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protocols::forge::remodel::RemodelData Class Reference

#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 LD_types
 
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::LineObjectblueprint
 
std::vector< core::SizedisulfMobileRange
 
std::vector< core::SizedisulfLandingRange
 
std::string parsed_string_for_resfile
 
core::pose::Pose insertPose
 
int insertionSize
 
std::string insertionSS
 
float total_chain_break_score
 

Constructor & Destructor Documentation

◆ RemodelData()

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

constructor

Member Function Documentation

◆ collectInsertionPose()

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.

References protocols::simple_filters::dssp(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and TR_REMODEL().

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

◆ getLoopsToBuildFromBlueprint()

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

◆ getLoopsToBuildFromFile()

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 protocols::abinitio::filename(), and TR_REMODEL().

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

◆ splitString()

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?

References protocols::kinmatch::str().

◆ translateDSSP_ABEGO()

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

◆ updateWithDsspAssignment()

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.

References TR_REMODEL().

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

Member Data Documentation

◆ abego

std::string protocols::forge::remodel::RemodelData::abego

◆ auto_design

bool protocols::forge::remodel::RemodelData::auto_design

◆ blueprint

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

◆ design_mode

int protocols::forge::remodel::RemodelData::design_mode

◆ design_neighbor

bool protocols::forge::remodel::RemodelData::design_neighbor

◆ disulfLandingRange

std::vector<core::Size> protocols::forge::remodel::RemodelData::disulfLandingRange

◆ disulfMobileRange

std::vector<core::Size> protocols::forge::remodel::RemodelData::disulfMobileRange

◆ dssp_updated_ss

std::string protocols::forge::remodel::RemodelData::dssp_updated_ss

◆ has_design_info_

bool protocols::forge::remodel::RemodelData::has_design_info_

◆ insertionSize

int protocols::forge::remodel::RemodelData::insertionSize

◆ insertionSS

std::string protocols::forge::remodel::RemodelData::insertionSS

◆ insertPose

core::pose::Pose protocols::forge::remodel::RemodelData::insertPose

◆ LD_types

std::string protocols::forge::remodel::RemodelData::LD_types

◆ loops_to_build

protocols::loops::Loops protocols::forge::remodel::RemodelData::loops_to_build

◆ natro_movemap_

core::kinematics::MoveMap protocols::forge::remodel::RemodelData::natro_movemap_

◆ parsed_string_for_resfile

std::string protocols::forge::remodel::RemodelData::parsed_string_for_resfile

◆ pdb_start

int protocols::forge::remodel::RemodelData::pdb_start

◆ pdb_stop

int protocols::forge::remodel::RemodelData::pdb_stop

◆ sequence

std::string protocols::forge::remodel::RemodelData::sequence

◆ ss

std::string protocols::forge::remodel::RemodelData::ss

◆ total_chain_break_score

float protocols::forge::remodel::RemodelData::total_chain_break_score

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