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Public Member Functions | Public Attributes | List of all members
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::LineObject
blueprint
 
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

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

constructor

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.

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

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

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

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.

References TR_REMODEL().

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

Member Data Documentation

std::string protocols::forge::remodel::RemodelData::abego
bool protocols::forge::remodel::RemodelData::auto_design
std::vector< protocols::forge::remodel::LineObject > protocols::forge::remodel::RemodelData::blueprint
int protocols::forge::remodel::RemodelData::design_mode
bool protocols::forge::remodel::RemodelData::design_neighbor
std::vector<core::Size> protocols::forge::remodel::RemodelData::disulfLandingRange
std::vector<core::Size> protocols::forge::remodel::RemodelData::disulfMobileRange
std::string protocols::forge::remodel::RemodelData::dssp_updated_ss
bool protocols::forge::remodel::RemodelData::has_design_info_
int protocols::forge::remodel::RemodelData::insertionSize
std::string protocols::forge::remodel::RemodelData::insertionSS
core::pose::Pose protocols::forge::remodel::RemodelData::insertPose
std::string protocols::forge::remodel::RemodelData::LD_types
protocols::loops::Loops protocols::forge::remodel::RemodelData::loops_to_build
core::kinematics::MoveMap protocols::forge::remodel::RemodelData::natro_movemap_
std::string protocols::forge::remodel::RemodelData::parsed_string_for_resfile
int protocols::forge::remodel::RemodelData::pdb_start
int protocols::forge::remodel::RemodelData::pdb_stop
std::string protocols::forge::remodel::RemodelData::sequence
std::string protocols::forge::remodel::RemodelData::ss
float protocols::forge::remodel::RemodelData::total_chain_break_score

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