apps::pilot::SampleSecondaryStructureAlignmentMover Class Reference

#include <util.hh>

Inheritance diagram for apps::pilot::SampleSecondaryStructureAlignmentMover:

Public Member Functions
	SampleSecondaryStructureAlignmentMover (numeric::random::RandomGenerator &RG, utility::vector1< utility::file::FileName > const &template_filenames)
void	read_template_structures (utility::vector1< core::pose::PoseOP > &template_structures, utility::vector1< utility::file::FileName > const &template_filenames)
void	set_loops_to_virt_ala (core::pose::Pose &pose, Loops loops)
void	revert_loops_to_original (core::pose::Pose &pose, Loops loops)
void	add_gap_constraints_to_pose (core::pose::Pose &pose, Size seq_distance_to_gap, Loops const &chunks, Real stdev=1.)
void	setup_startree (core::pose::Pose &pose)
numeric::xyzVector< Real >	center_of_mass (core::pose::Pose const &pose)
void	translate_virt_to_CoM (core::pose::Pose &pose)
Loops	loops ()
void	apply (core::pose::Pose &pose)
std::string	get_name () const

Private Attributes
numeric::random::RandomGenerator &	RG_
utility::vector1< core::pose::PoseOP >	template_poses_
Loops	ss_chunks_pose_
Loops	loops_pose_

Constructor & Destructor Documentation

SampleSecondaryStructureAlignmentMover()

apps::pilot::SampleSecondaryStructureAlignmentMover::SampleSecondaryStructureAlignmentMover ( numeric::random::RandomGenerator &  RG, utility::vector1< utility::file::FileName > const &  template_filenames  )

inline

References read_template_structures().

Member Function Documentation

add_gap_constraints_to_pose()

void apps::pilot::SampleSecondaryStructureAlignmentMover::add_gap_constraints_to_pose ( core::pose::Pose &  pose, Size  seq_distance_to_gap, Loops const &  chunks, Real  stdev = 1.  )

inline

References basic::options::OptionKeys::nonlocal::chunks, create_a3b_hbs::i, test.T110_numeric::I, beta_nonlocal::pose, myspace::stdev(), and TR.

apply()

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

inline

References apps::pilot::all_chunks, apps::pilot::MultiTemplateAlignChunkMover::apply(), basic::Tracer::Debug, pyrosetta.distributed.io::get_score_function(), create_a3b_hbs::i, test.T110_numeric::I, challenge::max_registry_shift, option, beta_nonlocal::pose, apps::pilot::random_chunk, challenge::revert_real_loops, oop_conformations::scorefxn, TR, and basic::options::OptionKeys::sc::weight.

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), and pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

center_of_mass()

numeric::xyzVector<Real> apps::pilot::SampleSecondaryStructureAlignmentMover::center_of_mass ( core::pose::Pose const &  pose )

inline

References val2thr::atom, create_a3b_hbs::i, create_a3b_hbs::j, create_a3b_hbs::nres, and beta_nonlocal::pose.

get_name()

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

inline

loops()

Loops apps::pilot::SampleSecondaryStructureAlignmentMover::loops ( )

inline

read_template_structures()

void apps::pilot::SampleSecondaryStructureAlignmentMover::read_template_structures ( utility::vector1< core::pose::PoseOP > &  template_structures, utility::vector1< utility::file::FileName > const &  template_filenames  )

inline

References pyrosetta.distributed.io::pose_from_file().

revert_loops_to_original()

void apps::pilot::SampleSecondaryStructureAlignmentMover::revert_loops_to_original ( core::pose::Pose &  pose, Loops  loops  )

inline

References in::file::fasta(), option, beta_nonlocal::pose, beta_sc_scan::restype_set, basic::options::OptionKeys::relax::sequence, and basic::options::OptionKeys::cutoutdomain::start.

set_loops_to_virt_ala()

void apps::pilot::SampleSecondaryStructureAlignmentMover::set_loops_to_virt_ala ( core::pose::Pose &  pose, Loops  loops  )

inline

References beta_nonlocal::pose, beta_sc_scan::restype_set, and basic::options::OptionKeys::cutoutdomain::start.

setup_startree()

void apps::pilot::SampleSecondaryStructureAlignmentMover::setup_startree ( core::pose::Pose &  pose )

inline

References basic::options::OptionKeys::nonlocal::chunks, basic::Tracer::Debug, basic::Tracer::flush(), create_a3b_hbs::i, option, beta_nonlocal::pose, basic::options::OptionKeys::in::file::psipred_ss2, set_secstruct_from_psipred_ss2(), challenge::ss, TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message, and challenge::virtual_loops.

translate_virt_to_CoM()

void apps::pilot::SampleSecondaryStructureAlignmentMover::translate_virt_to_CoM ( core::pose::Pose &  pose )

inline

References center_of_mass(), basic::Tracer::Debug, ObjexxFCL::format::F(), beta_nonlocal::pose, TR, and basic::options::OptionKeys::rigid::translation.

Member Data Documentation

loops_pose_

Loops apps::pilot::SampleSecondaryStructureAlignmentMover::loops_pose_

private

RG_

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

private

ss_chunks_pose_

Loops apps::pilot::SampleSecondaryStructureAlignmentMover::ss_chunks_pose_

private

template_poses_

utility::vector1< core::pose::PoseOP > apps::pilot::SampleSecondaryStructureAlignmentMover::template_poses_

private

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

• src/apps/pilot/yfsong/util.hh