protocols::forge::remodel::RemodelWorkingSet Class Reference

#include <RemodelWorkingSet.hh>

Public Member Functions
	RemodelWorkingSet ()
	RemodelWorkingSet (RemodelWorkingSet const &rval)
	copy constructor. More...
RemodelWorkingSet &	operator= (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

RemodelWorkingSet() [1/2]

protocols::forge::remodel::RemodelWorkingSet::RemodelWorkingSet

(

)

RemodelWorkingSet() [2/2]

protocols::forge::remodel::RemodelWorkingSet::RemodelWorkingSet

(

RemodelWorkingSet const &

rval

)

copy constructor.

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

~RemodelWorkingSet()

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

inline

Member Function Documentation

manualPackerTaskGen()

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.

operator=()

RemodelWorkingSet & protocols::forge::remodel::RemodelWorkingSet::operator=

(

RemodelWorkingSet const &

rval

)

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

workingSetGen()

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

checks value of option -remodel::generic_aa

References aa, protocols::forge::remodel::RemodelData::abego, abego, protocols::forge::build::BuildManager::add(), protocols::loops::Loops::add_loop(), begin, protocols::forge::remodel::RemodelData::blueprint, protocols::forge::remodel::RemodelData::dssp_updated_ss, end, protocols::forge::remodel::LineObject::index, protocols::forge::remodel::RemodelData::insertPose, protocols::forge::remodel::RemodelData::LD_types, LD_types, loops, manager, core::chemical::element::N, protocols::forge::build::SegmentInsertConnectionScheme::N, protocols::forge::remodel::LineObject::original_index, core::pose::Pose::residue_type_set_for_pose(), core::pose::residue_types_from_sequence(), protocols::forge::remodel::Segment::residues, safe_root_, protocols::forge::remodel::RemodelData::sequence, sequence, core::pose::Pose::size(), ss, core::pose::Pose::total_residue(), protocols::forge::remodel::TR(), and translate_index.

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

Member Data Documentation

aa

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

Referenced by workingSetGen().

abego

std::string protocols::forge::remodel::RemodelWorkingSet::abego

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

begin

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

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

buildDisulfide

bool protocols::forge::remodel::RemodelWorkingSet::buildDisulfide

copy_begin

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

Referenced by operator=().

copy_end

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

Referenced by operator=().

design_matrix

ObjexxFCL::FArray2D_bool protocols::forge::remodel::RemodelWorkingSet::design_matrix

disulfide_cutpoint

int protocols::forge::remodel::RemodelWorkingSet::disulfide_cutpoint

disulfide_jump_points

ObjexxFCL::FArray2D_int protocols::forge::remodel::RemodelWorkingSet::disulfide_jump_points

disulfide_ss

std::string protocols::forge::remodel::RemodelWorkingSet::disulfide_ss

end

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

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

hasInsertion

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

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

insertionEndIndex

int protocols::forge::remodel::RemodelWorkingSet::insertionEndIndex

insertionStartIndex

int protocols::forge::remodel::RemodelWorkingSet::insertionStartIndex

LD_types

std::string protocols::forge::remodel::RemodelWorkingSet::LD_types

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

loops

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().

manager

protocols::forge::build::BuildManager protocols::forge::remodel::RemodelWorkingSet::manager

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

rvjump_pose

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

Referenced by operator=().

safe_root_

int protocols::forge::remodel::RemodelWorkingSet::safe_root_

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

sequence

std::string protocols::forge::remodel::RemodelWorkingSet::sequence

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

src_begin

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

Referenced by operator=().

src_end

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

Referenced by operator=().

ss

std::string protocols::forge::remodel::RemodelWorkingSet::ss

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

task

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

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

translate_index

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

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

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

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