#include <DEERDataCache.hh>

Inheritance diagram for core::scoring::epr_deer::DEERDataCache:

Public Member Functions
	DEERDataCache ()=default
	Constructor. More...

	DEERDataCache (DEERDataCache const &)=default
	Copy constructor. More...

	~DEERDataCache () override
	Destructor. More...

basic::datacache::CacheableDataOP	clone () const override
	Copy function, overrides parent class. More...

metrics::DEERDataOP &	operator[] (Size const &i)
	Returns non-const data for a given ID (or nullptr if empty) More...

metrics::DEERDataOP const &	at (Size const &i) const
	Returns const data for a given ID (or nullptr if empty) More...

void	append (metrics::DEERDataOP const &data)
	Adds DEERDataOP object to DEERDataCache at earliest spot. More...

void	append (metrics::DEERDataOP const &data, Size const &i)
	Adds DEERDataOP object to DEERDataCache at predefined spot. More...

void	push_back (metrics::DEERDataOP const &data)
	Adds DEERDataOP object to DEERDataCache at last spot. More...

Size	size () const
	Returns number of DEERDataOPs stored here. More...

std::set< Size >	indices () const
	Returns set of keys in the data map. More...

void	fetch_and_organize_data (pose::Pose const &pose)
	Fetches are parses data from command line using DEERIO object. More...

void	set_up_residues ()
	Initializer function following reading of data. More...

std::map< Size, Real >	edge (Size const &rsd1, Size const &rsd2) const
	Returns number of edges corresponding to the pair of residues. More...

utility::vector1< std::pair < Size, std::string > >	labeled_residues () const
	Returns set of residues and appropriate spin labels to compute. More...

std::set< std::string >	label_types () const
	Returns list of residues spin labels to compute. More...

utility::vector1< EPRSpinLabel >	labels () const
	Stores the coordinates for residues with CUSTOM spin labels. More...

void	set_labels (utility::vector1< EPRSpinLabel > const &labels)
	Stores the normalized coordinates for residues with CUSTOM spin labels. More...

utility::vector1< Real > const &	sl_weights () const
	Returns the weights assigned to CUSTOM spin label coordinates. More...

void	set_sl_weights (utility::vector1< Real > const &weights)
	Stores the weights assigned to CUSTOM spin label coordinates. More...

bool	has_f1_force (Size const &res) const
	Returns if F1 force is stored for residue. More...

bool	has_f2_force (Size const &res) const
	Checks if residues has an F1 force, used for gradient minimzation. More...

void	f1_force (Size const &res, numeric::xyzVector< Real > const &vec)
	Sets F1 force stored for residue. More...

void	f2_force (Size const &res, numeric::xyzVector< Real > const &vec)
	Sets F2 force stored for residue. More...

numeric::xyzVector< Real > const &	f1_force (Size const &res) const
	Returns the F1 force applied to a residue. More...

numeric::xyzVector< Real > const &	f2_force (Size const &res) const
	Returns the F2 force applied to a residue. More...

void	delete_data (core::Size const &i)
	Removes data at specific spot and reparameterizes. More...

bool	has_data (core::Size const &i)
	Check and return if data in spot is occupied. More...

Private Attributes
std::map< Size, metrics::DEERDataOP >	data_
	Data container. More...

std::map< Size, numeric::xyzVector< Real > >	f1_forces_
	Container for F1 forces. More...

std::map< Size, numeric::xyzVector< Real > >	f2_forces_
	Container for F2 forces. More...

std::set< std::pair< Size, std::string > >	labeled_residues_
	Set of all labeled residues (string is SL type) More...

std::map< std::pair< Size, Size >, std::map< Size, Real > >	pair_data_
	Map of IDs and weights corresponding to residue pairs. More...

utility::vector1< EPRSpinLabel >	spin_labels_
	List of CUSTOM EPRSpin labels (obtained by multilateration) More...

utility::vector1< Real >	sl_weights_
	Weights for CUSTOM labels (obtained by multilateration) More...

Constructor & Destructor Documentation

core::scoring::epr_deer::DEERDataCache::DEERDataCache ( )

default

Constructor.

Referenced by clone().

core::scoring::epr_deer::DEERDataCache::DEERDataCache ( DEERDataCache const & )

default

Copy constructor.

core::scoring::epr_deer::DEERDataCache::~DEERDataCache ( )

override

Destructor.

Member Function Documentation

void core::scoring::epr_deer::DEERDataCache::append ( metrics::DEERDataOP const & data )

Adds DEERDataOP object to DEERDataCache at earliest spot.

Parameters

data	metrics::DEERDataOP object to insert
data	metrics::DEERDataOP object to insert Not threadsafe

References data_, and size().

void core::scoring::epr_deer::DEERDataCache::append	(	metrics::DEERDataOP const &	data,
		Size const &	i
	)

Adds DEERDataOP object to DEERDataCache at predefined spot.

Parameters

data	Object to insert
i	Position to insert object
data	Object to insert
i	Position to insert object Not threadsafe

References data_.

metrics::DEERDataOP const & core::scoring::epr_deer::DEERDataCache::at ( Size const & i ) const

Returns const data for a given ID (or nullptr if empty)

Parameters

i	Index of data object ()

Returns: Requested DEERDataOP object (or nullptr)

References data_, and core::id::to_string().

basic::datacache::CacheableDataOP core::scoring::epr_deer::DEERDataCache::clone ( ) const

override

Copy function, overrides parent class.

References DEERDataCache().

void core::scoring::epr_deer::DEERDataCache::delete_data ( core::Size const & i )

Removes data at specific spot and reparameterizes.

Parameters

i	Key of data in map

References data_, and set_up_residues().

std::map< Size, Real > core::scoring::epr_deer::DEERDataCache::edge	(	Size const &	rsd1,
		Size const &	rsd2
	)		const

Returns number of edges corresponding to the pair of residues.

Parameters

rsd1	identity of first residue (AA sequence)
rsd2	identity of second residue (AA sequence)

Returns: Map with edges and weights for residue pair

References protocols::mean_field::max(), protocols::mean_field::min(), and pair_data_.

Referenced by set_up_residues().

void core::scoring::epr_deer::DEERDataCache::f1_force	(	Size const &	res,
		numeric::xyzVector< Real > const &	vec
	)

Sets F1 force stored for residue.

Parameters

res	Residue ID of interest
vec	Vector of F1 force

References f1_forces_.

numeric::xyzVector< Real > const & core::scoring::epr_deer::DEERDataCache::f1_force ( Size const & res ) const

Returns the F1 force applied to a residue.

Parameters

res	Residue ID of interest

Returns: F1 force

References f1_forces_.

void core::scoring::epr_deer::DEERDataCache::f2_force	(	Size const &	res,
		numeric::xyzVector< Real > const &	vec
	)

Sets F2 force stored for residue.

Parameters

res	Residue ID of interest
vec	Vector of F2 force

References f2_forces_.

numeric::xyzVector< Real > const & core::scoring::epr_deer::DEERDataCache::f2_force ( Size const & res ) const

Returns the F2 force applied to a residue.

Parameters

res	Residue ID of interest

Returns: F2 force

References f2_forces_.

void core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data ( pose::Pose const & pose )

Fetches are parses data from command line using DEERIO object.

Parameters

pose	Pose object from which data will be fetched

References data_, core::scoring::epr_deer::DEERIO::generate_data(), core::scoring::epr_deer::DEERIO::pull_coords(), set_up_residues(), sl_weights_, and spin_labels_.

bool core::scoring::epr_deer::DEERDataCache::has_data ( core::Size const & i )

Check and return if data in spot is occupied.

Parameters

i	Key to check

Returns: Whether key is being used

References data_.

bool core::scoring::epr_deer::DEERDataCache::has_f1_force ( Size const & res ) const

Returns if F1 force is stored for residue.

Parameters

res	Residue ID of interest

Returns: True or false if residue is stored in F1 force map

References f1_forces_.

bool core::scoring::epr_deer::DEERDataCache::has_f2_force ( Size const & res ) const

Checks if residues has an F1 force, used for gradient minimzation.

Returns if F2 force is stored for residue.

Parameters

res	Residue ID of interest

Returns: True or false if residue is stored in F2 force map

References f2_forces_.

std::set< Size > core::scoring::epr_deer::DEERDataCache::indices ( ) const

Returns set of keys in the data map.

Returns: Set object containing all keys in map

References data_.

std::set< std::string > core::scoring::epr_deer::DEERDataCache::label_types ( ) const

Returns list of residues spin labels to compute.

Returns: Labels required by data

References labeled_residues_.

utility::vector1< std::pair< Size, std::string > > core::scoring::epr_deer::DEERDataCache::labeled_residues ( ) const

Returns set of residues and appropriate spin labels to compute.

Returns: Residues in data Returns vector of residues and appropriate spin labels to compute; Residues in data

References labeled_residues_.

utility::vector1< EPRSpinLabel > core::scoring::epr_deer::DEERDataCache::labels ( ) const

Stores the coordinates for residues with CUSTOM spin labels.

Returns: utility::vector1< EPRSpinLabel > of custom SL rotamers in data

References spin_labels_.

Referenced by set_labels().

metrics::DEERDataOP & core::scoring::epr_deer::DEERDataCache::operator[] ( Size const & i )

Returns non-const data for a given ID (or nullptr if empty)

Parameters

i	Index of data object ()

Returns: Requested DEERDataOP object (or nullptr)

References data_, and core::id::to_string().

void core::scoring::epr_deer::DEERDataCache::push_back ( metrics::DEERDataOP const & data )

Adds DEERDataOP object to DEERDataCache at last spot.

Parameters

data	metrics::DEERDataOP object to insert
data	metrics::DEERDataOP object to insert Not threadsafe

References data_.

void core::scoring::epr_deer::DEERDataCache::set_labels ( utility::vector1< EPRSpinLabel > const & labels )

Stores the normalized coordinates for residues with CUSTOM spin labels.

Parameters

labels Custom rotamers across model

References labels(), and spin_labels_.

void core::scoring::epr_deer::DEERDataCache::set_sl_weights ( utility::vector1< Real > const & weights )

Stores the weights assigned to CUSTOM spin label coordinates.

Parameters

weights Vector of weights for custom SLs

References sl_weights_.

void core::scoring::epr_deer::DEERDataCache::set_up_residues ( )

Initializer function following reading of data.

References data_, edge(), labeled_residues_, protocols::mean_field::max(), protocols::mean_field::min(), core::scoring::pair, and pair_data_.

Referenced by delete_data(), and fetch_and_organize_data().

Size core::scoring::epr_deer::DEERDataCache::size ( ) const

Returns number of DEERDataOPs stored here.

Returns: Size object ofnumber of DEERDataOPs in map Note: output could be less than data_.rbegin()->first)

References data_.

Referenced by append().

utility::vector1< Real > const & core::scoring::epr_deer::DEERDataCache::sl_weights ( ) const

Returns the weights assigned to CUSTOM spin label coordinates.

Returns: Vector of weights

References sl_weights_.

Member Data Documentation

std::map< Size, metrics::DEERDataOP > core::scoring::epr_deer::DEERDataCache::data_

private

Data container.

Referenced by append(), at(), delete_data(), fetch_and_organize_data(), has_data(), indices(), operator[](), push_back(), set_up_residues(), and size().

std::map< Size, numeric::xyzVector< Real > > core::scoring::epr_deer::DEERDataCache::f1_forces_

private

Container for F1 forces.

Referenced by f1_force(), and has_f1_force().

std::map< Size, numeric::xyzVector< Real > > core::scoring::epr_deer::DEERDataCache::f2_forces_

private

Container for F2 forces.

Referenced by f2_force(), and has_f2_force().

std::set< std::pair< Size, std::string > > core::scoring::epr_deer::DEERDataCache::labeled_residues_

private

Set of all labeled residues (string is SL type)

Referenced by label_types(), labeled_residues(), and set_up_residues().

std::map< std::pair< Size, Size >, std::map< Size, Real > > core::scoring::epr_deer::DEERDataCache::pair_data_

private

Map of IDs and weights corresponding to residue pairs.

Referenced by edge(), and set_up_residues().

utility::vector1< Real > core::scoring::epr_deer::DEERDataCache::sl_weights_

private

Weights for CUSTOM labels (obtained by multilateration)

Referenced by fetch_and_organize_data(), set_sl_weights(), and sl_weights().

utility::vector1< EPRSpinLabel > core::scoring::epr_deer::DEERDataCache::spin_labels_

private

List of CUSTOM EPRSpin labels (obtained by multilateration)

Referenced by fetch_and_organize_data(), labels(), and set_labels().

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

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

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation