SwapElementsMover2 Class Reference

Inheritance diagram for SwapElementsMover2:

Public Types
typedef core::Size	Size
typedef core::Real	Real
typedef core::pose::Pose	Pose
typedef core::pose::PoseOP	PoseOP
typedef core::id::AtomID	AtomID
typedef protocols::forge::build::BuildManager	BuildManager
typedef protocols::forge::build::Interval	Interval
typedef protocols::forge::build::SegmentRebuild	SegmentRebuild
typedef protocols::forge::build::SegmentRebuildOP	SegmentRebuildOP
typedef protocols::forge::components::VarLengthBuild	VarLengthBuild
typedef core::kinematics::MoveMap	MoveMap
typedef core::kinematics::MoveMapOP	MoveMapOP
typedef core::fragment::FrameList	FrameList
typedef core::fragment::FrameOP	FrameOP
typedef core::fragment::FragData	FragData
typedef numeric::xyzVector< Real >	Vector
typedef numeric::xyzMatrix< Real >	Matrix

Public Member Functions
	SwapElementsMover2 ()
FrameList	pick_fragments (std::string const &complete_ss, std::string const &complete_aa, utility::vector1< std::string > const &complete_abego, Interval const &interval, Size const frag_length, Size const n_frags)
	pick fragments of a given length, padding when necessary More...
Size	count_clashes (Pose const &pose)
virtual void	apply (Pose &pose)
virtual std::string	get_name () const

Private Attributes
Size	junction_start_
Size	junction_end_
Size	frag_length_
Size	nfrags_
std::string	junction_ss_
std::string	junction_abego_
std::string	junction_aa_
Real	distance_threshold_
Real	clash_distance_
bool	symm_min_

Member Typedef Documentation

AtomID

typedef core::id::AtomID SwapElementsMover2::AtomID

BuildManager

typedef protocols::forge::build::BuildManager SwapElementsMover2::BuildManager

FragData

typedef core::fragment::FragData SwapElementsMover2::FragData

FrameList

typedef core::fragment::FrameList SwapElementsMover2::FrameList

FrameOP

typedef core::fragment::FrameOP SwapElementsMover2::FrameOP

Interval

typedef protocols::forge::build::Interval SwapElementsMover2::Interval

Matrix

typedef numeric::xyzMatrix< Real > SwapElementsMover2::Matrix

MoveMap

typedef core::kinematics::MoveMap SwapElementsMover2::MoveMap

MoveMapOP

typedef core::kinematics::MoveMapOP SwapElementsMover2::MoveMapOP

Pose

typedef core::pose::Pose SwapElementsMover2::Pose

PoseOP

typedef core::pose::PoseOP SwapElementsMover2::PoseOP

Real

typedef core::Real SwapElementsMover2::Real

SegmentRebuild

typedef protocols::forge::build::SegmentRebuild SwapElementsMover2::SegmentRebuild

SegmentRebuildOP

typedef protocols::forge::build::SegmentRebuildOP SwapElementsMover2::SegmentRebuildOP

Size

typedef core::Size SwapElementsMover2::Size

VarLengthBuild

typedef protocols::forge::components::VarLengthBuild SwapElementsMover2::VarLengthBuild

Vector

typedef numeric::xyzVector< Real > SwapElementsMover2::Vector

Constructor & Destructor Documentation

SwapElementsMover2()

SwapElementsMover2::SwapElementsMover2 ( )

inline

Member Function Documentation

apply()

virtual void SwapElementsMover2::apply ( Pose &  pose )

inlinevirtual

References basic::options::OptionKeys::AnchoredDesign::anchor, numeric::angle_degrees(), center_of_mass(), numeric::kinematic_closure::frame(), score_vs_rmsd::frames, create_a3b_hbs::i, numeric::xyzMatrix< T >::identity(), basic::options::OptionKeys::ms::checkpoint::interval, subloop_histogram::iterator, create_a3b_hbs::j, basic::options::OptionKeys::in::file::movemap, pick_fragments(), beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::relax::sequence, challenge::ss, basic::options::TR, numeric::y_rotation_matrix_degrees(), and numeric::z_rotation_matrix_degrees().

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

count_clashes()

Size SwapElementsMover2::count_clashes ( Pose const &  pose )

inline

References create_a3b_hbs::i, create_a3b_hbs::j, and beta_nonlocal::pose.

get_name()

virtual std::string SwapElementsMover2::get_name ( ) const

inlinevirtual

pick_fragments()

FrameList SwapElementsMover2::pick_fragments ( std::string const &  complete_ss, std::string const &  complete_aa, utility::vector1< std::string > const &  complete_abego, Interval const &  interval, Size const  frag_length, Size const  n_frags  )

inline

pick fragments of a given length, padding when necessary

Parameters

[in]	complete_ss	The complete secondary structure string, typically from a Pose.
[in]	complete_aa	The complete amino acid string, typically from a Pose; can be empty. If empty, sequence bias is not used to pick fragments.
[in]	interval	The interval [left, right] to pick fragments from; Pose numbering (i.e. 1-based indexing).
[in]	frag_length	The desired length of the fragments
[in]	n_frags	The number of fragments to pick per position.

References demo.D080_Loop_modeling::frag_length, numeric::kinematic_closure::frame(), score_vs_rmsd::frames, create_a3b_hbs::ii, basic::options::OptionKeys::ms::checkpoint::interval, create_a3b_hbs::j, basic::options::OptionKeys::frags::n_frags, pick_fragments(), make_symmdef_file_denovo::pos, runtime_assert, and basic::options::TR.

Member Data Documentation

clash_distance_

Real SwapElementsMover2::clash_distance_

private

distance_threshold_

Real SwapElementsMover2::distance_threshold_

private

frag_length_

Size SwapElementsMover2::frag_length_

private

junction_aa_

std::string SwapElementsMover2::junction_aa_

private

junction_abego_

std::string SwapElementsMover2::junction_abego_

private

junction_end_

Size SwapElementsMover2::junction_end_

private

junction_ss_

std::string SwapElementsMover2::junction_ss_

private

junction_start_

Size SwapElementsMover2::junction_start_

private

nfrags_

Size SwapElementsMover2::nfrags_

private

symm_min_

bool SwapElementsMover2::symm_min_

private

---

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

• src/apps/pilot/javierbq/swap_elements.cc