#include <LoopsFileIO.hh>

Collaboration diagram for protocols::loops::LoopFromFileData:

Public Member Functions
	LoopFromFileData ()

	LoopFromFileData (ResidueIndexDescriptionFromFile const &start_res, ResidueIndexDescriptionFromFile const &cutpoint_res, ResidueIndexDescriptionFromFile const &end_res, core::Real skip_rate, bool extended, bool prohibit_single_residue_loops=true)

	LoopFromFileData (SerializedLoop const &loop, std::string const &fname, bool prohibit_single_residue_loops=true)
	constructed the other way around (for the the PoseNumberedLoopReader) More...

SerializedLoop	resolve_as_serialized_loop_from_pose (core::pose::Pose const &pose) const
	loop-index resolution function: construct a SerializedLoopData object by possibly retrieving data from a Pose. This function also performs the loop-index checks performed by the PoseNumberedLoopFileReader. More...

ResidueIndexDescriptionFromFile const &	start_res () const

void	start_res (ResidueIndexDescriptionFromFile const &setting)

ResidueIndexDescriptionFromFile const &	cutpoint_res () const

void	cutpoint_res (ResidueIndexDescriptionFromFile const &setting)

ResidueIndexDescriptionFromFile const &	end_res () const

void	end_res (ResidueIndexDescriptionFromFile const &setting)

core::Real	skip_rate () const

void	skip_rate (core::Real setting)

bool	extended () const

void	extended (bool setting)

bool	prohibit_single_residue_loops () const

void	prohibit_single_residue_loops (bool setting)

Private Attributes
ResidueIndexDescriptionFromFile	start_res_

ResidueIndexDescriptionFromFile	cutpoint_res_

ResidueIndexDescriptionFromFile	end_res_

core::Real	skip_rate_

bool	extended_

bool	prohibit_single_residue_loops_

Detailed Description

Definition at line 113 of file LoopsFileIO.hh.

Constructor & Destructor Documentation

protocols::loops::LoopFromFileData::LoopFromFileData ( )

Definition at line 175 of file LoopsFileIO.cc.

protocols::loops::LoopFromFileData::LoopFromFileData	(	ResidueIndexDescriptionFromFile const &	start_res,
		ResidueIndexDescriptionFromFile const &	cutpoint_res,
		ResidueIndexDescriptionFromFile const &	end_res,
		core::Real	skip_rate,
		bool	extended,
		bool	prohibit_single_residue_loops = `true`
	)

Definition at line 181 of file LoopsFileIO.cc.

protocols::loops::LoopFromFileData::LoopFromFileData	(	SerializedLoop const &	loop,
		std::string const &	fname,
		bool	prohibit_single_residue_loops = `true`
	)

constructed the other way around (for the the PoseNumberedLoopReader)

Definition at line 198 of file LoopsFileIO.cc.

Member Function Documentation

ResidueIndexDescriptionFromFile const& protocols::loops::LoopFromFileData::cutpoint_res ( ) const

inline

Definition at line 143 of file LoopsFileIO.hh.

References cutpoint_res_.

Referenced by protocols::loops::JSONFormattedLoopsFileReader::parse_json_formatted_data().

void protocols::loops::LoopFromFileData::cutpoint_res ( ResidueIndexDescriptionFromFile const & setting)

inline

Definition at line 144 of file LoopsFileIO.hh.

References cutpoint_res_.

ResidueIndexDescriptionFromFile const& protocols::loops::LoopFromFileData::end_res ( ) const

inline

Definition at line 146 of file LoopsFileIO.hh.

References end_res_.

Referenced by protocols::loops::JSONFormattedLoopsFileReader::parse_json_formatted_data().

void protocols::loops::LoopFromFileData::end_res ( ResidueIndexDescriptionFromFile const & setting)

inline

Definition at line 147 of file LoopsFileIO.hh.

References end_res_.

bool protocols::loops::LoopFromFileData::extended ( ) const

inline

Definition at line 152 of file LoopsFileIO.hh.

References extended_.

Referenced by protocols::loops::JSONFormattedLoopsFileReader::parse_configuration_options().

void protocols::loops::LoopFromFileData::extended ( bool setting)

inline

Definition at line 153 of file LoopsFileIO.hh.

References extended_.

bool protocols::loops::LoopFromFileData::prohibit_single_residue_loops ( ) const

inline

Definition at line 155 of file LoopsFileIO.hh.

References prohibit_single_residue_loops_.

Referenced by protocols::loops::JSONFormattedLoopsFileReader::parse_json_formatted_data().

void protocols::loops::LoopFromFileData::prohibit_single_residue_loops ( bool setting)

inline

Definition at line 156 of file LoopsFileIO.hh.

References prohibit_single_residue_loops_.

SerializedLoop protocols::loops::LoopFromFileData::resolve_as_serialized_loop_from_pose ( core::pose::Pose const & pose) const

loop-index resolution function: construct a SerializedLoopData object by possibly retrieving data from a Pose. This function also performs the loop-index checks performed by the PoseNumberedLoopFileReader.

Convert from the information read from the loop-definition file into residue indices that make sense in the context of this pose, and validate the input loop definition (i.e. that the index of the start residue is less than the index of the end residue ).

Definition at line 216 of file LoopsFileIO.cc.

References cutpoint_res_, end_res_, extended_, protocols::loops::ResidueIndexDescriptionFromFile::fname(), protocols::loops::ResidueIndexDescriptionFromFile::linenum(), prohibit_single_residue_loops_, protocols::loops::ResidueIndexDescriptionFromFile::resolve_index(), skip_rate_, protocols::loops::SerializedLoop::start, start_res_, and protocols::loops::validate_loop_start_stop().