#include <EPRSpinLabel.hh>

Public Member Functions
	EPRSpinLabel ()
	Constructor. More...

	~EPRSpinLabel ()
	Destructor. More...

void	init_vdw () const
	Initialize object used to calculate centroid clashes. More...

utility::vector1< PseudoSL >	read_db_file (std::string const &name)
	Read DB file for a given type of spin label. More...

utility::vector1< PseudoSL > &	operator[] (PairSizeString const &res)
	Operator to return nnn-const PseudoSL from specific residue. More...

utility::vector1< PseudoSL > const &	at (PairSizeString const &res) const
	Return const PseudoSL from specific residue. More...

std::map< Size, Real >	histogram (utility::vector1< PairSizeString > const &residues, Size const &bins_per_a, int const &mod=0, Real const &stdev=1.0, std::map< Size, Real > const &dist_ids={})
	Returns histogram between coordinate sets for residues. More...

std::map< Size, Real >	histogram (utility::vector1< PseudoSL > const &res1_coords, utility::vector1< PseudoSL > const &res2_coords, Size const &bins_per_a, int const &mod=0, Real const &stdev=1.0, std::map< Size, Real > const &dist_ids={})
	Return histogram for pair of coordinate sets. More...

std::map< Size, Real >	histogram (PairSizeString const &res1, PairSizeString const &res2, Size const &bins_per_a, int const &mod=0, Real const &stdev=1.0, std::map< Size, Real > const &dist_ids={})
	Returns histogram between coordinate sets for residues. More...

void	label (PairSizeString const &res_label, pose::Pose const &pose, bool const &skip_clash_eval=false)
	Label a residue with a certain spin label. More...

std::map< Size, Real >	normalize (std::map< Size, Real > sim_map) const
	Normalize distribution so that the sum is equal to 1.0. More...

utility::vector1< PseudoSL >	calc_sl_for_res (Size const &res, pose::Pose const &pose, utility::vector1< PseudoSL > const &sl_vec, bool const &skip_clash_eval=false, Real const &min_rad=0.0)
	Get positions of unpaired electrons at a residue. More...

Real	weight (Size const &res1, numeric::xyzVector< core::Real > const &clash_xyz, Real w, pose::Pose const &pose, Real const &rad)
	retrieve weight for given coordinate More...

Real	cutoff () const
	Getter for cutoff for weights. More...

void	load_custom_electrons (std::map< Size, utility::vector1< PseudoSL > > const &all_coords)
	Allows a custom set of electrons to be read without superimposition. More...

void	label_everything (pose::Pose &pose, utility::vector1< PairSizeString > const &residues, bool const &skip_clash_eval)
	Goes through every residue in provided list and calculates. More...

Private Member Functions
numeric::xyzVector< Real >	bulk (numeric::xyzVector< Real > const &coord, numeric::xyzVector< Real > const &cb) const
	Returns the center of mass between coordinate and CB. More...

Private Attributes
std::map< PairSizeString, utility::vector1< PseudoSL > >	coords_
	Coordinates for each residue being stored. More...

std::map< Size, utility::vector1< PseudoSL > >	custom_coords_
	Custom coordinates (residue-specific) More...

Real	cutoff_ = 0.001
	Cutoff for clash evaluation. More...

std::string	path_ = "scoring/epr_deer/"
	Path for files describing default PseudoSL objects to read. More...

Constructor & Destructor Documentation

◆ EPRSpinLabel()

core::scoring::epr_deer::EPRSpinLabel::EPRSpinLabel ( )

Constructor.

References init_vdw().

◆ ~EPRSpinLabel()

core::scoring::epr_deer::EPRSpinLabel::~EPRSpinLabel ( )

Destructor.

Member Function Documentation

◆ at()

utility::vector1< PseudoSL > const & core::scoring::epr_deer::EPRSpinLabel::at ( PairSizeString const & res ) const

Return const PseudoSL from specific residue.

Parameters

res	Residue info (number and spin label type)

Returns: Coords corresponding to residue

References coords_.

◆ bulk()

numeric::xyzVector< Real > core::scoring::epr_deer::EPRSpinLabel::bulk	(	numeric::xyzVector< Real > const &	coord,
		numeric::xyzVector< Real > const &	cb
	)		const

private

Returns the center of mass between coordinate and CB.

Parameters

coord	Coordinate xyz
cb	CB coordinate

Returns: XYZ of bulk / center of mass of nitroxide ring @detail See del Alamo et al 2020 Biophysical Journal for details on why 0.875 was computed/chosen

Referenced by calc_sl_for_res().

◆ calc_sl_for_res()

utility::vector1< PseudoSL > core::scoring::epr_deer::EPRSpinLabel::calc_sl_for_res	(	Size const &	res,
		pose::Pose const &	pose,
		utility::vector1< PseudoSL > const &	sl_vec,
		bool const &	skip_clash_eval = `false`,
		Real const &	min_rad = `0.0`
	)

Get positions of unpaired electrons at a residue.

Parameters

res	Residue number
pose	Pose for clash eval
sl_vec	Vector of PseudoSLs, which have positions of unpaired e
skip_clash_eval	Exactly what it suggested by the title
min_rad	Lowest radius for clash eval to check

Returns: Vector of PseudoSLs in local coordinate frame of residue

References bulk(), cutoff_, core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::scoring::epr_deer::vrt_cb_(), weight(), and core::conformation::Residue::xyz().

Referenced by label().

◆ cutoff()

Real core::scoring::epr_deer::EPRSpinLabel::cutoff ( ) const

Getter for cutoff for weights.

Returns: Weight cutoff

References cutoff_.

Referenced by protocols::simple_moves::DEEROptimizeCoordsMover::init_coords().

◆ histogram() [1/3]

std::map< Size, Real > core::scoring::epr_deer::EPRSpinLabel::histogram	(	PairSizeString const &	res1,
		PairSizeString const &	res2,
		Size const &	bins_per_a,
		int const &	mod = `0`,
		Real const &	stdev = `1.0`,
		std::map< Size, Real > const &	dist_ids = `{}`
	)

Returns histogram between coordinate sets for residues.

Parameters

res1	Residue 1
res2	Residue 2
bins_per_a	Granularity of histogram (bins per angstrom)
mod	What to add to the X-axis
dist_ids	If a custom X-axis is used (default: empty)

Returns: Histogram with X- and Y-values being keys and values @detail Note: the X-axis = bins_per_a * distance, rounded to an int

References coords_, histogram(), and core::scoring::epr_deer::TR().

◆ histogram() [2/3]

std::map< Size, Real > core::scoring::epr_deer::EPRSpinLabel::histogram	(	utility::vector1< PairSizeString > const &	residues,
		Size const &	bins_per_a,
		int const &	mod = `0`,
		Real const &	stdev = `1.0`,
		std::map< Size, Real > const &	dist_ids = `{}`
	)

Returns histogram between coordinate sets for residues.

Parameters

residues	Residues contributing to histogram
bins_per_a	Granularity of histogram (bins per angstrom)
mod	What to add to the X-axis
dist_ids	If a custom X-axis is used (default: empty)

Returns: Histogram with X- and Y-values being keys and values @detail Note: the X-axis = bins_per_a * distance, rounded to an int @detail Note: Equal labeling assumed for all sites @detail This matters if residues.size() > 2

References core::scoring::epr_deer::add_to_map(), and normalize().

Referenced by core::energy_methods::DEEREnergy::get_score(), and histogram().

◆ histogram() [3/3]

std::map< Size, Real > core::scoring::epr_deer::EPRSpinLabel::histogram	(	utility::vector1< PseudoSL > const &	res1_coords,
		utility::vector1< PseudoSL > const &	res2_coords,
		Size const &	bins_per_a,
		int const &	mod = `0`,
		Real const &	stdev = `1.0`,
		std::map< Size, Real > const &	dist_ids = `{}`
	)

Return histogram for pair of coordinate sets.

Parameters

res1_coords	Pair of PseudoSL coords for res1
res2_coords	Pair of PseudoSL coords for res2
bins_per_a	Bins per angstrom for distribution
mod	How much to shift X-axis
stdev	St deviation of gauss used to convolute pairwise dists
dist_ids	If a custom X-axis is used (default: empty)

Returns: Histogram with X- and Y-values being keys and values @detail Note: the X-axis = bins_per_a * distance, rounded to an int

References core::scoring::epr_deer::add_to_map(), core::scoring::epr_deer::gauss(), protocols::mean_field::max(), normalize(), and protocols::noesy_assign::round().

◆ init_vdw()

void core::scoring::epr_deer::EPRSpinLabel::init_vdw ( ) const

Initialize object used to calculate centroid clashes.

References core::scoring::epr_deer::atom_vdw_, and core::chemical::CENTROID.

Referenced by EPRSpinLabel().

◆ label()

void core::scoring::epr_deer::EPRSpinLabel::label	(	PairSizeString const &	res_label,
		pose::Pose const &	pose,
		bool const &	skip_clash_eval = `false`
	)

Label a residue with a certain spin label.

Parameters

res	Residue index
label	SL type
pose	Pose used for superimposition
skip_clash_eval	Whether clash evaluation is skipped @detail Clashes are skipped for custom coordinates for reasons @detail relating to the way they have been calculated

References calc_sl_for_res(), coords_, custom_coords_, core::scoring::epr_deer::deflt_coords_, and read_db_file().

Referenced by protocols::simple_moves::DEEROptimizeCoordsMover::init_coords(), label_everything(), and protocols::simple_moves::DEEROptimizeCoordsMover::print_coords().

◆ label_everything()

void core::scoring::epr_deer::EPRSpinLabel::label_everything	(	pose::Pose &	pose,
		utility::vector1< PairSizeString > const &	residues,
		bool const &	skip_clash_eval
	)

Goes through every residue in provided list and calculates.

Parameters

pose	Pose to label
residues	Residues that need to be labeled
skip_clash_eval	Whether clash evaluation should be skipped

References label().

Referenced by core::energy_methods::DEEREnergy::get_score().

◆ load_custom_electrons()

void core::scoring::epr_deer::EPRSpinLabel::load_custom_electrons ( std::map< Size, utility::vector1< PseudoSL > > const & all_coords )

Allows a custom set of electrons to be read without superimposition.

Parameters

all_coords Custom residue-specific PseudoSLs

References custom_coords_.

Referenced by core::scoring::epr_deer::DEERIO::pull_coords().

◆ normalize()

std::map< Size, Real > core::scoring::epr_deer::EPRSpinLabel::normalize ( std::map< Size, Real > sim_map ) const

Normalize distribution so that the sum is equal to 1.0.

Parameters

sim_map Simulated DEER distribution

Returns: Identical std::map except values add up to 1.0

References protocols::analysis::total.

Referenced by histogram().

◆ operator[]()

utility::vector1< PseudoSL > & core::scoring::epr_deer::EPRSpinLabel::operator[] ( PairSizeString const & res )

Operator to return nnn-const PseudoSL from specific residue.

Parameters

res	Residue info (number and spin label type)

Returns: Coords corresponding to residue

References coords_.

◆ read_db_file()

utility::vector1< PseudoSL > core::scoring::epr_deer::EPRSpinLabel::read_db_file ( std::string const & name )

Read DB file for a given type of spin label.

Parameters

Name	of file/SL type

Returns: PseudoSLs used for simulation of DEER distributions

References path_, protocols::sparta::split(), and protocols::hybridization::val.

Referenced by label().

◆ weight()

Real core::scoring::epr_deer::EPRSpinLabel::weight	(	Size const &	res1,
		numeric::xyzVector< core::Real > const &	clash_xyz,
		Real	w,
		pose::Pose const &	pose,
		Real const &	rad
	)

retrieve weight for given coordinate

Parameters

res1	Residue over which the coordinate is being superimposed
clash_xyz	Coordinate used for clash calculation
w	Weight, passed by value since we need a new obj to modify
pose	Pose with all the residues we check for clash evaluation
vdw_rad	Radius of the clash_xyz atom to consider

Returns: Weight of PseudoSL at position given local environment of pose

References core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_backbone(), core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::scoring::epr_deer::atom_vdw_, core::pose::Pose::energies(), core::pose::Pose::is_fullatom(), core::conformation::Residue::is_virtual_residue(), core::chemical::AtomType::lj_radius(), protocols::mean_field::min(), core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), core::scoring::vdw, and core::conformation::Atom::xyz().

Referenced by calc_sl_for_res().

Member Data Documentation

◆ coords_

std::map< PairSizeString, utility::vector1< PseudoSL > > core::scoring::epr_deer::EPRSpinLabel::coords_

private

Coordinates for each residue being stored.

Referenced by at(), histogram(), label(), and operator[]().

◆ custom_coords_

std::map< Size, utility::vector1< PseudoSL > > core::scoring::epr_deer::EPRSpinLabel::custom_coords_

private

Custom coordinates (residue-specific)

Referenced by label(), and load_custom_electrons().

◆ cutoff_

Real core::scoring::epr_deer::EPRSpinLabel::cutoff_ = 0.001

private

Cutoff for clash evaluation.

Referenced by calc_sl_for_res(), and cutoff().

◆ path_

std::string core::scoring::epr_deer::EPRSpinLabel::path_ = "scoring/epr_deer/"

private

Path for files describing default PseudoSL objects to read.

Referenced by read_db_file().

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

src/core/scoring/epr_deer/EPRSpinLabel.hh
src/core/scoring/epr_deer/EPRSpinLabel.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ EPRSpinLabel()

◆ ~EPRSpinLabel()

Member Function Documentation

◆ at()

◆ bulk()

◆ calc_sl_for_res()

◆ cutoff()

◆ histogram() [1/3]

◆ histogram() [2/3]

◆ histogram() [3/3]

◆ init_vdw()

◆ label()

◆ label_everything()

◆ load_custom_electrons()

◆ normalize()

◆ operator[]()

◆ read_db_file()

◆ weight()

Member Data Documentation

◆ coords_

◆ custom_coords_

◆ cutoff_

◆ path_