ChallengeMover Class Reference

Inheritance diagram for ChallengeMover:

Public Types
typedef boost::unordered_map< int, core::kinematics::Jump >	Jumps

Public Member Functions
void	initialize_template_structures ()
utility::vector1< core::Real >	count_alignment (core::pose::Pose &mod_pose, utility::vector1< std::map< core::Size, core::Size > > &seqpos_alignments)
protocols::loops::Loops	extract_chunks_from_alignment_counts (utility::vector1< core::Real > alignment_counts)
void	extract_ss_chunks_from_alignment_counts (utility::vector1< core::Real > alignment_counts, std::string const full_sequence, utility::vector1< SecondaryStructureChunk > &ss_chunks)
core::Size	pick_random_template ()
void	get_alignment_from_template (core::pose::PoseOP const template_pose, std::map< core::Size, core::Size > &seqpos_alignment)
	ChallengeMover ()
void	initialize_pose (core::pose::Pose &pose)
void	realign (core::pose::Pose &pose)
std::list< Size >	downstream_residues_from_jump (core::pose::Pose &pose, Size jump_number)
void	apply (core::pose::Pose &pose)
core::Size	num_trials ()
void	jumps_from_pose (const core::pose::Pose &pose, Jumps *jumps) const
void	do_rigid_body_moves (const core::scoring::ScoreFunctionOP &score, core::pose::Pose *pose) const
void	sample (core::pose::Pose &pose, core::scoring::ScoreFunctionOP &scorefxn)
std::string	get_name () const

Private Attributes
utility::vector1< core::pose::PoseOP >	template_structures_
utility::vector1< Loops >	template_ss_chunks_
utility::vector1< std::map< core::Size, core::Size > >	seqpos_alignments_
Loops	ss_chunks_target_
Loops	loops_target_
utility::vector1< core::fragment::FragSetOP >	frag_libs_

Member Typedef Documentation

Jumps

typedef boost::unordered_map<int, core::kinematics::Jump> ChallengeMover::Jumps

Constructor & Destructor Documentation

ChallengeMover()

ChallengeMover::ChallengeMover ( )

inline

Member Function Documentation

apply()

void ChallengeMover::apply ( core::pose::Pose &  pose )

inline

References challenge::close_loops, initialize_pose(), basic::options::option, beta_nonlocal::pose, oop_conformations::scorefxn, and basic::options::OptionKeys::remodel::vdw.

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

count_alignment()

utility::vector1<core::Real> ChallengeMover::count_alignment ( core::pose::Pose &  mod_pose, utility::vector1< std::map< core::Size, core::Size > > &  seqpos_alignments  )

inline

References end, ObjexxFCL::format::F(), detail::find(), basic::Tracer::flush(), test.T110_numeric::I, and TR.

do_rigid_body_moves()

void ChallengeMover::do_rigid_body_moves ( const core::scoring::ScoreFunctionOP &  score, core::pose::Pose *  pose  ) const

inline

References docking::jumps, option, beta_nonlocal::pose, basic::options::OptionKeys::fold_and_dock::rigid_body_cycles, local::temperature, and TR.

downstream_residues_from_jump()

std::list< Size > ChallengeMover::downstream_residues_from_jump ( core::pose::Pose &  pose, Size  jump_number  )

inline

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

extract_chunks_from_alignment_counts()

protocols::loops::Loops ChallengeMover::extract_chunks_from_alignment_counts ( utility::vector1< core::Real >  alignment_counts )

inline

References average(), and basic::options::OptionKeys::nonlocal::chunks.

extract_ss_chunks_from_alignment_counts()

void ChallengeMover::extract_ss_chunks_from_alignment_counts ( utility::vector1< core::Real >  alignment_counts, std::string const  full_sequence, utility::vector1< SecondaryStructureChunk > &  ss_chunks  )

inline

References utility::vectorL< L, T, A >::append(), average(), SecondaryStructureChunk::set_sequence(), SecondaryStructureChunk::set_start_seqpos(), and SecondaryStructureChunk::start_seqpos().

get_alignment_from_template()

void ChallengeMover::get_alignment_from_template ( core::pose::PoseOP const  template_pose, std::map< core::Size, core::Size > &  seqpos_alignment  )

inline

get_name()

std::string ChallengeMover::get_name ( ) const

inline

initialize_pose()

void ChallengeMover::initialize_pose ( core::pose::Pose &  pose )

inline

References align_backbone_by_chunk(), apps::pilot::downstream_residues_from_jump(), basic::Tracer::flush(), test.T110_numeric::I, oop_conformations::length, option, beta_nonlocal::pose, basic::options::OptionKeys::in::file::psipred_ss2, set_secstruct_from_psipred_ss2(), basic::options::OptionKeys::cutoutdomain::start, TR, basic::options::OptionKeys::inout::dbms::user, and utility_exit_with_message.

initialize_template_structures()

void ChallengeMover::initialize_template_structures ( )

inline

References read_template_structures().

jumps_from_pose()

void ChallengeMover::jumps_from_pose ( const core::pose::Pose &  pose, Jumps *  jumps  ) const

inline

References basic::Tracer::Debug, create_a3b_hbs::i, beta_nonlocal::pose, and TR.

num_trials()

core::Size ChallengeMover::num_trials ( )

inline

Referenced by schema.Move::efficiency().

pick_random_template()

core::Size ChallengeMover::pick_random_template ( )

inline

References numeric::random::RandomGenerator::random_range(), numeric::random::rg(), and subloop_histogram::size.

realign()

void ChallengeMover::realign ( core::pose::Pose &  pose )

inline

References align_backbone_by_chunk(), apps::pilot::downstream_residues_from_jump(), test.T110_numeric::I, challenge::max_registry_shift, beta_nonlocal::pose, numeric::random::RandomGenerator::random_range(), numeric::random::rg(), and TR.

sample()

void ChallengeMover::sample ( core::pose::Pose &  pose, core::scoring::ScoreFunctionOP &  scorefxn  )

inline

References erraser_util::copy(), basic::Tracer::flush(), create_a3b_hbs::i, basic::options::OptionKeys::MonteCarlo::MonteCarlo, local::num_trials, beta_nonlocal::pose, basic::options::OptionKeys::edensity::realign, oop_conformations::scorefxn, and TR.

Member Data Documentation

frag_libs_

utility::vector1< core::fragment::FragSetOP > ChallengeMover::frag_libs_

private

loops_target_

Loops ChallengeMover::loops_target_

private

seqpos_alignments_

utility::vector1< std::map <core::Size, core::Size> > ChallengeMover::seqpos_alignments_

private

ss_chunks_target_

Loops ChallengeMover::ss_chunks_target_

private

template_ss_chunks_

utility::vector1< Loops > ChallengeMover::template_ss_chunks_

private

template_structures_

utility::vector1< core::pose::PoseOP > ChallengeMover::template_structures_

private

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

• src/apps/pilot/yfsong/challenge.cc