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Public Member Functions | Static Private Member Functions | Static Private Attributes | List of all members
core::scoring::disulfides::CentroidDisulfidePotential Class Reference

#include <CentroidDisulfidePotential.hh>

Inheritance diagram for core::scoring::disulfides::CentroidDisulfidePotential:
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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 Cb_Distance_FuncCOP cb_distance_func_
 
static Cen_Distance_FuncCOP cen_distance_func_
 
static CaCbCb_Angle_FuncCOP cacbcb_angle_func_
 
static NCaCaC_Dihedral_FuncCOP ncacac_dihedral_func_
 
static 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_sqThe distance between Cbetas squared
centroid_distance_sqThe distance between centroids squared
cacbcb_angle_1The Ca1-Cb1-Cb2 planar angle, in degrees
cacbcb_angle_2The Ca2-Cb2-Cb1 planar angle, in degrees
cacbcbca_dihedralThe Ca1-Cb1-Cb2-Ca2 dihedral angle
backbone_dihedralThe 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_distanceThe distance between Cbetas squared
centroid_distanceThe distance between centroids squared
cacbcb_angle_1The Ca1-Cb1-Cb2 planar angle, in degrees
cacbcb_angle_2The Ca2-Cb2-Cb1 planar angle, in degrees
cacbcbca_dihedralThe Ca1-Cb1-Cb2-Ca2 dihedral angle
backbone_dihedralThe 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::scoring::disulfides::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: