#include <CentroidDisulfidePotential.hh>

Inheritance diagram for core::scoring::disulfides::CentroidDisulfidePotential:

Public Member Functions
	CentroidDisulfidePotential ()

	~CentroidDisulfidePotential () override

void	score_disulfide (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Energy &cbcb_distance_score, core::Energy &centroid_distance_score, core::Energy &cacbcb_angle_1_score, core::Energy &cacbcb_angle_2_score, core::Energy &cacbcbca_dihedral_score, core::Energy &backbone_dihedral_score) const
	Calculates scoring terms for the disulfide bond specified. More...

void	score_disulfide (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real &cbcb_distance_sq, core::Real &centroid_distance_sq, core::Real &cacbcb_angle_1, core::Real &cacbcb_angle_2, core::Real &cacbcbca_dihedral, core::Real &backbone_dihedral, core::Energy &cbcb_distance_score, core::Energy &centroid_distance_score, core::Energy &cacbcb_angle_1_score, core::Energy &cacbcb_angle_2_score, core::Energy &cacbcbca_dihedral_score, core::Energy &backbone_dihedral_score, core::Real &cb_score_factor) const
	Calculates scoring terms and geometry. More...

bool	is_disulfide (core::conformation::Residue const &res1, core::conformation::Residue const &res2) const
	Decide whether there is a disulfide bond between two residues. More...

Static Private Member Functions
static void	disulfide_params (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Real &cbcb_distance_sq, core::Real &centroid_distance_sq, core::Real &cacbcb_angle_1, core::Real &cacbcb_angle_2, core::Real &cacbcbca_dihedral, core::Real &backbone_dihedral)
	calculates some degrees of freedom between two centroid cys residues More...

Static Private Attributes
static core::scoring::disulfides::Cb_Distance_FuncCOP	cb_distance_func_

static core::scoring::disulfides::Cen_Distance_FuncCOP	cen_distance_func_

static core::scoring::disulfides::CaCbCb_Angle_FuncCOP	cacbcb_angle_func_

static core::scoring::disulfides::NCaCaC_Dihedral_FuncCOP	ncacac_dihedral_func_

static core::scoring::disulfides::CaCbCbCa_Dihedral_FuncCOP	cacbcbca_dihedral_func_

static const core::Real	disulfide_cb_dist_cutoff
	the Cysteines with cb dist scores less than this threshold are very likely (99%) to be disulfide bonded. More...

Detailed Description

This class scores centroid disulfide bonds It is intended to be a singleton with a single instance held by ScoringManager.

The energy functions are derived from those present in Rosetta++

Constructor & Destructor Documentation

core::scoring::disulfides::CentroidDisulfidePotential::CentroidDisulfidePotential ( )

default

Constructor

core::scoring::disulfides::CentroidDisulfidePotential::~CentroidDisulfidePotential ( )

overridedefault

Deconstructor

Member Function Documentation

void core::scoring::disulfides::CentroidDisulfidePotential::disulfide_params	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		core::Real &	cbcb_distance_sq,
		core::Real &	centroid_distance_sq,
		core::Real &	cacbcb_angle_1,
		core::Real &	cacbcb_angle_2,
		core::Real &	cacbcbca_dihedral,
		core::Real &	backbone_dihedral
	)

staticprivate

calculates some degrees of freedom between two centroid cys residues

Parameters

cbcb_distance_sq	The distance between Cbetas squared
centroid_distance_sq	The distance between centroids squared
cacbcb_angle_1	The Ca1-Cb1-Cb2 planar angle, in degrees
cacbcb_angle_2	The Ca2-Cb2-Cb1 planar angle, in degrees
cacbcbca_dihedral	The Ca1-Cb1-Cb2-Ca2 dihedral angle
backbone_dihedral	The N-Ca1-Ca2-C2 dihedral angle

If one of the residues is glycine it will be substituted with an idealize alanine geometry for the calculations which require a Cb molecule.

centroid_distance requires CEN atoms be defined. If full atom residues are specified this function returns centroid_distance of -1.

Parameters

cbcb_distance	The distance between Cbetas squared
centroid_distance	The distance between centroids squared
cacbcb_angle_1	The Ca1-Cb1-Cb2 planar angle, in degrees
cacbcb_angle_2	The Ca2-Cb2-Cb1 planar angle, in degrees
cacbcbca_dihedral	The Ca1-Cb1-Cb2-Ca2 dihedral angle
backbone_dihedral	The N-Ca1-Ca2-C2 dihedral angle

References core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::CENTROID, and core::conformation::Residue::get_self_ptr().

bool core::scoring::disulfides::CentroidDisulfidePotential::is_disulfide	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2
	)		const

Decide whether there is a disulfide bond between two residues.

Does not require that the residues be cysteines, so if this is important you should check for CYS first. (The relaxed requirements are useful for design.)

Referenced by protocols::protein_interface_design::movers::DisulfideMover::disulfide_list().

void core::scoring::disulfides::CentroidDisulfidePotential::score_disulfide	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		core::Energy &	cbcb_distance_score,
		core::Energy &	centroid_distance_score,
		core::Energy &	cacbcb_angle_1_score,
		core::Energy &	cacbcb_angle_2_score,
		core::Energy &	cacbcbca_dihedral_score,
		core::Energy &	backbone_dihedral_score
	)		const

Calculates scoring terms for the disulfide bond specified.

Note: Equivalent to the expanded form, but discards geometry info

Referenced by core::energy_methods::CentroidDisulfideEnergy::residue_pair_energy().

void core::scoring::disulfides::CentroidDisulfidePotential::score_disulfide	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		core::Real &	cbcb_distance_sq,
		core::Real &	centroid_distance_sq,
		core::Real &	cacbcb_angle_1,
		core::Real &	cacbcb_angle_2,
		core::Real &	cacbcbca_dihedral,
		core::Real &	backbone_dihedral,
		core::Energy &	cbcb_distance_score,
		core::Energy &	centroid_distance_score,
		core::Energy &	cacbcb_angle_1_score,
		core::Energy &	cacbcb_angle_2_score,
		core::Energy &	cacbcbca_dihedral_score,
		core::Energy &	backbone_dihedral_score,
		core::Real &	cb_score_factor
	)		const

Calculates scoring terms and geometry.

If a full atom pose is given, centroid_distance_score will be zero.

If one of the residues is glycine it will be replaced with alanine for the scores which require a CB atom.

Note: distances are given squared to avoid calling std::sqrt unnecessarily

Member Data Documentation

CaCbCb_Angle_FuncCOP core::scoring::disulfides::CentroidDisulfidePotential::cacbcb_angle_func_

staticprivate

CaCbCbCa_Dihedral_FuncCOP core::scoring::disulfides::CentroidDisulfidePotential::cacbcbca_dihedral_func_

staticprivate

Cb_Distance_FuncCOP core::scoring::disulfides::CentroidDisulfidePotential::cb_distance_func_

staticprivate

Cen_Distance_FuncCOP core::scoring::disulfides::CentroidDisulfidePotential::cen_distance_func_

staticprivate

const Real core::scoring::disulfides::CentroidDisulfidePotential::disulfide_cb_dist_cutoff

staticprivate

the Cysteines with cb dist scores less than this threshold are very likely (99%) to be disulfide bonded.

NCaCaC_Dihedral_FuncCOP core::scoring::disulfides::CentroidDisulfidePotential::ncacac_dihedral_func_

staticprivate

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

src/core/scoring/disulfides/CentroidDisulfidePotential.hh
src/core/scoring/disulfides/CentroidDisulfidePotential.cc

Public Member Functions

Static Private Member Functions

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation