#include <NearNativeLoopCloser.hh>

Inheritance diagram for protocols::pose_length_moves::PossibleLoop:

Public Member Functions
	PossibleLoop (int resAdjustmentBeforeLoop, int resAdjustmentAfterLoop, core::Size loopLength, core::Size resBeforeLoop, core::Size resAfterLoop, char resTypeBeforeLoop, char resTypeAfterLoop, core::Size insertedBeforeLoopRes, core::Size insertedAfterLoopRes, core::pose::PoseOP fullLengthPoseOP, core::pose::PoseOP orig_atom_type_fullLengthPoseOP, std::string fragment_store_path, std::string fragment_store_format, std::string fragment_store_compression, core::Size numb_stubs_to_consider)

	~PossibleLoop () override

void	evaluate_distance_closure ()

void	generate_stub_rmsd (core::Real stubRmsdThreshold)

void	generate_output_pose (bool output_closed, bool ideal_loop, core::Real rms_threshold, std::string allowed_loop_abegos, std::string closure_type)

void	setup_finalPose_copy_labels ()

void	setup_finalPose_copy_rotamers ()

core::pose::PoseOP	get_finalPoseOP ()

core::Real	get_stubRMSD ()

core::Real	get_final_RMSD ()

bool	outputed ()

void	outputed (bool outputed)

bool	get_below_distance_threshold ()

void	label_loop (std::string label)

std::string	get_description ()

Private Member Functions
void	trimRegion (core::pose::PoseOP &poseOP, core::Size resStart, core::Size resStop)

void	extendRegion (bool towardCTerm, core::Size resStart, core::Size numberAddRes, core::pose::PoseOP &poseOP)

void	generate_overlap_range (core::Size &front_overlap, core::Size &back_overlap)

bool	check_loop_abego (core::pose::PoseOP &poseOP, core::Size loopStart, core::Size loopStop, std::string allowed_loop_abegos, core::Real current_rmsd)

void	assign_phi_psi_omega_from_lookback (core::Size db_index, core::Size fragment_index, core::pose::PoseOP &poseOP, core::Size front_overlap_res_length)

std::vector< core::Real >	get_center_of_mass (const core::Real *coordinates, int number_of_atoms)

void	output_fragment_debug (std::vector< numeric::xyzVector< numeric::Real > > coordinates, std::string filename)

void	add_coordinate_csts_from_lookback (core::Size stub_ss_index_match, core::Size fragment_index, core::Size pose_residue, bool match_stub_alone, core::Size front_overlap_res_length, core::pose::PoseOP &poseOP)

void	add_dihedral_csts_from_lookback (core::Size stub_ss_index_match, core::Size fragment_index, core::Size pose_residue, core::pose::PoseOP &poseOP)

core::Size	get_valid_resid (int resid, core::pose::Pose const pose)

std::vector< numeric::xyzVector< numeric::Real > >	get_coordinates_from_pose (core::pose::PoseOP const poseOP, core::Size resid, core::Size length)

core::Real	rmsd_between_coordinates (std::vector< numeric::xyzVector< numeric::Real > > fragCoordinates, std::vector< numeric::xyzVector< numeric::Real > > coordinates)

bool	kic_closure (core::scoring::ScoreFunctionOP scorefxn_, core::pose::PoseOP &poseOP, core::Size firstLoopRes, core::Size lastLoopRes, core::Size numb_kic_cycles)

void	minimize_loop (core::scoring::ScoreFunctionOP scorefxn, bool ideal_loop, core::pose::PoseOP &poseOP)

Private Attributes
core::Size	insertedBeforeLoopRes_

core::Size	insertedAfterLoopRes_

int	resAdjustmentBeforeLoop_

int	resAdjustmentAfterLoop_

char	resTypeBeforeLoop_

char	resTypeAfterLoop_

core::Size	loopLength_

core::Size	resBeforeLoop_

core::Size	resAfterLoop_

core::Size	fullLength_resBeforeLoop_

bool	below_distance_threshold_

core::Size	numb_stubs_to_consider_

utility::vector1< indexed_structure_store::BackboneStub >	stubVector_

core::Real	stub_rmsd_top_match_

bool	outputed_

core::pose::PoseOP	original_atom_type_fullLengthPoseOP_

core::pose::PoseOP	fullLengthPoseOP_

core::pose::PoseOP	finalPoseOP_

protocols::indexed_structure_store::SSHashedFragmentStoreOP	SSHashedFragmentStoreOP_

core::Real	final_rmsd_

std::string	fragment_store_path_

std::string	fragment_store_format_

std::string	fragment_store_compression_

Constructor & Destructor Documentation

◆ PossibleLoop()

protocols::pose_length_moves::PossibleLoop::PossibleLoop	(	int	resAdjustmentBeforeLoop,
		int	resAdjustmentAfterLoop,
		core::Size	loopLength,
		core::Size	resBeforeLoop,
		core::Size	resAfterLoop,
		char	resTypeBeforeLoop,
		char	resTypeAfterLoop,
		core::Size	insertedBeforeLoopRes,
		core::Size	insertedAfterLoopRes,
		core::pose::PoseOP	fullLengthPoseOP,
		core::pose::PoseOP	orig_atom_type_fullLengthPoseOP,
		std::string	fragment_store_path,
		std::string	fragment_store_format,
		std::string	fragment_store_compression,
		core::Size	numb_stubs_to_consider
	)

References protocols::TR().

◆ ~PossibleLoop()

protocols::pose_length_moves::PossibleLoop::~PossibleLoop ( )

overridedefault

Member Function Documentation

◆ add_coordinate_csts_from_lookback()

void protocols::pose_length_moves::PossibleLoop::add_coordinate_csts_from_lookback	(	core::Size	stub_ss_index_match,
		core::Size	fragment_index,
		core::Size	pose_residue,
		bool	match_stub_alone,
		core::Size	front_overlap_res_length,
		core::pose::PoseOP &	poseOP
	)

private

References protocols::seeded_abinitio::superposition_transform(), and protocols::TR().

◆ add_dihedral_csts_from_lookback()

void protocols::pose_length_moves::PossibleLoop::add_dihedral_csts_from_lookback	(	core::Size	stub_ss_index_match,
		core::Size	fragment_index,
		core::Size	pose_residue,
		core::pose::PoseOP &	poseOP
	)

private

◆ assign_phi_psi_omega_from_lookback()

void protocols::pose_length_moves::PossibleLoop::assign_phi_psi_omega_from_lookback	(	core::Size	db_index,
		core::Size	fragment_index,
		core::pose::PoseOP &	poseOP,
		core::Size	front_overlap_res_length
	)

private

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), and core::kinematics::Edge::PEPTIDE.

◆ check_loop_abego()

bool protocols::pose_length_moves::PossibleLoop::check_loop_abego	(	core::pose::PoseOP &	poseOP,
		core::Size	loopStart,
		core::Size	loopStop,
		std::string	allowed_loop_abegos,
		core::Real	current_rmsd
	)

private

References core::scoring::abego, core::sequence::get_abego(), core::sequence::ABEGOManager::get_abego_string(), and protocols::TR().

◆ evaluate_distance_closure()

void protocols::pose_length_moves::PossibleLoop::evaluate_distance_closure ( )

◆ extendRegion()

void protocols::pose_length_moves::PossibleLoop::extendRegion	(	bool	towardCTerm,
		core::Size	resStart,
		core::Size	numberAddRes,
		core::pose::PoseOP &	poseOP
	)

private

References core::chemical::aa_from_oneletter_code(), core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::conformation::ResidueFactory::create_residue(), core::chemical::name_from_aa(), core::kinematics::Edge::PEPTIDE, and core::pose::renumber_pdbinfo_based_on_conf_chains().

◆ generate_output_pose()

void protocols::pose_length_moves::PossibleLoop::generate_output_pose	(	bool	output_closed,
		bool	ideal_loop,
		core::Real	rms_threshold,
		std::string	allowed_loop_abegos,
		std::string	closure_type
	)

References core::scoring::cart_bonded, core::scoring::cart_bonded_angle, core::scoring::cart_bonded_length, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, core::scoring::dssp::Dssp::dssp_reduced(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::sequence::SSManager::index2symbolString(), core::scoring::linear_chainbreak, core::scoring::rama, core::select::resids(), and core::scoring::vdw.

◆ generate_overlap_range()

void protocols::pose_length_moves::PossibleLoop::generate_overlap_range	(	core::Size &	front_overlap,
		core::Size &	back_overlap
	)

private

◆ generate_stub_rmsd()

void protocols::pose_length_moves::PossibleLoop::generate_stub_rmsd ( core::Real stubRmsdThreshold )

◆ get_below_distance_threshold()

bool protocols::pose_length_moves::PossibleLoop::get_below_distance_threshold ( )

inline

References below_distance_threshold_.

◆ get_center_of_mass()

vector< Real > protocols::pose_length_moves::PossibleLoop::get_center_of_mass	(	const core::Real *	coordinates,
		int	number_of_atoms
	)

private

References core::conformation::membrane::center.

◆ get_coordinates_from_pose()

std::vector< numeric::xyzVector< numeric::Real > > protocols::pose_length_moves::PossibleLoop::get_coordinates_from_pose	(	core::pose::PoseOP const	poseOP,
		core::Size	resid,
		core::Size	length
	)

private

◆ get_description()

std::string protocols::pose_length_moves::PossibleLoop::get_description ( )

◆ get_final_RMSD()

core::Real protocols::pose_length_moves::PossibleLoop::get_final_RMSD ( )

inline

References final_rmsd_.

◆ get_finalPoseOP()

core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::get_finalPoseOP ( )

◆ get_stubRMSD()

core::Real protocols::pose_length_moves::PossibleLoop::get_stubRMSD ( )

inline

References stub_rmsd_top_match_.

◆ get_valid_resid()

Size protocols::pose_length_moves::PossibleLoop::get_valid_resid	(	int	resid,
		core::pose::Pose const	pose
	)

private

References core::pose::Pose::size(), and protocols::TR().

◆ kic_closure()

bool protocols::pose_length_moves::PossibleLoop::kic_closure	(	core::scoring::ScoreFunctionOP	scorefxn_,
		core::pose::PoseOP &	poseOP,
		core::Size	firstLoopRes,
		core::Size	lastLoopRes,
		core::Size	numb_kic_cycles
	)

private

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), and core::kinematics::Edge::PEPTIDE.

◆ label_loop()

void protocols::pose_length_moves::PossibleLoop::label_loop ( std::string label )

◆ minimize_loop()

void protocols::pose_length_moves::PossibleLoop::minimize_loop	(	core::scoring::ScoreFunctionOP	scorefxn,
		bool	ideal_loop,
		core::pose::PoseOP &	poseOP
	)

private

References core::kinematics::FoldTree::add_edge(), core::pose::add_variant_type_to_pose_residue(), core::kinematics::FoldTree::clear(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::Edge::PEPTIDE, core::pose::remove_variant_type_from_pose_residue(), core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_bb_true_range(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), and core::optimization::MinimizerOptions::silent().

◆ output_fragment_debug()

void protocols::pose_length_moves::PossibleLoop::output_fragment_debug	(	std::vector< numeric::xyzVector< numeric::Real > >	coordinates,
		std::string	filename
	)

private

References core::chemical::element::F, protocols::abinitio::filename(), core::chemical::element::I, and core::conformation::membrane::out.

◆ outputed() [1/2]

bool protocols::pose_length_moves::PossibleLoop::outputed ( )

inline

References outputed_.

◆ outputed() [2/2]

void protocols::pose_length_moves::PossibleLoop::outputed ( bool outputed )

inline

References outputed(), and outputed_.

Referenced by outputed().

◆ rmsd_between_coordinates()

Real protocols::pose_length_moves::PossibleLoop::rmsd_between_coordinates	(	std::vector< numeric::xyzVector< numeric::Real > >	fragCoordinates,
		std::vector< numeric::xyzVector< numeric::Real > >	coordinates
	)

private

◆ setup_finalPose_copy_labels()

void protocols::pose_length_moves::PossibleLoop::setup_finalPose_copy_labels ( )

◆ setup_finalPose_copy_rotamers()

void protocols::pose_length_moves::PossibleLoop::setup_finalPose_copy_rotamers ( )

References core::chemical::FA_STANDARD, and core::util::switch_to_residue_type_set().

◆ trimRegion()

void protocols::pose_length_moves::PossibleLoop::trimRegion	(	core::pose::PoseOP &	poseOP,
		core::Size	resStart,
		core::Size	resStop
	)

private

References core::pose::renumber_pdbinfo_based_on_conf_chains().

Member Data Documentation

◆ below_distance_threshold_

bool protocols::pose_length_moves::PossibleLoop::below_distance_threshold_

private

Referenced by get_below_distance_threshold().

◆ final_rmsd_

core::Real protocols::pose_length_moves::PossibleLoop::final_rmsd_

private

Referenced by get_final_RMSD().

◆ finalPoseOP_

core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::finalPoseOP_

private

◆ fragment_store_compression_

std::string protocols::pose_length_moves::PossibleLoop::fragment_store_compression_

private

◆ fragment_store_format_

std::string protocols::pose_length_moves::PossibleLoop::fragment_store_format_

private

◆ fragment_store_path_

std::string protocols::pose_length_moves::PossibleLoop::fragment_store_path_

private

◆ fullLength_resBeforeLoop_

core::Size protocols::pose_length_moves::PossibleLoop::fullLength_resBeforeLoop_

private

◆ fullLengthPoseOP_

core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::fullLengthPoseOP_

private

◆ insertedAfterLoopRes_

core::Size protocols::pose_length_moves::PossibleLoop::insertedAfterLoopRes_

private

◆ insertedBeforeLoopRes_

core::Size protocols::pose_length_moves::PossibleLoop::insertedBeforeLoopRes_

private

◆ loopLength_

core::Size protocols::pose_length_moves::PossibleLoop::loopLength_

private

◆ numb_stubs_to_consider_

core::Size protocols::pose_length_moves::PossibleLoop::numb_stubs_to_consider_

private

◆ original_atom_type_fullLengthPoseOP_

core::pose::PoseOP protocols::pose_length_moves::PossibleLoop::original_atom_type_fullLengthPoseOP_

private

◆ outputed_

bool protocols::pose_length_moves::PossibleLoop::outputed_

private

Referenced by outputed().

◆ resAdjustmentAfterLoop_

int protocols::pose_length_moves::PossibleLoop::resAdjustmentAfterLoop_

private

◆ resAdjustmentBeforeLoop_

int protocols::pose_length_moves::PossibleLoop::resAdjustmentBeforeLoop_

private

◆ resAfterLoop_

core::Size protocols::pose_length_moves::PossibleLoop::resAfterLoop_

private

◆ resBeforeLoop_

core::Size protocols::pose_length_moves::PossibleLoop::resBeforeLoop_

private

◆ resTypeAfterLoop_

char protocols::pose_length_moves::PossibleLoop::resTypeAfterLoop_

private

◆ resTypeBeforeLoop_

char protocols::pose_length_moves::PossibleLoop::resTypeBeforeLoop_

private

◆ SSHashedFragmentStoreOP_

protocols::indexed_structure_store::SSHashedFragmentStoreOP protocols::pose_length_moves::PossibleLoop::SSHashedFragmentStoreOP_

private

◆ stub_rmsd_top_match_

core::Real protocols::pose_length_moves::PossibleLoop::stub_rmsd_top_match_

private

Referenced by get_stubRMSD().

◆ stubVector_

utility::vector1<indexed_structure_store::BackboneStub> protocols::pose_length_moves::PossibleLoop::stubVector_

private

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

src/protocols/pose_length_moves/NearNativeLoopCloser.hh
src/protocols/pose_length_moves/NearNativeLoopCloser.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ PossibleLoop()

◆ ~PossibleLoop()

Member Function Documentation

◆ add_coordinate_csts_from_lookback()

◆ add_dihedral_csts_from_lookback()

◆ assign_phi_psi_omega_from_lookback()

◆ check_loop_abego()

◆ evaluate_distance_closure()

◆ extendRegion()

◆ generate_output_pose()

◆ generate_overlap_range()

◆ generate_stub_rmsd()

◆ get_below_distance_threshold()

◆ get_center_of_mass()

◆ get_coordinates_from_pose()

◆ get_description()

◆ get_final_RMSD()

◆ get_finalPoseOP()

◆ get_stubRMSD()

◆ get_valid_resid()

◆ kic_closure()

◆ label_loop()

◆ minimize_loop()

◆ output_fragment_debug()

◆ outputed() [1/2]

◆ outputed() [2/2]

◆ rmsd_between_coordinates()

◆ setup_finalPose_copy_labels()

◆ setup_finalPose_copy_rotamers()

◆ trimRegion()

Member Data Documentation

◆ below_distance_threshold_

◆ final_rmsd_

◆ finalPoseOP_

◆ fragment_store_compression_

◆ fragment_store_format_

◆ fragment_store_path_

◆ fullLength_resBeforeLoop_

◆ fullLengthPoseOP_

◆ insertedAfterLoopRes_

◆ insertedBeforeLoopRes_

◆ loopLength_

◆ numb_stubs_to_consider_

◆ original_atom_type_fullLengthPoseOP_

◆ outputed_

◆ resAdjustmentAfterLoop_

◆ resAdjustmentBeforeLoop_

◆ resAfterLoop_

◆ resBeforeLoop_

◆ resTypeAfterLoop_

◆ resTypeBeforeLoop_

◆ SSHashedFragmentStoreOP_

◆ stub_rmsd_top_match_

◆ stubVector_