Rosetta
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#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... | |
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default |
Constructor.
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default |
Copy Constructor.
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default |
Destructor.
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.
pose | Input pose (used for residue numbering) |
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.
pose | Pose (used for residue renumbering) |
sorted_data | Input lines sorted by linetype |
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.
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().
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.
pose | Pose (used for residue numbering) |
idx | Index of datum (used for error messages) |
lines | Lines associated with this dataset |
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.
pose | Pose (used for residue renumbering) |
sorted_data | Input lines sorted by linetype |
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.
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().
void core::scoring::epr_deer::DEERIO::parse_decay_lines | ( | SplitLines const & | decay_lines, |
metrics::DEERDataOP & | data | ||
) | const |
Parses decay data for DEERDecayData object.
decay_lines | Lines labeled "DECAY" in input file |
data | Proper 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.
pose | Pose (used for residue renumbering) |
desc_lines | Input lines containing this information |
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.
pose | Pose (used for residue renumbering) |
sorted_data | Input lines sorted by linetype |
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.
info_lines | Lines labeled "INFO" in input file |
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.
info_lines | Lines with the information (as strings) |
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.
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().
std::map< Size, SplitLines > core::scoring::epr_deer::DEERIO::parse_input | ( | ) | const |
Parses file.
pose | Pose (for residue numbering) |
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().
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.
pose | Pose (used for residue renumbering) |
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.
line | Line of interest |
References protocols::sparta::split().
Referenced by parse_input(), and pull_coords().
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Defines the default max distance (for DEERDecayData objects)
Referenced by parse_decay_info_lines().
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Defines the default bins per angstrom in distributions.
Referenced by parse_decay_info_lines(), and parse_dist_info_lines().
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Sets the first line that will replace "PAIR" lines.
Referenced by parse_input().
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Sets the second line that will replace "PAIR" lines.
Referenced by parse_input().