apps::pilot::AlignChunkMover Class Reference

#include <AlignChunkMover.hh>

Inheritance diagram for apps::pilot::AlignChunkMover:

Public Member Functions
	AlignChunkMover (numeric::random::RandomGenerator &RG)
void	get_superposition_transformation (pose::Pose const &mod_pose, pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT)
void	apply_transform (pose::Pose &mod_pose, std::list< Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT)
void	align_chunk (core::pose::Pose &pose)
void	set_template (core::pose::PoseCOP template_pose, std::map< core::Size, core::Size > const &sequence_alignment)
void	set_aligned_chunk (core::pose::Pose const &pose, Size const jump_number)
void	set_reset_torsion_unaligned (bool reset_torsion_unaligned)
void	steal_torsion_from_template (core::pose::Pose &pose)
bool	get_local_sequence_mapping (core::pose::Pose const &pose, int registry_shift=0, Size MAX_TRIAL=10)
void	set_registry_shift (int registry_shift)
Size	trial_counter (Size ires)
void	apply (core::pose::Pose &pose)
std::string	get_name () const

Private Attributes
numeric::random::RandomGenerator &	RG_
core::pose::PoseCOP	template_pose_
std::map< core::Size, core::Size >	sequence_alignment_
Size	jump_number_
Size	seqpos_start_
Size	seqpos_stop_
int	registry_shift_
char	secstruct_
bool	reset_torsion_unaligned_
bool	align_to_ss_only_
bool	copy_ss_torsion_only_
std::map< core::Size, core::Size >	sequence_alignment_local_
core::id::AtomID_Map< core::id::AtomID >	atom_map_
utility::vector1< Size >	align_trial_counter_

Constructor & Destructor Documentation

AlignChunkMover()

apps::pilot::AlignChunkMover::AlignChunkMover ( numeric::random::RandomGenerator &  RG )

inline

Member Function Documentation

align_chunk()

void apps::pilot::AlignChunkMover::align_chunk ( core::pose::Pose &  pose )

inline

References apply_transform(), get_superposition_transformation(), beta_nonlocal::pose, and docking::R.

apply()

void apps::pilot::AlignChunkMover::apply ( core::pose::Pose &  pose )

inline

References beta_nonlocal::pose, and loops_kic::success.

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

apply_transform()

void apps::pilot::AlignChunkMover::apply_transform ( pose::Pose &  mod_pose, std::list< Size > const &  residue_list, numeric::xyzMatrix< core::Real > const &  R, numeric::xyzVector< core::Real > const &  preT, numeric::xyzVector< core::Real > const &  postT  )

inline

References natoms(), and docking::R.

get_local_sequence_mapping()

bool apps::pilot::AlignChunkMover::get_local_sequence_mapping ( core::pose::Pose const &  pose, int  registry_shift = 0, Size  MAX_TRIAL = 10  )

inline

References demo.D060_Folding::counter, apps::pilot::discontinued_lower(), apps::pilot::discontinued_upper(), and beta_nonlocal::pose.

get_name()

std::string apps::pilot::AlignChunkMover::get_name ( ) const

inline

get_superposition_transformation()

void apps::pilot::AlignChunkMover::get_superposition_transformation ( pose::Pose const &  mod_pose, pose::Pose const &  ref_pose, id::AtomID_Map< id::AtomID > const &  atom_map, numeric::xyzMatrix< core::Real > &  R, numeric::xyzVector< core::Real > &  preT, numeric::xyzVector< core::Real > &  postT  )

inline

References numeric::model_quality::findUU(), run_backbone::float, create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, natoms(), and docking::R.

set_aligned_chunk()

void apps::pilot::AlignChunkMover::set_aligned_chunk ( core::pose::Pose const &  pose, Size const  jump_number  )

inline

References apps::pilot::downstream_residues_from_jump(), and beta_nonlocal::pose.

set_registry_shift()

void apps::pilot::AlignChunkMover::set_registry_shift ( int  registry_shift )

inline

set_reset_torsion_unaligned()

void apps::pilot::AlignChunkMover::set_reset_torsion_unaligned ( bool  reset_torsion_unaligned )

inline

set_template()

void apps::pilot::AlignChunkMover::set_template ( core::pose::PoseCOP  template_pose, std::map< core::Size, core::Size > const &  sequence_alignment  )

inline

steal_torsion_from_template()

void apps::pilot::AlignChunkMover::steal_torsion_from_template ( core::pose::Pose &  pose )

inline

References basic::Tracer::Debug, apps::pilot::discontinued_lower(), apps::pilot::discontinued_upper(), ObjexxFCL::format::F(), test.T110_numeric::I, beta_nonlocal::pose, and TR.

trial_counter()

Size apps::pilot::AlignChunkMover::trial_counter ( Size  ires )

inline

Member Data Documentation

align_to_ss_only_

bool apps::pilot::AlignChunkMover::align_to_ss_only_

private

align_trial_counter_

utility::vector1<Size> apps::pilot::AlignChunkMover::align_trial_counter_

private

atom_map_

core::id::AtomID_Map< core::id::AtomID > apps::pilot::AlignChunkMover::atom_map_

private

copy_ss_torsion_only_

bool apps::pilot::AlignChunkMover::copy_ss_torsion_only_

private

jump_number_

Size apps::pilot::AlignChunkMover::jump_number_

private

registry_shift_

int apps::pilot::AlignChunkMover::registry_shift_

private

reset_torsion_unaligned_

bool apps::pilot::AlignChunkMover::reset_torsion_unaligned_

private

RG_

numeric::random::RandomGenerator& apps::pilot::AlignChunkMover::RG_

private

secstruct_

char apps::pilot::AlignChunkMover::secstruct_

private

seqpos_start_

Size apps::pilot::AlignChunkMover::seqpos_start_

private

seqpos_stop_

Size apps::pilot::AlignChunkMover::seqpos_stop_

private

sequence_alignment_

std::map<core::Size, core::Size> apps::pilot::AlignChunkMover::sequence_alignment_

private

sequence_alignment_local_

std::map<core::Size, core::Size> apps::pilot::AlignChunkMover::sequence_alignment_local_

private

template_pose_

core::pose::PoseCOP apps::pilot::AlignChunkMover::template_pose_

private

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

• src/apps/pilot/yfsong/AlignChunkMover.hh