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::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

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

)

Parses the blueprint text.

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::scoring::abego, protocols::forge::remodel::LineObject::aminoAcidList, protocols::forge::remodel::LineObject::constraint_definition, core::pack::task::create_command_map(), protocols::forge::remodel::LineObject::design_type, core::sequence::end, protocols::forge::remodel::LineObject::has_constraints, protocols::forge::remodel::LineObject::has_ncaa, protocols::forge::remodel::LineObject::index, protocols::forge::remodel::LineObject::isDesignable, protocols::forge::remodel::LineObject::original_index, protocols::forge::remodel::LineObject::resname, protocols::forge::remodel::LineObject::sstype, and TR_REMODEL().

Referenced by protocols::forge::remodel::RemodelMover::apply(), and protocols::forge::remodel::RemodelMover::setup_remodel_data_for_loop_btw_parametric_components().

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
	)

References core::scoring::abego, and TR_REMODEL().

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

Referenced by protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

auto_design

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

blueprint

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

Referenced by protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelEnzdesCstModule::blueprint_cst_definition(), protocols::forge::components::VarLengthBuild::centroid_build(), protocols::forge::remodel::RemodelMover::centroid_build(), protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover(), protocols::forge::remodel::RemodelGlobalFrame::RemodelGlobalFrame(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

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

Referenced by protocols::forge::components::VarLengthBuild::centroid_build(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

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

Referenced by protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

LD_types

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

Referenced by protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

loops_to_build

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

natro_movemap_

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

Referenced by protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), and protocols::forge::remodel::RemodelMover::design_refine_cart_relax().

parsed_string_for_resfile

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

Referenced by protocols::forge::remodel::RemodelWorkingSet::manualPackerTaskGen().

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

Referenced by protocols::forge::components::VarLengthBuild::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelMover::centroid_build(), and protocols::forge::remodel::RemodelWorkingSet::workingSetGen().

ss

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

Referenced by protocols::forge::remodel::RemodelLoopMover::apply(), protocols::forge::remodel::RemodelLoopMover::generate_residues_to_sample(), and protocols::forge::remodel::RemodelLoopMover::set_ideal_helices().

total_chain_break_score

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

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

• src/protocols/forge/remodel/RemodelData.hh
• src/protocols/forge/remodel/RemodelData.cc