#include <StepWiseProteinKIC_LoopBridger.hh>

Inheritance diagram for protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger:

[legend]

Public Member Functions
	StepWiseProteinKIC_LoopBridger (sampler::StepWiseSamplerSizedOP sampler, protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters)

	~StepWiseProteinKIC_LoopBridger () override

void	apply (core::pose::Pose &pose_to_visualize) override
	Apply the minimizer to one pose. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

utility::vector1< utility::vector1< core::Real > > const &	main_chain_torsion_set_lists () const

utility::vector1< core::id::TorsionID > const &	which_torsions () const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	setup_torsions (core::pose::Pose const &pose)

void	figure_out_loop (core::pose::Pose const &pose)

void	output_chainTORS (utility::vector1< core::Real > const &dt_ang, utility::vector1< core::Real > const &db_ang, utility::vector1< core::Real > const &db_len) const

void	fill_chainTORS_info (core::pose::Pose const &pose, utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &atoms, utility::vector1< core::Real > &dt_ang, utility::vector1< core::Real > &db_ang, utility::vector1< core::Real > &db_len, core::Size const &start_res_, core::Size const &end_res_) const

void	KIC_loop_close_with_perturbations (core::pose::Pose &pose)

void	KIC_loop_close (core::pose::Pose &pose)

void	grab_main_chain_torsion_set_list (core::pose::Pose const &pose)

void	save_phi_psi_offsets (core::pose::Pose const &pose)

void	fix_phi_psi_offsets (core::pose::Pose &pose) const

void	sample_omega_recursively (core::pose::Pose &pose, int const offset, utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &atoms, utility::vector1< core::Real > &dt_ang, utility::vector1< core::Real > &db_ang, utility::vector1< core::Real > &db_len, utility::vector1< core::Size > const &pivots, utility::vector1< core::Size > const &order)

void	initialize_is_fixed_res (utility::vector1< core::Size > const &fixed_res, std::string const &working_sequence)

Private Attributes
sampler::StepWiseSamplerSizedOP	sampler_

utility::vector1< core::Size >	working_bridge_res_

utility::vector1< bool >	is_pre_proline_

utility::vector1< bool >	is_fixed_res_

loops::Loop	loop_

utility::vector1< core::id::TorsionID >	which_torsions_

utility::vector1< utility::vector1< core::Real > >	main_chain_torsion_sets_for_moving_residues_

core::scoring::Ramachandran	ramachandran_

int const	num_perturb_steps_

core::Real const	perturb_torsion_

core::Real const	idl_CA_C_N_

core::Real const	idl_C_N_CA_

core::Real const	idl_C_N_

core::Real const	OMEGA_MEAN_

bool const	use_icoor_geometry_

bool const	verbose_

utility::vector1< core::Real >	phi_offsets_

utility::vector1< core::Real >	psi_offsets_

core::Size	start_res_

core::Size	middle_res_

core::Size	end_res_

core::Size	middle_offset_

core::Size	seg_len_

core::Size	pose_count_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

◆ StepWiseProteinKIC_LoopBridger()

protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::StepWiseProteinKIC_LoopBridger	(	sampler::StepWiseSamplerSizedOP	sampler,
		protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP	working_parameters
	)

References initialize_is_fixed_res(), and working_bridge_res_.

◆ ~StepWiseProteinKIC_LoopBridger()

protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::~StepWiseProteinKIC_LoopBridger ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::apply ( core::pose::Pose & pose_to_visualize )

overridevirtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References figure_out_loop(), grab_main_chain_torsion_set_list(), KIC_loop_close_with_perturbations(), main_chain_torsion_sets_for_moving_residues_, pose_count_, sampler_, and setup_torsions().

Referenced by protocols::stepwise::modeler::protein::loop_close::kic_close_loops_in_samples().

◆ figure_out_loop()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::figure_out_loop ( core::pose::Pose const & pose )

private

References core::pose::Pose::annotated_sequence(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueTypeBase::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), loop_, core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and working_bridge_res_.

Referenced by apply().

◆ fill_chainTORS_info()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::fill_chainTORS_info	(	core::pose::Pose const &	pose,
		utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &	atoms,
		utility::vector1< core::Real > &	dt_ang,
		utility::vector1< core::Real > &	db_ang,
		utility::vector1< core::Real > &	db_len,
		core::Size const &	start_res_,
		core::Size const &	end_res_
	)		const

private

References end_res_, output_chainTORS(), core::pose::Pose::residue(), start_res_, verbose_, and core::conformation::Residue::xyz().

Referenced by KIC_loop_close(), and sample_omega_recursively().

◆ fix_phi_psi_offsets()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::fix_phi_psi_offsets ( core::pose::Pose & pose ) const

private

◆ get_name()

std::string protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

◆ grab_main_chain_torsion_set_list()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::grab_main_chain_torsion_set_list ( core::pose::Pose const & pose )

private

References main_chain_torsion_sets_for_moving_residues_, core::pose::Pose::torsion(), and which_torsions_.

Referenced by apply(), and sample_omega_recursively().

◆ initialize_is_fixed_res()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::initialize_is_fixed_res	(	utility::vector1< core::Size > const &	fixed_res,
		std::string const &	working_sequence
	)

private

References is_fixed_res_, and core::pose::rna::remove_bracketed().

Referenced by StepWiseProteinKIC_LoopBridger().

◆ KIC_loop_close()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close ( core::pose::Pose & pose )

private

◆ KIC_loop_close_with_perturbations()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::KIC_loop_close_with_perturbations ( core::pose::Pose & pose )

private

References KIC_loop_close(), num_perturb_steps_, perturb_torsion_, core::pose::Pose::phi(), pose_count_, core::pose::Pose::psi(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and working_bridge_res_.

Referenced by apply().

◆ main_chain_torsion_set_lists()

utility::vector1< utility::vector1< core::Real > > const & protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::main_chain_torsion_set_lists ( ) const

References main_chain_torsion_sets_for_moving_residues_.

Referenced by protocols::stepwise::modeler::protein::loop_close::kic_close_loops_in_samples().

◆ output_chainTORS()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::output_chainTORS	(	utility::vector1< core::Real > const &	dt_ang,
		utility::vector1< core::Real > const &	db_ang,
		utility::vector1< core::Real > const &	db_len
	)		const

private

References core::chemical::element::F.

Referenced by fill_chainTORS_info(), and KIC_loop_close().

◆ sample_omega_recursively()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::sample_omega_recursively	(	core::pose::Pose &	pose,
		int const	offset,
		utility::vector1< utility::fixedsizearray1< core::Real, 3 > > &	atoms,
		utility::vector1< core::Real > &	dt_ang,
		utility::vector1< core::Real > &	db_ang,
		utility::vector1< core::Real > &	db_len,
		utility::vector1< core::Size > const &	pivots,
		utility::vector1< core::Size > const &	order
	)

private

References core::pose::Pose::dump_pdb(), end_res_, fill_chainTORS_info(), grab_main_chain_torsion_set_list(), is_pre_proline_, OMEGA_MEAN_, protocols::forge::methods::order(), seg_len_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), start_res_, and verbose_.

Referenced by KIC_loop_close().

◆ save_phi_psi_offsets()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::save_phi_psi_offsets ( core::pose::Pose const & pose )

private

◆ setup_torsions()

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::setup_torsions ( core::pose::Pose const & pose )

private

References core::id::BB, is_fixed_res_, core::pose::Pose::size(), and which_torsions_.

Referenced by apply().

◆ which_torsions()

utility::vector1< core::id::TorsionID > const & protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::which_torsions ( ) const

References which_torsions_.

Referenced by protocols::stepwise::modeler::protein::loop_close::kic_close_loops_in_samples().

Member Data Documentation

◆ end_res_

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::end_res_

private

Referenced by fill_chainTORS_info(), KIC_loop_close(), and sample_omega_recursively().

◆ idl_C_N_

core::Real const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::idl_C_N_

private

Referenced by KIC_loop_close().

◆ idl_C_N_CA_

core::Real const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::idl_C_N_CA_

private

Referenced by KIC_loop_close().

◆ idl_CA_C_N_

core::Real const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::idl_CA_C_N_

private

Referenced by KIC_loop_close().

◆ is_fixed_res_

utility::vector1< bool > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::is_fixed_res_

private

Referenced by initialize_is_fixed_res(), and setup_torsions().

◆ is_pre_proline_

utility::vector1< bool > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::is_pre_proline_

private

Referenced by sample_omega_recursively().

◆ loop_

loops::Loop protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::loop_

private

Referenced by figure_out_loop(), and KIC_loop_close().

◆ main_chain_torsion_sets_for_moving_residues_

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::main_chain_torsion_sets_for_moving_residues_

private

Referenced by apply(), grab_main_chain_torsion_set_list(), and main_chain_torsion_set_lists().

◆ middle_offset_

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::middle_offset_

private

Referenced by KIC_loop_close().

◆ middle_res_

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::middle_res_

private

Referenced by KIC_loop_close().

◆ num_perturb_steps_

int const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::num_perturb_steps_

private

Referenced by KIC_loop_close_with_perturbations().

◆ OMEGA_MEAN_

core::Real const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::OMEGA_MEAN_

private

Referenced by KIC_loop_close(), and sample_omega_recursively().

◆ perturb_torsion_

core::Real const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::perturb_torsion_

private

Referenced by KIC_loop_close_with_perturbations().

◆ phi_offsets_

utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::phi_offsets_

private

◆ pose_count_

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::pose_count_

private

Referenced by apply(), and KIC_loop_close_with_perturbations().

◆ psi_offsets_

utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::psi_offsets_

private

◆ ramachandran_

core::scoring::Ramachandran protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::ramachandran_

private

◆ sampler_

sampler::StepWiseSamplerSizedOP protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::sampler_

private

Referenced by apply().

◆ seg_len_

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::seg_len_

private

Referenced by KIC_loop_close(), and sample_omega_recursively().

◆ start_res_

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::start_res_

private

Referenced by fill_chainTORS_info(), KIC_loop_close(), and sample_omega_recursively().

◆ use_icoor_geometry_

bool const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::use_icoor_geometry_

private

Referenced by KIC_loop_close().

◆ verbose_

bool const protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::verbose_

private

Referenced by fill_chainTORS_info(), KIC_loop_close(), and sample_omega_recursively().

◆ which_torsions_

utility::vector1< core::id::TorsionID > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::which_torsions_

private

Referenced by grab_main_chain_torsion_set_list(), setup_torsions(), and which_torsions().

◆ working_bridge_res_

utility::vector1< core::Size > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinKIC_LoopBridger::working_bridge_res_

private

Referenced by figure_out_loop(), KIC_loop_close_with_perturbations(), and StepWiseProteinKIC_LoopBridger().

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

src/protocols/stepwise/modeler/protein/loop_close/StepWiseProteinKIC_LoopBridger.hh
src/protocols/stepwise/modeler/protein/loop_close/StepWiseProteinKIC_LoopBridger.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWiseProteinKIC_LoopBridger()

◆ ~StepWiseProteinKIC_LoopBridger()

Member Function Documentation

◆ apply()

◆ figure_out_loop()

◆ fill_chainTORS_info()

◆ fix_phi_psi_offsets()

◆ get_name()

◆ grab_main_chain_torsion_set_list()

◆ initialize_is_fixed_res()

◆ KIC_loop_close()

◆ KIC_loop_close_with_perturbations()

◆ main_chain_torsion_set_lists()

◆ output_chainTORS()

◆ sample_omega_recursively()

◆ save_phi_psi_offsets()

◆ setup_torsions()

◆ which_torsions()

Member Data Documentation

◆ end_res_

◆ idl_C_N_

◆ idl_C_N_CA_

◆ idl_CA_C_N_

◆ is_fixed_res_

◆ is_pre_proline_

◆ loop_

◆ main_chain_torsion_sets_for_moving_residues_

◆ middle_offset_

◆ middle_res_

◆ num_perturb_steps_

◆ OMEGA_MEAN_

◆ perturb_torsion_

◆ phi_offsets_

◆ pose_count_

◆ psi_offsets_

◆ ramachandran_

◆ sampler_

◆ seg_len_

◆ start_res_

◆ use_icoor_geometry_

◆ verbose_

◆ which_torsions_

◆ working_bridge_res_