1< Real > >	b_

utility::vector1 < utility::vector1< Real > >	c_

utility::vector1< Real >	d_

Detailed Description

This is an implementation of the "CarboHydrate Intrinsic" (CHI) energy function developed by Woods Lab.
The Gaussian parameters for the function depend on whether the glycosidic bond in question is a phi or psi angle.
The parameters further depend on if the phi angles are at alpha or beta linkages and on if the psi angles are at ->2-axial, ->3-equatorial, or ->4-axial OR ->2-equatorial, ->3-axial, or ->4-equatorial linkages.
The function has not been developed for ->6 linkages (with omega angles). A.K. Nivedha et al. J. Comput. Chem. 2014, 35, 526-39

Definition at line 40 of file CHIEnergyFunction.hh.

Constructor & Destructor Documentation

core::scoring::carbohydrates::CHIEnergyFunction::CHIEnergyFunction ( )

Default constructor.

This class is only intended to be instantiated by the ScoringManager.

Definition at line 42 of file CHIEnergyFunction.cc.

References init().

core::scoring::carbohydrates::CHIEnergyFunction::~CHIEnergyFunction ( )

virtual

Definition at line 47 of file CHIEnergyFunction.cc.

Member Function Documentation

Real core::scoring::carbohydrates::CHIEnergyFunction::evaluate_derivative	(	LinkageType	type,
		core::Angle	x
	)		const

E'(x) = Sum of -2((x-b)/c)[ae^-((x-b)^2/c)], where the parameters for a, b, and c depend on the linkage type.

Parameters

<x>	an angle, in degrees, between 0 and 360: phi, if type is ALPHA_LINKS or BETA_LINKS; psi, if type is _2AX_3EQ_4AX_LINKS or _2EQ_3AX_4EQ_LINKS A.K. Nivedha et al. J. Comput. Chem. 2014, 35, 526-39

Definition at line 68 of file CHIEnergyFunction.cc.

References a_, b_, c_, evaluate_term(), and core::chemical::element::N.

Referenced by core::scoring::methods::carbohydrates::SugarBackboneEnergy::eval_residue_dof_derivative().

Energy core::scoring::carbohydrates::CHIEnergyFunction::evaluate_function	(	LinkageType	type,
		core::Angle	x
	)		const

private

Definition at line 131 of file CHIEnergyFunction.cc.

References a_, d_, protocols::comparative_modeling::features::E, evaluate_term(), and core::chemical::element::N.

Referenced by operator()().

Energy core::scoring::carbohydrates::CHIEnergyFunction::evaluate_term	(	LinkageType	type,
		uint	i,
		core::Angle	x
	)		const

private

Definition at line 124 of file CHIEnergyFunction.cc.

References a_, b_, and c_.

Referenced by evaluate_derivative(), and evaluate_function().

void core::scoring::carbohydrates::CHIEnergyFunction::init ( void )

private

Definition at line 83 of file CHIEnergyFunction.cc.

References core::scoring::carbohydrates::_2AX_3EQ_4AX_LINKS, core::scoring::carbohydrates::_2EQ_3AX_4EQ_LINKS, a_, core::scoring::carbohydrates::ALPHA_LINKS, b_, core::scoring::carbohydrates::BETA_LINKS, c_, d_, protocols::abinitio::filename(), core::scoring::carbohydrates::FIRST_LINK_TYPE, core::scoring::carbohydrates::N_LINK_TYPES, and core::scoring::carbohydrates::read_Gaussian_parameters_from_database_file().

Referenced by CHIEnergyFunction().

Energy core::scoring::carbohydrates::CHIEnergyFunction::operator()	(	LinkageType	type,
		core::Angle	x
	)		const

E(x) = d + Sum of ae^-((x-b)^2/c), where the parameters for a, b, c, and d depend on the linkage type.

Parameters

<x>	an angle, in degrees phi (between -180 and 180), if type is ALPHA_LINKS or BETA_LINKS; psi (between 0 and 360), if type is _2AX_3EQ_4AX_LINKS or _2EQ_3AX_4EQ_LINKS A.K. Nivedha et al. J. Comput. Chem. 2014, 35, 526-39

Definition at line 58 of file CHIEnergyFunction.cc.

References evaluate_function().