#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)

	~PossibleLoop () override

void	evaluate_distance_closure ()

void	generate_stub_rmsd ()

void	generate_uncached_stub_rmsd ()

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

core::pose::PoseOP	get_finalPoseOP ()

core::Real	get_stubRMSD ()

core::Real	get_uncached_stubRMSD ()

core::Real	get_final_RMSD ()

bool	outputed ()

void	outputed (bool outputed)

bool	get_below_distance_threshold ()

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)

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

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

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::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)

Constructor & Destructor Documentation

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
	)

References protocols::TR().

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

overridedefault

Member Function Documentation

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::pose::PoseOP &	poseOP
	)

private

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

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

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

private

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

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	loop_rmsd
	)

private

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

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

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

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::rama, core::select::resids(), and core::scoring::vdw.

void protocols::pose_length_moves::PossibleLoop::generate_stub_rmsd ( )

void protocols::pose_length_moves::PossibleLoop::generate_uncached_stub_rmsd ( )

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

inline

References below_distance_threshold_.

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.

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

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

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

inline

References final_rmsd_.

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

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

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

inline

References stub_rmsd_match_.

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

inline

References uncached_stub_rmsd_.

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().

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::clear(), and core::kinematics::Edge::PEPTIDE.

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

private

References core::kinematics::FoldTree::clear(), core::kinematics::Edge::PEPTIDE, core::optimization::AtomTreeMinimizer::run(), core::optimization::CartesianMinimizer::run(), and core::kinematics::MoveMap::set_bb().

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, core::chemical::element::I, and core::conformation::membrane::out.

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

inline

References outputed_.

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

inline

References outputed(), and outputed_.

Referenced by outputed().

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

private

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

bool protocols::pose_length_moves::PossibleLoop::below_distance_threshold_

private

Referenced by get_below_distance_threshold().

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

private

Referenced by get_final_RMSD().

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

private

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

private

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

private

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

private

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

private

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

private

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

private

bool protocols::pose_length_moves::PossibleLoop::outputed_

private

Referenced by outputed().

int protocols::pose_length_moves::PossibleLoop::resAdjustmentAfterLoop_

private

int protocols::pose_length_moves::PossibleLoop::resAdjustmentBeforeLoop_

private

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

private

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

private

char protocols::pose_length_moves::PossibleLoop::resTypeAfterLoop_

private

char protocols::pose_length_moves::PossibleLoop::resTypeBeforeLoop_

private

protocols::indexed_structure_store::SSHashedFragmentStore* protocols::pose_length_moves::PossibleLoop::SSHashedFragmentStore_

private

core::Size protocols::pose_length_moves::PossibleLoop::stub_index_match_

private

core::Real protocols::pose_length_moves::PossibleLoop::stub_rmsd_match_

private

Referenced by get_stubRMSD().

core::Size protocols::pose_length_moves::PossibleLoop::stub_ss_index_match_

private

core::Size protocols::pose_length_moves::PossibleLoop::uncached_stub_index_

private

core::Real protocols::pose_length_moves::PossibleLoop::uncached_stub_rmsd_

private

Referenced by get_uncached_stubRMSD().

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

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::Real	stub_rmsd_match_

core::Size	stub_index_match_

core::Size	stub_ss_index_match_

core::Real	uncached_stub_rmsd_

core::Size	uncached_stub_index_

bool	outputed_

core::pose::PoseOP	original_atom_type_fullLengthPoseOP_

core::pose::PoseOP	fullLengthPoseOP_

core::pose::PoseOP	finalPoseOP_

protocols::indexed_structure_store::SSHashedFragmentStore *	SSHashedFragmentStore_

core::Real	final_rmsd_

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation