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protocols::forge::remodel::WorkingRemodelSet Class Reference

#include <RemodelWorkingSet.hh>

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Public Member Functions

void workingSetGen (core::pose::Pose const &input_pose, protocols::forge::remodel::RemodelData const &data)
 
void manualPackerTaskGen (core::pose::Pose const &built_pose, protocols::forge::remodel::RemodelData const &data)
 
 WorkingRemodelSet ()
 If remodel loop setup is calling for n-terminus movement then return true, otherwise false. More...
 
 WorkingRemodelSet (WorkingRemodelSet const &rval)
 copy constructor More...
 
WorkingRemodelSet & operator= (WorkingRemodelSet const &rval)
 
 ~WorkingRemodelSet ()
 

Public Attributes

protocols::loops::Loops loops
 
int safe_root_
 
std::string sequence
 
std::string ss
 
std::string abego
 
std::map< int, int > translate_index
 
std::vector< int > begin
 
std::vector< int > end
 
std::vector< int > copy_begin
 
std::vector< int > copy_end
 
std::vector< int > src_begin
 
std::vector< int > src_end
 
std::string aa
 
bool hasInsertion
 
protocols::forge::build::BuildManager manager
 
core::pack::task::PackerTaskOP task
 
core::pose::Pose rvjump_pose
 
bool buildDisulfide
 
ObjexxFCL::FArray2D_int disulfide_jump_points
 
int disulfide_cutpoint
 
std::string disulfide_ss
 
int insertionStartIndex
 
int insertionEndIndex
 
ObjexxFCL::FArray2D_bool design_matrix
 

Detailed Description

Definition at line 31 of file RemodelWorkingSet.hh.

Constructor & Destructor Documentation

protocols::forge::remodel::WorkingRemodelSet::WorkingRemodelSet ( )
inline

If remodel loop setup is calling for n-terminus movement then return true, otherwise false.

build a fold tree for loop modeling using the defined loops

Note
builds directly from internal loop data and does not randomize cutpoints, so inside a fully stochastic loop building routine you most likely do not want to use this function

Definition at line 84 of file RemodelWorkingSet.hh.

References buildDisulfide, and hasInsertion.

protocols::forge::remodel::WorkingRemodelSet::WorkingRemodelSet ( WorkingRemodelSet const &  rval)

copy constructor

Definition at line 102 of file RemodelWorkingSet.cc.

References abego, hasInsertion, sequence, and ss.

protocols::forge::remodel::WorkingRemodelSet::~WorkingRemodelSet ( )
inline

Definition at line 95 of file RemodelWorkingSet.hh.

Member Function Documentation

void protocols::forge::remodel::WorkingRemodelSet::manualPackerTaskGen ( core::pose::Pose const &  built_pose,
protocols::forge::remodel::RemodelData const &  data 
)

Definition at line 620 of file RemodelWorkingSet.cc.

References core::pack::task::parse_resfile_string(), protocols::forge::remodel::RemodelData::parsed_string_for_resfile, and protocols::forge::methods::remodel_generic_taskfactory().

Referenced by protocols::forge::remodel::RemodelDesignMover::mode4_packertask().

WorkingRemodelSet & protocols::forge::remodel::WorkingRemodelSet::operator= ( WorkingRemodelSet const &  rval)

Definition at line 121 of file RemodelWorkingSet.cc.

References abego, begin, copy_begin, copy_end, end, hasInsertion, loops, manager, rvjump_pose, sequence, src_begin, src_end, ss, task, and translate_index.

void protocols::forge::remodel::WorkingRemodelSet::workingSetGen ( core::pose::Pose const &  input_pose,
protocols::forge::remodel::RemodelData const &  data 
)

Definition at line 147 of file RemodelWorkingSet.cc.

References protocols::forge::remodel::RemodelData::abego, core::scoring::abego, protocols::forge::remodel::RemodelData::blueprint, protocols::forge::remodel::RemodelData::dssp_updated_ss, core::sequence::end, protocols::forge::remodel::LineObject::index, protocols::forge::remodel::RemodelData::insertPose, protocols::forge::build::SegmentInsertConnectionScheme::N, protocols::forge::remodel::LineObject::original_index, protocols::forge::remodel::RemodelData::sequence, core::pose::Pose::total_residue(), and protocols::forge::remodel::TR().

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

Member Data Documentation

std::string protocols::forge::remodel::WorkingRemodelSet::aa

Definition at line 48 of file RemodelWorkingSet.hh.

std::string protocols::forge::remodel::WorkingRemodelSet::abego

Definition at line 40 of file RemodelWorkingSet.hh.

Referenced by protocols::forge::remodel::RemodelMover::centroid_build(), operator=(), and WorkingRemodelSet().

std::vector<int> protocols::forge::remodel::WorkingRemodelSet::begin

Definition at line 42 of file RemodelWorkingSet.hh.

Referenced by operator=().

bool protocols::forge::remodel::WorkingRemodelSet::buildDisulfide

Definition at line 56 of file RemodelWorkingSet.hh.

Referenced by WorkingRemodelSet().

std::vector<int> protocols::forge::remodel::WorkingRemodelSet::copy_begin

Definition at line 44 of file RemodelWorkingSet.hh.

Referenced by operator=().

std::vector<int> protocols::forge::remodel::WorkingRemodelSet::copy_end

Definition at line 45 of file RemodelWorkingSet.hh.

Referenced by operator=().

ObjexxFCL::FArray2D_bool protocols::forge::remodel::WorkingRemodelSet::design_matrix

Definition at line 63 of file RemodelWorkingSet.hh.

int protocols::forge::remodel::WorkingRemodelSet::disulfide_cutpoint

Definition at line 58 of file RemodelWorkingSet.hh.

ObjexxFCL::FArray2D_int protocols::forge::remodel::WorkingRemodelSet::disulfide_jump_points

Definition at line 57 of file RemodelWorkingSet.hh.

std::string protocols::forge::remodel::WorkingRemodelSet::disulfide_ss

Definition at line 59 of file RemodelWorkingSet.hh.

std::vector<int> protocols::forge::remodel::WorkingRemodelSet::end

Definition at line 43 of file RemodelWorkingSet.hh.

Referenced by operator=().

bool protocols::forge::remodel::WorkingRemodelSet::hasInsertion

Definition at line 49 of file RemodelWorkingSet.hh.

Referenced by operator=(), and WorkingRemodelSet().

int protocols::forge::remodel::WorkingRemodelSet::insertionEndIndex

Definition at line 62 of file RemodelWorkingSet.hh.

int protocols::forge::remodel::WorkingRemodelSet::insertionStartIndex

Definition at line 61 of file RemodelWorkingSet.hh.

protocols::loops::Loops protocols::forge::remodel::WorkingRemodelSet::loops

Definition at line 36 of file RemodelWorkingSet.hh.

Referenced by protocols::forge::remodel::RemodelAccumulator::cluster_loop(), and operator=().

protocols::forge::build::BuildManager protocols::forge::remodel::WorkingRemodelSet::manager

Definition at line 51 of file RemodelWorkingSet.hh.

Referenced by operator=(), and protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover().

core::pose::Pose protocols::forge::remodel::WorkingRemodelSet::rvjump_pose

Definition at line 55 of file RemodelWorkingSet.hh.

Referenced by operator=().

int protocols::forge::remodel::WorkingRemodelSet::safe_root_

Definition at line 37 of file RemodelWorkingSet.hh.

std::string protocols::forge::remodel::WorkingRemodelSet::sequence

Definition at line 38 of file RemodelWorkingSet.hh.

Referenced by operator=(), and WorkingRemodelSet().

std::vector<int> protocols::forge::remodel::WorkingRemodelSet::src_begin

Definition at line 46 of file RemodelWorkingSet.hh.

Referenced by operator=().

std::vector<int> protocols::forge::remodel::WorkingRemodelSet::src_end

Definition at line 47 of file RemodelWorkingSet.hh.

Referenced by operator=().

std::string protocols::forge::remodel::WorkingRemodelSet::ss

Definition at line 39 of file RemodelWorkingSet.hh.

Referenced by protocols::forge::remodel::RemodelMover::centroid_build(), operator=(), and WorkingRemodelSet().

core::pack::task::PackerTaskOP protocols::forge::remodel::WorkingRemodelSet::task

Definition at line 52 of file RemodelWorkingSet.hh.

Referenced by protocols::forge::remodel::RemodelDesignMover::apply(), protocols::forge::remodel::RemodelDesignMover::mode1_packertask(), protocols::forge::remodel::RemodelDesignMover::mode2_packertask(), protocols::forge::remodel::RemodelDesignMover::mode3_packertask(), protocols::forge::remodel::RemodelDesignMover::mode5_packertask(), protocols::forge::remodel::RemodelDesignMover::mode6_packertask(), operator=(), protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover(), protocols::forge::remodel::RemodelDesignMover::set_state(), and protocols::forge::remodel::RemodelDesignMover::task().

std::map<int,int> protocols::forge::remodel::WorkingRemodelSet::translate_index

Definition at line 41 of file RemodelWorkingSet.hh.

Referenced by operator=().

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