#include <DEERIO.hh>

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

	DEERIO (DEERIO const &io)=default
	Copy Constructor. More...

	~DEERIO ()=default
	Destructor. More...

SplitLine	split_line (std::string const &line) const
	Split an input line into vector of strings. More...

std::map< Size, metrics::DEERDataOP >	generate_data (core::pose::Pose const &pose) const
	Generates the data for use. Core function. More...

std::map< Size, SplitLines >	parse_input () const
	Parses file. More...

metrics::DEERDataOP	parse_data (pose::Pose const &pose, SplitLines const &lines) const
	Parse the input lines into actual data containers. More...

metrics::DEERDataOP	parse_decay_data (pose::Pose const &pose, std::map< std::string, SplitLines > const &sorted_data) const
	Parse inputs lines into DEERDecayDataOP. More...

metrics::DEERDataOP	parse_bounds_data (pose::Pose const &pose, std::map< std::string, SplitLines > const &sorted_data) const
	Parse inputs lines into DEERDistanceBoundsOP. More...

metrics::DEERDataOP	parse_dist_data (pose::Pose const &pose, std::map< std::string, SplitLines > const &sorted_data) const
	Parse inputs lines into DEERDistanceDistributionOP. More...

metrics::DEERDataOP	parse_dist_info_lines (SplitLines const &info_lines) const
	Parses lines labeled "INFO" into information usable by Rosetta. More...

void	parse_dist_lines (SplitLines const &dist_lines, metrics::DEERDataOP data) const
	Parses lines labeled "DIST" into information usable by Rosetta. More...

metrics::DEERDataOP	parse_dist_datatype (SplitLines const &info_lines) const
	Determines function used by DEERDistanceDistribution. More...

void	parse_bounds_lines (SplitLines const &bounds_lines, metrics::DEERDataOP bounds_data) const
	Parses data for DEERDistanceBounds object. More...

void	parse_decay_info_lines (SplitLines const &info_lines, metrics::DEERDataOP data) const
	Parses information data for DEERDecayData object. More...

void	parse_decay_lines (SplitLines const &decay_lines, metrics::DEERDataOP &data) const
	Parses decay data for DEERDecayData object. More...

utility::vector1< PairSizeString >	parse_desc_lines (pose::Pose const &pose, SplitLines const &desc_lines) const
	Parse input lines for information on residues involved in data. More...

utility::vector1< std::pair< EPRSpinLabel, Real > >	pull_coords (pose::Pose const &pose) const
	Parse coordinate files for custom spin labels. More...

Private Attributes
Size const	ANGSTROM_LIMIT_ = 100
	Defines the default max distance (for DEERDecayData objects) More...

Size const	BINS_PER_A_ = 2
	Defines the default bins per angstrom in distributions. More...

utility::vector1< std::string > const	pairline1_
	Sets the first line that will replace "PAIR" lines. More...

utility::vector1< std::string > const	pairline2_
	Sets the second line that will replace "PAIR" lines. More...

Constructor & Destructor Documentation

◆ DEERIO() [1/2]

core::scoring::epr_deer::DEERIO::DEERIO ( )

default

Constructor.

◆ DEERIO() [2/2]

core::scoring::epr_deer::DEERIO::DEERIO ( DEERIO const & io )

default

Copy Constructor.

◆ ~DEERIO()

core::scoring::epr_deer::DEERIO::~DEERIO ( )

default

Destructor.

Member Function Documentation

◆ generate_data()

std::map< Size, metrics::DEERDataOP > core::scoring::epr_deer::DEERIO::generate_data ( core::pose::Pose const & pose ) const

Generates the data for use. Core function.

Parameters

pose	Input pose (used for residue numbering)

Returns: Map of input data @detail Will only compute this once! Otherwise, the data is saved @detail in a static/global object (epr_deer_input_data_) defined in @detail header file

References core::scoring::epr_deer::epr_deer_input_data_, parse_data(), and parse_input().

Referenced by core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data().

◆ parse_bounds_data()

metrics::DEERDataOP core::scoring::epr_deer::DEERIO::parse_bounds_data	(	pose::Pose const &	pose,
		std::map< std::string, SplitLines > const &	sorted_data
	)		const

Parse inputs lines into DEERDistanceBoundsOP.

Parameters

pose	Pose (used for residue renumbering)
sorted_data	Input lines sorted by linetype

Returns: Proper data container that can be used by Rosetta

References parse_bounds_lines(), and parse_desc_lines().

Referenced by parse_data().

◆ parse_bounds_lines()

void core::scoring::epr_deer::DEERIO::parse_bounds_lines	(	SplitLines const &	bounds_lines,
		metrics::DEERDataOP	bounds_data
	)		const

Parses data for DEERDistanceBounds object.

Parameters

bounds_lines	Lines labeled "BOUNDS" in input file
data	Proper data container that can be used by Rosetta @detail Note that only the last BOUNDS line will be used

References core::scoring::epr_deer::TR().

Referenced by parse_bounds_data().

◆ parse_data()

metrics::DEERDataOP core::scoring::epr_deer::DEERIO::parse_data	(	pose::Pose const &	pose,
		SplitLines const &	lines
	)		const

Parse the input lines into actual data containers.

Parameters

pose	Pose (used for residue numbering)
idx	Index of datum (used for error messages)
lines	Lines associated with this dataset

Returns: Proper data container that can be used by Rosetta

References core::scoring::epr_deer::append_to_map(), parse_bounds_data(), parse_decay_data(), and parse_dist_data().

Referenced by generate_data().

◆ parse_decay_data()

metrics::DEERDataOP core::scoring::epr_deer::DEERIO::parse_decay_data	(	pose::Pose const &	pose,
		std::map< std::string, SplitLines > const &	sorted_data
	)		const

Parse inputs lines into DEERDecayDataOP.

Parameters

pose	Pose (used for residue renumbering)
sorted_data	Input lines sorted by linetype

Returns: Proper data container that can be used by Rosetta

References parse_decay_info_lines(), parse_decay_lines(), and parse_desc_lines().

Referenced by parse_data().

◆ parse_decay_info_lines()

void core::scoring::epr_deer::DEERIO::parse_decay_info_lines	(	SplitLines const &	info_lines,
		metrics::DEERDataOP	data
	)		const

Parses information data for DEERDecayData object.

Parameters

info_lines	Lines labeled "INFO" in input file
data	Proper data container that can be used by Rosetta

References ANGSTROM_LIMIT_, core::scoring::epr_deer::metrics::DEERData::bins_per_a(), BINS_PER_A_, and core::scoring::epr_deer::TR().

Referenced by parse_decay_data().

◆ parse_decay_lines()

void core::scoring::epr_deer::DEERIO::parse_decay_lines	(	SplitLines const &	decay_lines,
		metrics::DEERDataOP &	data
	)		const

Parses decay data for DEERDecayData object.

Parameters

decay_lines	Lines labeled "DECAY" in input file
data	Proper data container that can be used by Rosetta

Referenced by parse_decay_data().

◆ parse_desc_lines()

utility::vector1< PairSizeString > core::scoring::epr_deer::DEERIO::parse_desc_lines	(	pose::Pose const &	pose,
		SplitLines const &	desc_lines
	)		const

Parse input lines for information on residues involved in data.

Parameters

pose	Pose (used for residue renumbering)
desc_lines	Input lines containing this information

Returns: List of residues describing both the ID# and spin label type

References core::pose::parse_resnum(), core::pose::Pose::size(), and core::scoring::epr_deer::TR().

Referenced by parse_bounds_data(), parse_decay_data(), and parse_dist_data().

◆ parse_dist_data()

metrics::DEERDataOP core::scoring::epr_deer::DEERIO::parse_dist_data	(	pose::Pose const &	pose,
		std::map< std::string, SplitLines > const &	sorted_data
	)		const

Parse inputs lines into DEERDistanceDistributionOP.

Parameters

pose	Pose (used for residue renumbering)
sorted_data	Input lines sorted by linetype

Returns: Proper data container that can be used by Rosetta

References parse_desc_lines(), parse_dist_info_lines(), and parse_dist_lines().

Referenced by parse_data().

◆ parse_dist_datatype()

metrics::DEERDataOP core::scoring::epr_deer::DEERIO::parse_dist_datatype ( SplitLines const & info_lines ) const

Determines function used by DEERDistanceDistribution.

Parameters

info_lines Lines labeled "INFO" in input file

Returns: Proper data container that can be used by Rosetta @detail Note that this container, upon output, is incomplete!

References core::scoring::epr_deer::metrics::DEERDistanceDistribution::bb(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::integral(), core::scoring::epr_deer::metrics::DEERMiscMethod::mode(), core::scoring::epr_deer::metrics::DEERDistanceDistribution::singleval(), and core::scoring::epr_deer::TR().

Referenced by parse_dist_info_lines().

◆ parse_dist_info_lines()

metrics::DEERDataOP core::scoring::epr_deer::DEERIO::parse_dist_info_lines ( SplitLines const & info_lines ) const

Parses lines labeled "INFO" into information usable by Rosetta.

Parameters

info_lines Lines with the information (as strings)

Returns: Proper data container that can be used by Rosetta @detail Note that this container, upon output, is incomplete!

References BINS_PER_A_, and parse_dist_datatype().

Referenced by parse_dist_data().

◆ parse_dist_lines()

void core::scoring::epr_deer::DEERIO::parse_dist_lines	(	SplitLines const &	dist_lines,
		metrics::DEERDataOP	data
	)		const

Parses lines labeled "DIST" into information usable by Rosetta.

Parameters

dist_lines	Lines with the distance distributions
data	DEERData object (passed by reference and modified here)

References core::scoring::epr_deer::metrics::DEERDistanceDistribution::best_fit(), protocols::mean_field::max(), protocols::mean_field::min(), protocols::noesy_assign::round(), and protocols::analysis::total.

Referenced by parse_dist_data().

◆ parse_input()

std::map< Size, SplitLines > core::scoring::epr_deer::DEERIO::parse_input ( ) const

Parses file.

Parameters

pose	Pose (for residue numbering)

Returns: Map of strings (grouped by data index)

References core::scoring::epr_deer::append_to_map(), core::conformation::membrane::in, update_ResidueType_enum_files::input_file, pairline1_, pairline2_, split_line(), and core::id::to_string().

Referenced by generate_data().

◆ pull_coords()

utility::vector1< std::pair< EPRSpinLabel, Real > > core::scoring::epr_deer::DEERIO::pull_coords ( pose::Pose const & pose ) const

Parse coordinate files for custom spin labels.

Parameters

pose	Pose (used for residue renumbering)

Returns: List of spin labels and corresponding weights

References core::scoring::epr_deer::append_to_map(), core::conformation::membrane::in, core::scoring::epr_deer::EPRSpinLabel::load_custom_electrons(), core::pose::parse_resnum(), core::pose::Pose::size(), split_line(), and core::scoring::epr_deer::TR().

Referenced by core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data().

◆ split_line()

SplitLine core::scoring::epr_deer::DEERIO::split_line ( std::string const & line ) const

Split an input line into vector of strings.

Parameters

line	Line of interest

Returns: Vector of strings @detail Ignores lines starting with "#"

References protocols::sparta::split().

Referenced by parse_input(), and pull_coords().

Member Data Documentation

◆ ANGSTROM_LIMIT_

Size const core::scoring::epr_deer::DEERIO::ANGSTROM_LIMIT_ = 100

private

Defines the default max distance (for DEERDecayData objects)

Referenced by parse_decay_info_lines().

◆ BINS_PER_A_

Size const core::scoring::epr_deer::DEERIO::BINS_PER_A_ = 2

private

Defines the default bins per angstrom in distributions.

Referenced by parse_decay_info_lines(), and parse_dist_info_lines().

◆ pairline1_

utility::vector1< std::string > const core::scoring::epr_deer::DEERIO::pairline1_

private

Initial value:

=

{ "DESC", "", "DEFAULT", "", "DEFAULT", "" }

Sets the first line that will replace "PAIR" lines.

Referenced by parse_input().

◆ pairline2_

utility::vector1< std::string > const core::scoring::epr_deer::DEERIO::pairline2_

private

Initial value:

=

{ "BOUNDS", "", "", "", "1.0" }

Sets the second line that will replace "PAIR" lines.

Referenced by parse_input().

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

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

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ DEERIO() [1/2]

◆ DEERIO() [2/2]

◆ ~DEERIO()

Member Function Documentation

◆ generate_data()

◆ parse_bounds_data()

◆ parse_bounds_lines()

◆ parse_data()

◆ parse_decay_data()

◆ parse_decay_info_lines()

◆ parse_decay_lines()

◆ parse_desc_lines()

◆ parse_dist_data()

◆ parse_dist_datatype()

◆ parse_dist_info_lines()

◆ parse_dist_lines()

◆ parse_input()

◆ pull_coords()

◆ split_line()

Member Data Documentation

◆ ANGSTROM_LIMIT_

◆ BINS_PER_A_

◆ pairline1_

◆ pairline2_