#include <StepWiseProteinCCD_Closer.hh>

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

Public Member Functions
	StepWiseProteinCCD_Closer (protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters)

	~StepWiseProteinCCD_Closer () override

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

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

void	get_closure_solution (core::pose::Pose &pose_to_visualize)

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

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

void	set_ccd_close_res (core::Size const value)

void	set_working_moving_res_list (utility::vector1< core::Size > const &setting)

utility::vector1< core::Real >	grab_main_chain_torsion_set_list (core::pose::Pose const &pose)

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

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

core::Size	ntries () const

bool	closed_loop () 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
bool	CCD_loop_close (core::pose::Pose &pose)

void	CCD_loop_close_sample_omega_recursively (core::pose::Pose &pose, int const offset)

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

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

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

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

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

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

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

core::Size	check_for_unique_cutpoint_flanked_by_bridge_res (core::pose::Pose const &pose)

core::Size	check_for_unique_cutpoint (core::pose::Pose const &pose)

Private Attributes
loops::loop_closure::ccd::CCDLoopClosureMoverOP	ccd_loop_closure_mover_

utility::vector1< core::Size >	working_bridge_res_

utility::vector1< core::Size >	moving_residues_

utility::vector1< bool >	is_pre_proline_

core::Size	ccd_close_res_

loops::Loop	loop_

core::kinematics::MoveMapOP	mm_

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

utility::vector1< core::Real >	main_chain_torsion_set_

utility::vector1< core::Real >	main_chain_torsion_set_save_

bool	closed_loop_

core::Size	ntries_

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

protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::StepWiseProteinCCD_Closer ( protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters )

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

overridedefault

Member Function Documentation

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

overridevirtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References protocols::simple_moves::TorsionSetMover::apply(), get_closure_solution(), main_chain_torsion_set(), and which_torsions().

bool protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close ( core::pose::Pose & pose )

private

References ccd_loop_closure_mover_, grab_main_chain_torsion_set_list(), loop_, mm_, ntries_, and protocols::TR().

Referenced by CCD_loop_close_sample_omega_recursively().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::CCD_loop_close_sample_omega_recursively	(	core::pose::Pose &	pose,
		int const	offset
	)

private

References CCD_loop_close(), closed_loop_, is_pre_proline_, loop_, restore_phi_psi_over_loop_residues(), core::pose::Pose::set_omega(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::TR().

Referenced by get_closure_solution().

Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint ( core::pose::Pose const & pose )

private

References protocols::stepwise::modeler::is_cutpoint_closed(), and core::pose::Pose::size().

Referenced by figure_out_loop().

Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::check_for_unique_cutpoint_flanked_by_bridge_res ( core::pose::Pose const & pose )

private

References protocols::stepwise::modeler::is_cutpoint_closed(), core::pose::Pose::size(), and working_bridge_res_.

Referenced by figure_out_loop().

bool protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::closed_loop ( ) const

inline

References closed_loop_.

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

private

References ccd_close_res_, check_for_unique_cutpoint(), check_for_unique_cutpoint_flanked_by_bridge_res(), protocols::stepwise::modeler::is_cutpoint_closed(), loop_, core::pose::Pose::size(), and working_bridge_res_.

Referenced by init().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::figure_out_movemap ( core::pose::Pose const & pose )

private

References core::id::BB, loop_, core::conformation::Residue::mainchain_torsions(), mm_, core::pose::Pose::residue(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by init().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries ( core::pose::Pose & pose )

private

References protocols::stepwise::modeler::fix_protein_jump_atom(), loop_, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by init().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::get_closure_solution ( core::pose::Pose & pose_to_visualize )

References CCD_loop_close_sample_omega_recursively(), closed_loop_, restore_phi_psi_omega_over_loop_residues(), and save_phi_psi_omega_over_loop_residues().

Referenced by apply().

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

overridevirtual

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

Implements protocols::moves::Mover.

utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::grab_main_chain_torsion_set_list ( core::pose::Pose const & pose )

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

Referenced by CCD_loop_close().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::init ( core::pose::Pose & pose )

References figure_out_loop(), figure_out_movemap(), fix_jump_atoms_at_loop_boundaries(), ntries_, and setup_torsions().

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

References main_chain_torsion_set_.

Referenced by apply().

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

References main_chain_torsion_set_save_.

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ntries ( ) const

inline

References ntries_.

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::restore_phi_psi_omega_over_loop_residues ( core::pose::Pose & pose )

private

References main_chain_torsion_set_save_, core::pose::Pose::set_torsion(), and which_torsions_.

Referenced by get_closure_solution().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::restore_phi_psi_over_loop_residues ( core::pose::Pose & pose )

private

References main_chain_torsion_set_save_, core::pose::Pose::set_torsion(), and which_torsions_.

Referenced by CCD_loop_close_sample_omega_recursively().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::save_phi_psi_omega_over_loop_residues ( core::pose::Pose const & pose )

private

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

Referenced by get_closure_solution().

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::set_ccd_close_res ( core::Size const value )

inline

References ccd_close_res_.

void protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::set_working_moving_res_list ( utility::vector1< core::Size > const & setting )

inline

References moving_residues_.

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

private

References core::id::BB, loop_, core::pose::Pose::residue(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and which_torsions_.

Referenced by init().

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

References which_torsions_.

Referenced by apply().

Member Data Documentation

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ccd_close_res_

private

Referenced by figure_out_loop(), and set_ccd_close_res().

loops::loop_closure::ccd::CCDLoopClosureMoverOP protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ccd_loop_closure_mover_

private

Referenced by CCD_loop_close().

bool protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::closed_loop_

private

Referenced by CCD_loop_close_sample_omega_recursively(), closed_loop(), and get_closure_solution().

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

private

Referenced by CCD_loop_close_sample_omega_recursively().

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

private

Referenced by CCD_loop_close(), CCD_loop_close_sample_omega_recursively(), figure_out_loop(), figure_out_movemap(), fix_jump_atoms_at_loop_boundaries(), and setup_torsions().

utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::main_chain_torsion_set_

private

Referenced by grab_main_chain_torsion_set_list(), and main_chain_torsion_set().

utility::vector1< core::Real > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::main_chain_torsion_set_save_

private

Referenced by main_chain_torsion_set_save(), restore_phi_psi_omega_over_loop_residues(), restore_phi_psi_over_loop_residues(), and save_phi_psi_omega_over_loop_residues().

core::kinematics::MoveMapOP protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::mm_

private

Referenced by CCD_loop_close(), and figure_out_movemap().

utility::vector1< core::Size > protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::moving_residues_

private

Referenced by set_working_moving_res_list().

core::Size protocols::stepwise::modeler::protein::loop_close::StepWiseProteinCCD_Closer::ntries_

private

Referenced by CCD_loop_close(), init(), and ntries().

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

private

Referenced by grab_main_chain_torsion_set_list(), restore_phi_psi_omega_over_loop_residues(), restore_phi_psi_over_loop_residues(), save_phi_psi_omega_over_loop_residues(), setup_torsions(), and which_torsions().

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

private

Referenced by check_for_unique_cutpoint_flanked_by_bridge_res(), and figure_out_loop().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation