#include <RemodelData.hh>

Public Member Functions
	RemodelData ()
	constructor More...

void	getLoopsToBuildFromBlueprint (std::string text_blueprint)
	Parses the blueprint text. More...

void	getLoopsToBuildFromFile (std::string filename)
	Reads in the blueprint file and passes the text data to the blueprint file parser. More...

void	splitString (std::string str, std::string delim, std::vector< std::string > &results)
	Splits a string on the passed in delimeter and places the tokens in the passed in vector. Isn't there a function in utility that can do this already? More...

void	updateWithDsspAssignment (ObjexxFCL::FArray1D_char &dsspSS)
	Updates the dssp_updated_ss vector with secondary structure information. Uses the information obtained from DSSP unless the secondary structure was specified in the blueprint file. More...

void	collectInsertionPose ()
	If users are trying to do domain insertion with remodel (by specifying the insert_segment_from_pdb command-line option), then this function is called to read in the PDB file for that segment. More...

void	translateDSSP_ABEGO (std::string &ss, std::string &abego)

Public Attributes
protocols::loops::Loops	loops_to_build

std::string	sequence

std::string	ss

std::string	abego

std::string	dssp_updated_ss

bool	has_design_info_

int	pdb_start

int	pdb_stop

int	design_mode

bool	auto_design

bool	design_neighbor

core::kinematics::MoveMap	natro_movemap_

std::vector < protocols::forge::remodel::LineObject >	blueprint

std::vector< core::Size >	disulfMobileRange

std::vector< core::Size >	disulfLandingRange

std::string	parsed_string_for_resfile

core::pose::Pose	insertPose

int	insertionSize

std::string	insertionSS

float	total_chain_break_score

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelData::RemodelData ( )

constructor

RemodelData::RemodelData

Member Function Documentation

void protocols::forge::remodel::RemodelData::collectInsertionPose ( )

If users are trying to do domain insertion with remodel (by specifying the insert_segment_from_pdb command-line option), then this function is called to read in the PDB file for that segment.

RemodelData::collectInsertionPose

References dssp, core::scoring::dssp::Dssp::dssp_reduced(), basic::options::OptionKeys::remodel::domainFusion::insert_segment_from_pdb, basic::options::option, and TR_REMODEL.

Referenced by protocols::forge::remodel::RemodelMover::apply().

void protocols::forge::remodel::RemodelData::getLoopsToBuildFromBlueprint ( std::string text_blueprint )

Parses the blueprint text.

Referenced by protocols::forge::remodel::RemodelMover::apply().

void protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile ( std::string filename )

Reads in the blueprint file and passes the text data to the blueprint file parser.

References utility::exit(), getline(), and TR_REMODEL.

Referenced by protocols::forge::remodel::RemodelMover::apply().

void protocols::forge::remodel::RemodelData::splitString	(	std::string	str,
		std::string	delim,
		std::vector< std::string > &	results
	)

Splits a string on the passed in delimeter and places the tokens in the passed in vector. Isn't there a function in utility that can do this already?

RemodelData::splitString

void protocols::forge::remodel::RemodelData::translateDSSP_ABEGO	(	std::string &	ss,
		std::string &	abego
	)

References TR_REMODEL.

void protocols::forge::remodel::RemodelData::updateWithDsspAssignment ( ObjexxFCL::FArray1D_char & dsspSS )

Updates the dssp_updated_ss vector with secondary structure information. Uses the information obtained from DSSP unless the secondary structure was specified in the blueprint file.

RemodelData::updateWithDsspAssignment

References blueprint, ss, and TR_REMODEL.

Referenced by protocols::forge::remodel::RemodelMover::apply().