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core::scoring::epr_deer::DEERIO Class Reference

#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, SplitLinesparse_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< PairSizeStringparse_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

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

Constructor.

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

Copy Constructor.

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

Destructor.

Member Function Documentation

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
poseInput pose (used for residue numbering)
Returns
Map of input data Will only compute this once! Otherwise, the data is saved in a static/global object (epr_deer_input_data_) defined in 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().

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
posePose (used for residue renumbering)
sorted_dataInput 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().

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_linesLines labeled "BOUNDS" in input file
dataProper data container that can be used by Rosetta Note that only the last BOUNDS line will be used

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

Referenced by parse_bounds_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
posePose (used for residue numbering)
idxIndex of datum (used for error messages)
linesLines 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().

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
posePose (used for residue renumbering)
sorted_dataInput 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().

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_linesLines labeled "INFO" in input file
dataProper 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().

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_linesLines labeled "DECAY" in input file
dataProper data container that can be used by Rosetta

Referenced by parse_decay_data().

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
posePose (used for residue renumbering)
desc_linesInput 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().

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
posePose (used for residue renumbering)
sorted_dataInput 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().

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

Determines function used by DEERDistanceDistribution.

Parameters
info_linesLines labeled "INFO" in input file
Returns
Proper data container that can be used by Rosetta 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().

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_linesLines with the information (as strings)
Returns
Proper data container that can be used by Rosetta Note that this container, upon output, is incomplete!

References BINS_PER_A_, and parse_dist_datatype().

Referenced by parse_dist_data().

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_linesLines with the distance distributions
dataDEERData 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().

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

Parses file.

Parameters
posePose (for residue numbering)
Returns
Map of strings (grouped by data index)

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

Referenced by generate_data().

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
posePose (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().

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

Split an input line into vector of strings.

Parameters
lineLine of interest
Returns
Vector of strings Ignores lines starting with "#"

References protocols::sparta::split().

Referenced by parse_input(), and pull_coords().

Member Data Documentation

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().

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().

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().

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: