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

#include <RemodelData.hh>

Collaboration diagram for protocols::forge::remodel::RemodelData:

Public Member Functions
	RemodelData ()
void	translateDSSP_ABEGO (std::string &ss, std::string &abego)
void	getLoopsToBuildFromFile (std::string filename)
void	splitString (std::string str, std::string delim, std::vector< std::string > &results)
void	updateWithDsspAssignment (ObjexxFCL::FArray1D_char &dsspSS)
void	collectInsertionPose ()

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

Detailed Description

Definition at line 43 of file RemodelData.hh.

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelData::RemodelData

(

)

Definition at line 104 of file RemodelData.cc.

Member Function Documentation

void protocols::forge::remodel::RemodelData::collectInsertionPose

(

)

Definition at line 447 of file RemodelData.cc.

References core::scoring::dssp::Dssp::dssp_reduced(), and core::import_pose::pose_from_pdb().

void protocols::forge::remodel::RemodelData::getLoopsToBuildFromFile

(

std::string

filename)

Definition at line 112 of file RemodelData.cc.

References core::chemical::aa_from_oneletter_code(), core::scoring::abego, protocols::forge::remodel::LineObject::aminoAcidList, core::io::serialization::at(), 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::index, protocols::forge::remodel::LineObject::isDesignable, protocols::forge::remodel::LineObject::original_index, protocols::forge::remodel::LineObject::resname, core::io::serialization::size(), protocols::forge::remodel::LineObject::sstype, and protocols::forge::remodel::TR_REMODEL().

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

Definition at line 91 of file RemodelData.cc.

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

Definition at line 383 of file RemodelData.cc.

void protocols::forge::remodel::RemodelData::updateWithDsspAssignment

(

ObjexxFCL::FArray1D_char &

dsspSS)

Definition at line 430 of file RemodelData.cc.

References protocols::forge::remodel::TR_REMODEL().

Member Data Documentation

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

Definition at line 56 of file RemodelData.hh.

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

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

Definition at line 71 of file RemodelData.hh.

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

Definition at line 76 of file RemodelData.hh.

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

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

Definition at line 69 of file RemodelData.hh.

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

Definition at line 72 of file RemodelData.hh.

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

Definition at line 79 of file RemodelData.hh.

Referenced by protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood().

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

Definition at line 78 of file RemodelData.hh.

Referenced by protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood().

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

Definition at line 60 of file RemodelData.hh.

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

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

Definition at line 64 of file RemodelData.hh.

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

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

Definition at line 85 of file RemodelData.hh.

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

Definition at line 86 of file RemodelData.hh.

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

Definition at line 84 of file RemodelData.hh.

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

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

Definition at line 50 of file RemodelData.hh.

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

Definition at line 74 of file RemodelData.hh.

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

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

Definition at line 81 of file RemodelData.hh.

Referenced by protocols::forge::remodel::WorkingRemodelSet::manualPackerTaskGen(), and protocols::forge::remodel::RemodelDesignMover::mode5_packertask().

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

Definition at line 66 of file RemodelData.hh.

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

Definition at line 67 of file RemodelData.hh.

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

Definition at line 51 of file RemodelData.hh.

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

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

Definition at line 54 of file RemodelData.hh.

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

Definition at line 88 of file RemodelData.hh.

---

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

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