core::scoring::disulfides::DisulfideMatchingPotential Class Reference

#include <DisulfideMatchingPotential.hh>

Inheritance diagram for core::scoring::disulfides::DisulfideMatchingPotential:

Public Member Functions
	DisulfideMatchingPotential ()
	~DisulfideMatchingPotential () override
void	score_disulfide (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Energy &match_t, core::Energy &match_r, core::Energy &match_rt, bool const mirror=false) const
	Calculates scoring terms for the disulfide bond specified. More...
Energy	compute_matching_energy (pose::Pose const &pose) const

Private Member Functions
core::kinematics::RT	disulfide_RT (core::conformation::Residue const &res1, core::conformation::Residue const &res2, bool const mirror=false) const
	calculates RT object for residue pair More...

Private Attributes
disulfides::DisulfideMatchingDatabase	matching_database_

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

DisulfideMatchingPotential()

core::scoring::disulfides::DisulfideMatchingPotential::DisulfideMatchingPotential ( )

default

Constructor

~DisulfideMatchingPotential()

core::scoring::disulfides::DisulfideMatchingPotential::~DisulfideMatchingPotential ( )

overridedefault

Deconstructor

Member Function Documentation

compute_matching_energy()

Energy core::scoring::disulfides::DisulfideMatchingPotential::compute_matching_energy

(

pose::Pose const &

pose

)

const

References core::pose::Pose::conformation(), core::conformation::disulfide_bonds(), core::pose::Pose::residue(), and score_disulfide().

disulfide_RT()

core::kinematics::RT core::scoring::disulfides::DisulfideMatchingPotential::disulfide_RT ( core::conformation::Residue const &  res1, core::conformation::Residue const &  res2, bool const  mirror = false  ) const

private

calculates RT object for residue pair

calculates some degrees of freedom between two centroid cys residues

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::atom(), core::conformation::Residue::atom_index(), core::scoring::disulfides::RT_helper::RT_from_epos(), and core::conformation::Atom::xyz().

Referenced by score_disulfide().

score_disulfide()

void core::scoring::disulfides::DisulfideMatchingPotential::score_disulfide	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		core::Energy &	match_t,
		core::Energy &	match_r,
		core::Energy &	match_rt,
		bool const	mirror = false
	)		const

Calculates scoring terms for the disulfide bond specified.

Calculates scoring terms.

References core::kinematics::distance(), disulfide_RT(), core::scoring::disulfides::DisulfideMatchingDatabase::get_all_disulfides(), core::kinematics::RT::get_rotation(), core::kinematics::RT::get_translation(), and matching_database_.

Referenced by protocols::pose_sewing::movers::OmnibusDisulfideAnalysisLabelerMover::apply(), protocols::denovo_design::DisulfidizeMover::check_disulfide_match_rt(), compute_matching_energy(), protocols::simple_moves::DisulfideInsertionMover::determine_cyclization_viability(), and core::energy_methods::DisulfideMatchingEnergy::residue_pair_energy().

Member Data Documentation

matching_database_

disulfides::DisulfideMatchingDatabase core::scoring::disulfides::DisulfideMatchingPotential::matching_database_

private

Referenced by score_disulfide().

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

• src/core/scoring/disulfides/DisulfideMatchingPotential.hh
• src/core/scoring/disulfides/DisulfideMatchingPotential.cc