#include <StepWiseProteinCCD_Closer.hh>

Public Member Functions
	StepWiseProteinCCD_Closer (rotamer_sampler::RotamerSizedOP sampler, protocols::stepwise::sampling::protein::StepWiseProteinJobParametersCOP job_parameters)

	~StepWiseProteinCCD_Closer ()

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

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

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

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

void	set_ccd_close_res (Size const value)

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

void	set_choose_random (bool const &setting)

bool	choose_random () const

void	set_num_random_samples (Size const &setting)

Size	num_random_samples () const

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

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

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

std::string	get_type () const

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...

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Member Functions
bool	CCD_loop_close (pose::Pose &pose)

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

void	setup_torsions (pose::Pose const &pose)

void	figure_out_loop (pose::Pose const &pose)

void	grab_main_chain_torsion_set_list (pose::Pose const &pose)

void	save_phi_psi_omega_over_loop_residues (pose::Pose const &pose)

void	restore_phi_psi_omega_over_loop_residues (pose::Pose &pose)

void	restore_phi_psi_over_loop_residues (pose::Pose &pose)

void	fix_jump_atoms_at_loop_boundaries (pose::Pose &pose)

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 protocols::filters::Filters_map	Filters_map

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::sampling::protein::StepWiseProteinCCD_Closer::StepWiseProteinCCD_Closer	(	rotamer_sampler::RotamerSizedOP	sampler,
		protocols::stepwise::sampling::protein::StepWiseProteinJobParametersCOP	job_parameters
	)

References utility_exit_with_message, and working_bridge_res_.

protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::~StepWiseProteinCCD_Closer ( )

Member Function Documentation

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::apply ( pose::Pose & pose_to_visualize )

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References CCD_loop_close_sample_omega_recursively(), choose_random_, figure_out_loop(), fix_jump_atoms_at_loop_boundaries(), grab_main_chain_torsion_set_list(), main_chain_torsion_sets_for_moving_residues_, max_ntries_, num_random_samples_, pose_count_, restore_phi_psi_omega_over_loop_residues(), sampler_, save_phi_psi_omega_over_loop_residues(), and setup_torsions().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples().

bool protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::CCD_loop_close ( pose::Pose & pose )

private

References protocols::loops::Loop::cut(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), grab_main_chain_torsion_set_list(), loop_, mm_, n_cycles, pose_count_, protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::TR.

Referenced by CCD_loop_close_sample_omega_recursively().

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

private

References CCD_loop_close(), 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 apply().

bool protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::choose_random ( ) const

inline

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::figure_out_loop ( pose::Pose const & pose )

private

References ccd_close_res_, core::kinematics::MoveMap::clear(), CUTPOINT_LOWER, CUTPOINT_UPPER, core::chemical::ResidueType::has_variant_type(), loop_, mm_, core::pose::Pose::residue_type(), core::kinematics::MoveMap::set(), core::pose::Pose::total_residue(), utility_exit_with_message, and working_bridge_res_.

Referenced by apply().

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::fix_jump_atoms_at_loop_boundaries ( pose::Pose & pose )

private

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

Referenced by apply().

std::string protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::grab_main_chain_torsion_set_list ( pose::Pose const & pose )

private

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

Referenced by apply(), and CCD_loop_close().

utility::vector1< utility::vector1< core::Real > > const & protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::main_chain_torsion_set_lists ( ) const

References main_chain_torsion_sets_for_moving_residues_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples().

Size protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::num_random_samples ( ) const

inline

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::restore_phi_psi_omega_over_loop_residues ( pose::Pose & pose )

private

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

Referenced by apply().

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::restore_phi_psi_over_loop_residues ( pose::Pose & pose )

private

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

Referenced by CCD_loop_close_sample_omega_recursively().

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::save_phi_psi_omega_over_loop_residues ( pose::Pose const & pose )

private

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

Referenced by apply().

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::set_ccd_close_res ( Size const value )

inline

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::set_choose_random ( bool const & setting )

inline

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples().

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::set_num_random_samples ( Size const & setting )

inline

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples().

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

inline

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples().

void protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::setup_torsions ( pose::Pose const & pose )

private

References BB, moving_residues_, core::pose::Pose::total_residue(), which_torsions_, and working_bridge_res_.

Referenced by apply().

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

References which_torsions_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples().

Member Data Documentation

Size protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::ccd_close_res_

private

Referenced by figure_out_loop().

bool protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::choose_random_

private

Referenced by apply().

utility::vector1< bool > protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::is_pre_proline_

private

Referenced by CCD_loop_close_sample_omega_recursively().

loops::Loop protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::loop_

private

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

utility::vector1< Real > protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::main_chain_torsion_set_for_moving_residues_save_

private

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

utility::vector1< utility::vector1< Real > > protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::main_chain_torsion_sets_for_moving_residues_

private

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

Size protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::max_ntries_

private

Referenced by apply().

kinematics::MoveMap protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::mm_

private

Referenced by CCD_loop_close(), and figure_out_loop().

utility::vector1< Size > protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::moving_residues_

private

Referenced by setup_torsions().

Size protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::num_random_samples_

private

Referenced by apply().

Size protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::pose_count_

private

Referenced by apply(), and CCD_loop_close().

rotamer_sampler::RotamerSizedOP protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::sampler_

private

Referenced by apply().

bool const protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::verbose_

private

utility::vector1< id::TorsionID > protocols::stepwise::sampling::protein::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< Size > protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::working_bridge_res_

private

Referenced by figure_out_loop(), setup_torsions(), and StepWiseProteinCCD_Closer().

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

symlinks/rosetta/src/protocols/stepwise/sampling/protein/loop_close/StepWiseProteinCCD_Closer.hh
symlinks/rosetta/src/protocols/stepwise/sampling/protein/loop_close/StepWiseProteinCCD_Closer.cc

Private Attributes
rotamer_sampler::RotamerSizedOP	sampler_

utility::vector1< Size >	working_bridge_res_

utility::vector1< Size >	moving_residues_

utility::vector1< bool >	is_pre_proline_

Size	ccd_close_res_

loops::Loop	loop_

kinematics::MoveMap	mm_

utility::vector1< id::TorsionID >	which_torsions_

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

utility::vector1< Real >	main_chain_torsion_set_for_moving_residues_save_

bool const	verbose_

Size	pose_count_

bool	choose_random_

Size	num_random_samples_

Size	max_ntries_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation