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Rosetta
2020.50
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#include <DEERIO.hh>
Public Member Functions | |
DEERIO () | |
Constructor. More... | |
~DEERIO () | |
Destructor. More... | |
std::map< Size, DEERDataOP > | generate_data (core::pose::Pose const &pose) |
Generates the data for use. Core function. More... | |
utility::vector1 < utility::vector1 < std::string > > | get_splitlines () |
Reads the input file(s) and makes an unsorted vector of their whitespace-separated contents. More... | |
void | read_desc_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines, pose::Pose const &pose) |
Reads lines that start with DESC, which contain residue and spin label information. More... | |
void | read_info_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines) |
Reads lines that start with INFO, which gives additional options specific for each bit of data. More... | |
void | read_decay_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &data_lines) |
Read lines for decay data (raw data) More... | |
void | read_bounds_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines) |
Read lines for bounded distance restraints. More... | |
void | read_gauss_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines) |
Read lines for gaussian-distributed distance data. More... | |
void | read_dist_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines) |
Read lines for non-gaussian-distributed distance data. More... | |
void | read_pair_lines (std::map< Size, DEERDataOP > &output, utility::vector1< utility::vector1< std::string > > const &splitlines, pose::Pose const &pose) |
Read the lines starting with PAIR, which are for easy input. More... | |
Real | normalize_distribution (std::map< Size, Real > &in_map) |
Normalize distance distributions so their integrals equal 1. More... | |
utility::vector1< std::pair < EPRSpinLabel, Real > > | pull_coords () const |
Get custom spin label coordinates. More... | |
Private Attributes | |
Size | ANGSTROM_LIMIT_ = 100 |
Size | BINS_PER_ANGSTROM_ = 2 |
core::scoring::epr_deer::DEERIO::DEERIO | ( | ) |
Constructor.
core::scoring::epr_deer::DEERIO::~DEERIO | ( | ) |
Destructor.
std::map< Size, DEERDataOP > core::scoring::epr_deer::DEERIO::generate_data | ( | core::pose::Pose const & | pose | ) |
Generates the data for use. Core function.
References get_splitlines(), read_bounds_lines(), read_decay_lines(), read_desc_lines(), read_dist_lines(), read_gauss_lines(), read_info_lines(), and read_pair_lines().
Referenced by core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data().
utility::vector1< utility::vector1< std::string > > core::scoring::epr_deer::DEERIO::get_splitlines | ( | ) |
Reads the input file(s) and makes an unsorted vector of their whitespace-separated contents.
References core::conformation::membrane::in, and protocols::sparta::split().
Referenced by generate_data().
Normalize distance distributions so their integrals equal 1.
Referenced by read_dist_lines(), and read_gauss_lines().
utility::vector1< std::pair< EPRSpinLabel, Real > > core::scoring::epr_deer::DEERIO::pull_coords | ( | ) | const |
Get custom spin label coordinates.
References core::conformation::membrane::in, core::scoring::epr_deer::EPRSpinLabel::load_custom_electrons(), and protocols::sparta::split().
Referenced by core::scoring::epr_deer::DEERDataCache::fetch_and_organize_data().
void core::scoring::epr_deer::DEERIO::read_bounds_lines | ( | std::map< Size, DEERDataOP > & | output, |
utility::vector1< utility::vector1< std::string > > const & | splitlines | ||
) |
Read lines for bounded distance restraints.
References core::scoring::epr_deer::TR().
Referenced by generate_data().
void core::scoring::epr_deer::DEERIO::read_decay_lines | ( | std::map< Size, DEERDataOP > & | output, |
utility::vector1< utility::vector1< std::string > > const & | data_lines | ||
) |
Read lines for decay data (raw data)
References ANGSTROM_LIMIT_, and core::scoring::epr_deer::TR().
Referenced by generate_data().
void core::scoring::epr_deer::DEERIO::read_desc_lines | ( | std::map< Size, DEERDataOP > & | output, |
utility::vector1< utility::vector1< std::string > > const & | splitlines, | ||
pose::Pose const & | pose | ||
) |
Reads lines that start with DESC, which contain residue and spin label information.
References BINS_PER_ANGSTROM_, core::pose::parse_resnum(), and core::scoring::epr_deer::TR().
Referenced by generate_data().
void core::scoring::epr_deer::DEERIO::read_dist_lines | ( | std::map< Size, DEERDataOP > & | output, |
utility::vector1< utility::vector1< std::string > > const & | splitlines | ||
) |
Read lines for non-gaussian-distributed distance data.
References BINS_PER_ANGSTROM_, protocols::mean_field::max(), protocols::mean_field::min(), normalize_distribution(), protocols::noesy_assign::round(), core::scoring::epr_deer::TR(), and protocols::hybridization::val.
Referenced by generate_data().
void core::scoring::epr_deer::DEERIO::read_gauss_lines | ( | std::map< Size, DEERDataOP > & | output, |
utility::vector1< utility::vector1< std::string > > const & | splitlines | ||
) |
Read lines for gaussian-distributed distance data.
References ANGSTROM_LIMIT_, core::scoring::epr_deer::DEERDistanceDistribution::best_fit(), BINS_PER_ANGSTROM_, core::sequence::end, core::scoring::epr_deer::EPRSpinLabel::gauss(), protocols::mean_field::max(), core::simple_metrics::metrics::mean, protocols::mean_field::min(), normalize_distribution(), and core::scoring::epr_deer::TR().
Referenced by generate_data().
void core::scoring::epr_deer::DEERIO::read_info_lines | ( | std::map< Size, DEERDataOP > & | output, |
utility::vector1< utility::vector1< std::string > > const & | splitlines | ||
) |
Reads lines that start with INFO, which gives additional options specific for each bit of data.
References core::scoring::epr_deer::TR().
Referenced by generate_data().
void core::scoring::epr_deer::DEERIO::read_pair_lines | ( | std::map< Size, DEERDataOP > & | output, |
utility::vector1< utility::vector1< std::string > > const & | splitlines, | ||
pose::Pose const & | pose | ||
) |
Read the lines starting with PAIR, which are for easy input.
References BINS_PER_ANGSTROM_, core::kinematics::distance(), core::pose::parse_resnum(), and core::scoring::epr_deer::DEERData::residues().
Referenced by generate_data().
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Referenced by read_decay_lines(), and read_gauss_lines().
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Referenced by read_desc_lines(), read_dist_lines(), read_gauss_lines(), and read_pair_lines().