protocols::loops::JSONFormattedLoopsFileReader Class Reference

#include <LoopsFileIO.hh>

Collaboration diagram for protocols::loops::JSONFormattedLoopsFileReader:

Public Member Functions
void	set_linecount_offset (core::Size)
	if the input stream has had some number of lines already removed from it, indicate how many. More...
LoopsFileDataOP	read_loop_file (std::istream &is, std::string const &filename, bool prohibit_single_residue_loops)

Private Member Functions
LoopsFileDataOP	parse_json_formatted_data (utility::json_spirit::mValue &json_data, bool prohibit_single_residue_loops, std::string const &filename)
void	ensure_all_fields_are_valid (utility::json_spirit::mValue &json_data, std::string const &filename)
ResidueIndexDescriptionFromFile	parse_json_residue_info (utility::json_spirit::mValue &json_loop_data, ResidueIdentifier residue_identifier, std::string const &filename, core::Size &approximate_linenumber)
void	parse_configuration_options (utility::json_spirit::mValue &json_loop_data, LoopFromFileData &loop)
void	setup_residue_type_map ()
std::string	name_from_residue_identifier (ResidueIdentifier residue_identifier)
std::string	name_from_loop_configuration (LoopConfiguration loop_configuration)

Private Attributes
core::Size	linecount_offset_

Static Private Attributes
static bool	initialized_
static utility::vector1 < std::string >	valid_loop_file_keys_

Detailed Description

Definition at line 345 of file LoopsFileIO.hh.

Member Function Documentation

void protocols::loops::JSONFormattedLoopsFileReader::ensure_all_fields_are_valid ( utility::json_spirit::mValue &  json_data, std::string const &  filename  )

private

Definition at line 689 of file LoopsFileIO.cc.

References setup_residue_type_map(), and valid_loop_file_keys_.

Referenced by parse_json_formatted_data(), and parse_json_residue_info().

std::string protocols::loops::JSONFormattedLoopsFileReader::name_from_loop_configuration ( LoopConfiguration  loop_configuration)

private

Definition at line 866 of file LoopsFileIO.cc.

References setup_residue_type_map(), and valid_loop_file_keys_.

Referenced by parse_configuration_options(), and parse_json_residue_info().

std::string protocols::loops::JSONFormattedLoopsFileReader::name_from_residue_identifier ( ResidueIdentifier  residue_identifier)

private

Definition at line 860 of file LoopsFileIO.cc.

References setup_residue_type_map(), and valid_loop_file_keys_.

Referenced by parse_json_residue_info().

void protocols::loops::JSONFormattedLoopsFileReader::parse_configuration_options ( utility::json_spirit::mValue &  json_loop_data, LoopFromFileData &  loop  )

private

Definition at line 783 of file LoopsFileIO.cc.

References protocols::loops::extend, protocols::loops::LoopFromFileData::extended(), protocols::loops::extras, name_from_loop_configuration(), protocols::loops::LoopFromFileData::skip_rate(), protocols::loops::skip_rate, and protocols::loops::use_pose_numbering.

Referenced by parse_json_formatted_data().

LoopsFileDataOP protocols::loops::JSONFormattedLoopsFileReader::parse_json_formatted_data ( utility::json_spirit::mValue &  json_data, bool  prohibit_single_residue_loops, std::string const &  filename  )

private

Definition at line 660 of file LoopsFileIO.cc.

References protocols::loops::cut_point, protocols::loops::LoopFromFileData::cutpoint_res(), protocols::loops::LoopFromFileData::end_res(), ensure_all_fields_are_valid(), linecount_offset_, parse_configuration_options(), parse_json_residue_info(), protocols::loops::LoopFromFileData::prohibit_single_residue_loops(), protocols::loops::start, protocols::loops::LoopFromFileData::start_res(), and protocols::loops::stop.

Referenced by read_loop_file().

ResidueIndexDescriptionFromFile protocols::loops::JSONFormattedLoopsFileReader::parse_json_residue_info ( utility::json_spirit::mValue &  json_loop_data, ResidueIdentifier  residue_identifier, std::string const &  filename, core::Size &  approximate_linenumber  )

private

Definition at line 715 of file LoopsFileIO.cc.

References protocols::loops::chainID, protocols::loops::cut_point, ensure_all_fields_are_valid(), protocols::abinitio::filename(), protocols::loops::iCode, name_from_loop_configuration(), name_from_residue_identifier(), and protocols::loops::resSeq.

Referenced by parse_json_formatted_data().

LoopsFileDataOP protocols::loops::JSONFormattedLoopsFileReader::read_loop_file	(	std::istream &	is,
		std::string const &	filename,
		bool	prohibit_single_residue_loops
	)

Definition at line 645 of file LoopsFileIO.cc.

References parse_json_formatted_data().

Referenced by protocols::loops::LoopsFileIO::read_loop_file_stream().

void protocols::loops::JSONFormattedLoopsFileReader::set_linecount_offset

(

core::Size

setting)

if the input stream has had some number of lines already removed from it, indicate how many.

Definition at line 707 of file LoopsFileIO.cc.

References linecount_offset_.

Referenced by protocols::loops::LoopsFileIO::read_loop_file_stream().

void protocols::loops::JSONFormattedLoopsFileReader::setup_residue_type_map ( )

private

Definition at line 842 of file LoopsFileIO.cc.

References protocols::loops::chainID, protocols::loops::cut_point, protocols::loops::extend, protocols::loops::extras, protocols::loops::iCode, initialized_, protocols::loops::number_of_configuration_keywords, protocols::loops::resSeq, protocols::loops::skip_rate, protocols::loops::start, protocols::loops::stop, protocols::loops::use_pose_numbering, and valid_loop_file_keys_.

Referenced by ensure_all_fields_are_valid(), name_from_loop_configuration(), and name_from_residue_identifier().

Member Data Documentation

bool protocols::loops::JSONFormattedLoopsFileReader::initialized_

staticprivate

Definition at line 391 of file LoopsFileIO.hh.

Referenced by setup_residue_type_map().

core::Size protocols::loops::JSONFormattedLoopsFileReader::linecount_offset_

private

Definition at line 389 of file LoopsFileIO.hh.

Referenced by parse_json_formatted_data(), and set_linecount_offset().

utility::vector1< std::string > protocols::loops::JSONFormattedLoopsFileReader::valid_loop_file_keys_

staticprivate

Definition at line 392 of file LoopsFileIO.hh.

Referenced by ensure_all_fields_are_valid(), name_from_loop_configuration(), name_from_residue_identifier(), and setup_residue_type_map().

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

• src/protocols/loops/LoopsFileIO.hh
• src/protocols/loops/LoopsFileIO.cc