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Public Member Functions | Public Attributes | List of all members
protocols::forge::remodel::RemodelWorkingSet Class Reference

#include <RemodelWorkingSet.hh>

Public Member Functions

 RemodelWorkingSet ()
 
 RemodelWorkingSet (RemodelWorkingSet const &rval)
 copy constructor. More...
 
RemodelWorkingSetoperator= (RemodelWorkingSet const &rval)
 
 ~RemodelWorkingSet ()
 
void workingSetGen (core::pose::Pose const &input_pose, protocols::forge::remodel::RemodelData const &data)
 checks value of option -remodel::generic_aa More...
 
void manualPackerTaskGen (core::pose::Pose const &built_pose, protocols::forge::remodel::RemodelData const &data)
 Takes in a pose and remodel data objects and constructs a packer task for that pose. Uses the resfile string that was created while reading in the blueprint file. What happens if the resfile string is "" ? More...
 

Public Attributes

protocols::loops::Loops loops
 If remodel loop setup is calling for n-terminus movement then return true, otherwise false. More...
 
int safe_root_
 
std::string sequence
 
std::string ss
 
std::string abego
 
std::string LD_types
 
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
 

Constructor & Destructor Documentation

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

copy constructor.

References abego, hasInsertion, LD_types, sequence, and ss.

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

Member Function Documentation

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

Takes in a pose and remodel data objects and constructs a packer task for that pose. Uses the resfile string that was created while reading in the blueprint file. What happens if the resfile string is "" ?

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

RemodelWorkingSet & protocols::forge::remodel::RemodelWorkingSet::operator= ( RemodelWorkingSet const &  rval)
void protocols::forge::remodel::RemodelWorkingSet::workingSetGen ( core::pose::Pose const &  input_pose,
protocols::forge::remodel::RemodelData const &  data 
)

Member Data Documentation

std::string protocols::forge::remodel::RemodelWorkingSet::aa

Referenced by workingSetGen().

std::string protocols::forge::remodel::RemodelWorkingSet::abego
std::vector<int> protocols::forge::remodel::RemodelWorkingSet::begin

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

bool protocols::forge::remodel::RemodelWorkingSet::buildDisulfide
std::vector<int> protocols::forge::remodel::RemodelWorkingSet::copy_begin

Referenced by operator=().

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

Referenced by operator=().

ObjexxFCL::FArray2D_bool protocols::forge::remodel::RemodelWorkingSet::design_matrix
int protocols::forge::remodel::RemodelWorkingSet::disulfide_cutpoint
ObjexxFCL::FArray2D_int protocols::forge::remodel::RemodelWorkingSet::disulfide_jump_points
std::string protocols::forge::remodel::RemodelWorkingSet::disulfide_ss
std::vector<int> protocols::forge::remodel::RemodelWorkingSet::end

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

bool protocols::forge::remodel::RemodelWorkingSet::hasInsertion

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

int protocols::forge::remodel::RemodelWorkingSet::insertionEndIndex
int protocols::forge::remodel::RemodelWorkingSet::insertionStartIndex
std::string protocols::forge::remodel::RemodelWorkingSet::LD_types
protocols::loops::Loops protocols::forge::remodel::RemodelWorkingSet::loops

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

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

protocols::forge::build::BuildManager protocols::forge::remodel::RemodelWorkingSet::manager
core::pose::Pose protocols::forge::remodel::RemodelWorkingSet::rvjump_pose

Referenced by operator=().

int protocols::forge::remodel::RemodelWorkingSet::safe_root_
std::string protocols::forge::remodel::RemodelWorkingSet::sequence
std::vector<int> protocols::forge::remodel::RemodelWorkingSet::src_begin

Referenced by operator=().

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

Referenced by operator=().

std::string protocols::forge::remodel::RemodelWorkingSet::ss
core::pack::task::PackerTaskOP protocols::forge::remodel::RemodelWorkingSet::task
std::map<int,int> protocols::forge::remodel::RemodelWorkingSet::translate_index

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


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