ExposedStrandMover Class Reference

Inheritance diagram for ExposedStrandMover:

Public Member Functions
	ExposedStrandMover ()
void	apply (core::pose::Pose &pose) override
virtual void	print_sheets (core::pose::Pose &pose, core::Size &start_sheet, core::Size &end_sheet, core::Size &nhbonds)
virtual void	print_sheets_extras (core::pose::Pose &pose, core::pose::Pose &native_pose, core::Size &start_sheet, core::Size &end_sheet, core::Size &nhbonds, Real &rmsd, Real &energy, Size &match_res)
virtual void	parse_strand_ids (core::pose::Pose &pose, utility::vector1< std::string > &strand_id)
virtual Real	bb_score (pose::Pose &pose, core::Size aligned_chain_num, core::scoring::ScoreFunctionOP &scorefxn)
virtual pose::Pose	move_superimpose (core::pose::Pose &pose1, core::pose::Pose &pose2, core::Size &start_res1, core::Size &start_res2, core::Size &end_res1, core::Size &end_res2)
virtual Real	bb_rmsd (const core::pose::Pose &pose1, const core::pose::Pose &pose2)
virtual bool	is_exposed (pose::Pose &pose, Size &resid, vector1< Real > sasa_values)
MoverOP	clone () const override
std::string	get_name () const override
MoverOP	fresh_instance () const override

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_
bool	check_rmsd_
vector1< std::string >	strand_def_vector_
vector1< core::Size >	strand_pose_nums_
core::pose::Pose	native_pose_
Size	beta_length_
Size	sat_allow_
Size	num_satisfied_
core::Real	maxE_
core::Real	maxRMSD_
char	chain_char_
std::string	struct_filename_
vector1< core::Real >	best_rmsd_values_
utility::vector1< core::Size >	res_to_loose_
vector1< pose::Pose >	master_poses_
vector1< Real >	full_scores_
vector1< Size >	start_res_list_
vector1< Size >	end_res_list_

Constructor & Destructor Documentation

ExposedStrandMover()

ExposedStrandMover::ExposedStrandMover

(

)

References beta_length, check_rmsd, option, and sat_allow.

Member Function Documentation

apply()

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

override

References utility::file::FileName::base(), cal_NBR_radius::current_res, basic::options::OptionKeys::in::file::dssp, indel::end_res, create_a3b_hbs::first, test.T200_Scoring::hbond_set, create_a3b_hbs::ii, beta_nonlocal::jj, create_a3b_hbs::k, kk, max(), max_E_allow, max_RMSD, min(), in::file::native(), basic::options::option, option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, strand_span, struct_file, TR, basic::options::OptionKeys::inout::dbms::user, utility_exit_with_message_status, and basic::MetricValue< T >::value().

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

bb_rmsd()

core::Real ExposedStrandMover::bb_rmsd ( const core::pose::Pose &  pose1, const core::pose::Pose &  pose2  )

virtual

References test.T008_Serialization::pose1, test.T008_Serialization::pose2, and loops_kic::rms.

bb_score()

core::Real ExposedStrandMover::bb_score ( pose::Pose &  pose, core::Size  aligned_chain_num, core::scoring::ScoreFunctionOP &  scorefxn  )

virtual

References numeric::distance_squared(), create_a3b_hbs::ii, create_a3b_hbs::j, beta_nonlocal::jj, beta_nonlocal::pose, res, oop_conformations::scorefxn, TR, and basic::options::OptionKeys::in::file::xyz.

clone()

MoverOP ExposedStrandMover::clone ( ) const

inlineoverride

fresh_instance()

MoverOP ExposedStrandMover::fresh_instance ( ) const

inlineoverride

References clone().

get_name()

std::string ExposedStrandMover::get_name ( ) const

inlineoverride

is_exposed()

bool ExposedStrandMover::is_exposed ( pose::Pose &  pose, Size &  resid, vector1< Real >  sasa_values  )

virtual

References basic::options::OptionKeys::legacy_sewing::neighbor_cutoff, beta_nonlocal::pose, and TR.

move_superimpose()

pose::Pose ExposedStrandMover::move_superimpose ( core::pose::Pose &  pose1, core::pose::Pose &  pose2, core::Size &  start_res1, core::Size &  start_res2, core::Size &  end_res1, core::Size &  end_res2  )

virtual

References create_a3b_hbs::ii, oop_conformations::length, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, test.T008_Serialization::pose1, test.T008_Serialization::pose2, runtime_assert, and superimpose_pose().

parse_strand_ids()

void ExposedStrandMover::parse_strand_ids ( core::pose::Pose &  pose, utility::vector1< std::string > &  strand_id  )

virtual

References chain_index, end_index, beta_nonlocal::pose, start_index, and TR.

print_sheets()

void ExposedStrandMover::print_sheets ( core::pose::Pose &  pose, core::Size &  start_sheet, core::Size &  end_sheet, core::Size &  nhbonds  )

virtual

References lactamize::filename, beta_nonlocal::pose, and TRout.

print_sheets_extras()

void ExposedStrandMover::print_sheets_extras ( core::pose::Pose &  pose, core::pose::Pose &  native_pose, core::Size &  start_sheet, core::Size &  end_sheet, core::Size &  nhbonds, Real &  rmsd, Real &  energy, Size &  match_res  )

virtual

References oop_conformations::energy, lactamize::filename, docking::native_pose, beta_nonlocal::pose, average_rmsds::rmsd, and TRout.

Member Data Documentation

best_rmsd_values_

vector1<core::Real> ExposedStrandMover::best_rmsd_values_

private

beta_length_

Size ExposedStrandMover::beta_length_

private

chain_char_

char ExposedStrandMover::chain_char_

private

check_rmsd_

bool ExposedStrandMover::check_rmsd_

private

end_res_list_

vector1<Size> ExposedStrandMover::end_res_list_

private

full_scores_

vector1<Real> ExposedStrandMover::full_scores_

private

master_poses_

vector1<pose::Pose> ExposedStrandMover::master_poses_

private

maxE_

core::Real ExposedStrandMover::maxE_

private

maxRMSD_

core::Real ExposedStrandMover::maxRMSD_

private

native_pose_

core::pose::Pose ExposedStrandMover::native_pose_

private

num_satisfied_

Size ExposedStrandMover::num_satisfied_

private

res_to_loose_

utility::vector1< core::Size > ExposedStrandMover::res_to_loose_

private

sat_allow_

Size ExposedStrandMover::sat_allow_

private

scorefxn_

core::scoring::ScoreFunctionOP ExposedStrandMover::scorefxn_

private

start_res_list_

vector1<Size> ExposedStrandMover::start_res_list_

private

strand_def_vector_

vector1< std::string > ExposedStrandMover::strand_def_vector_

private

strand_pose_nums_

vector1< core::Size > ExposedStrandMover::strand_pose_nums_

private

struct_filename_

std::string ExposedStrandMover::struct_filename_

private

---

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

• src/apps/public/scenarios/beta_strand_homodimer_design/exposed_strand_finder.cc