#include <StepWiseProteinLoopBridger.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinLoopBridger:

Collaboration diagram for protocols::swa::protein::StepWiseProteinLoopBridger:

Public Member Functions
	StepWiseProteinLoopBridger (protocols::swa::StepWisePoseSampleGeneratorOP sample_generator, protocols::swa::StepWiseJobParametersOP job_parameters)

	~StepWiseProteinLoopBridger ()

virtual void	apply (core::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< 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	~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
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

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::vector1< core::Real > > &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::vector1< core::Real > > &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
protocols::swa::StepWisePoseSampleGeneratorOP	sample_generator_

utility::vector1< 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_

Size	start_res_

Size	middle_res_

Size	end_res_

Size	middle_offset_

Size	seg_len_

Size	pose_count_

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

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 39 of file StepWiseProteinLoopBridger.hh.

Constructor & Destructor Documentation

protocols::swa::protein::StepWiseProteinLoopBridger::StepWiseProteinLoopBridger	(	protocols::swa::StepWisePoseSampleGeneratorOP	sample_generator,
		protocols::swa::StepWiseJobParametersOP	job_parameters
	)

Definition at line 77 of file StepWiseProteinLoopBridger.cc.

References initialize_is_fixed_res(), and working_bridge_res_.

protocols::swa::protein::StepWiseProteinLoopBridger::~StepWiseProteinLoopBridger ( )

Definition at line 99 of file StepWiseProteinLoopBridger.cc.

Member Function Documentation

void protocols::swa::protein::StepWiseProteinLoopBridger::apply ( core::pose::Pose & pose_to_visualize)

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 111 of file StepWiseProteinLoopBridger.cc.

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

void protocols::swa::protein::StepWiseProteinLoopBridger::figure_out_loop ( core::pose::Pose const & pose)

private

Definition at line 189 of file StepWiseProteinLoopBridger.cc.

References core::pose::Pose::annotated_sequence(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::chemical::ResidueType::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().

void protocols::swa::protein::StepWiseProteinLoopBridger::fill_chainTORS_info	(	core::pose::Pose const &	pose,
		utility::vector1< utility::vector1< core::Real > > &	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

Definition at line 319 of file StepWiseProteinLoopBridger.cc.

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

Referenced by KIC_loop_close(), and sample_omega_recursively().

void protocols::swa::protein::StepWiseProteinLoopBridger::fix_phi_psi_offsets ( core::pose::Pose & pose) const

private

std::string protocols::swa::protein::StepWiseProteinLoopBridger::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 103 of file StepWiseProteinLoopBridger.cc.

void protocols::swa::protein::StepWiseProteinLoopBridger::grab_main_chain_torsion_set_list ( core::pose::Pose const & pose)

private

Definition at line 264 of file StepWiseProteinLoopBridger.cc.

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

Referenced by apply(), and sample_omega_recursively().

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

private

Definition at line 485 of file StepWiseProteinLoopBridger.cc.

References is_fixed_res_.

Referenced by StepWiseProteinLoopBridger().

void protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close ( core::pose::Pose & pose)

private

void protocols::swa::protein::StepWiseProteinLoopBridger::KIC_loop_close_with_perturbations ( core::pose::Pose & pose)

private

Definition at line 148 of file StepWiseProteinLoopBridger.cc.

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().

utility::vector1< utility::vector1< core::Real > > const & protocols::swa::protein::StepWiseProteinLoopBridger::main_chain_torsion_set_lists ( ) const

Definition at line 279 of file StepWiseProteinLoopBridger.cc.

References main_chain_torsion_sets_for_moving_residues_.

void protocols::swa::protein::StepWiseProteinLoopBridger::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

Definition at line 294 of file StepWiseProteinLoopBridger.cc.

Referenced by fill_chainTORS_info(), and KIC_loop_close().

void protocols::swa::protein::StepWiseProteinLoopBridger::sample_omega_recursively	(	core::pose::Pose &	pose,
		int const	offset,
		utility::vector1< utility::vector1< core::Real > > &	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

Definition at line 428 of file StepWiseProteinLoopBridger.cc.

References core::pose::Pose::dump_pdb(), end_res_, fill_chainTORS_info(), grab_main_chain_torsion_set_list(), is_pre_proline_, OMEGA_MEAN_, 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().

void protocols::swa::protein::StepWiseProteinLoopBridger::save_phi_psi_offsets ( core::pose::Pose const & pose)

private

void protocols::swa::protein::StepWiseProteinLoopBridger::setup_torsions ( core::pose::Pose const & pose)

private

Definition at line 230 of file StepWiseProteinLoopBridger.cc.

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

Referenced by apply().

utility::vector1< core::id::TorsionID > const & protocols::swa::protein::StepWiseProteinLoopBridger::which_torsions ( ) const

Definition at line 286 of file StepWiseProteinLoopBridger.cc.

References which_torsions_.

Member Data Documentation

Size protocols::swa::protein::StepWiseProteinLoopBridger::end_res_

private

Definition at line 126 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close(), and sample_omega_recursively().

core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::idl_C_N_

private

Definition at line 118 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close().

core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::idl_C_N_CA_

private

Definition at line 118 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close().

core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::idl_CA_C_N_

private

Definition at line 118 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close().

utility::vector1< bool > protocols::swa::protein::StepWiseProteinLoopBridger::is_fixed_res_

private

Definition at line 105 of file StepWiseProteinLoopBridger.hh.

Referenced by initialize_is_fixed_res(), and setup_torsions().

utility::vector1< bool > protocols::swa::protein::StepWiseProteinLoopBridger::is_pre_proline_

private

Definition at line 104 of file StepWiseProteinLoopBridger.hh.

Referenced by sample_omega_recursively().

loops::Loop protocols::swa::protein::StepWiseProteinLoopBridger::loop_

private

Definition at line 107 of file StepWiseProteinLoopBridger.hh.

Referenced by figure_out_loop(), and KIC_loop_close().

utility::vector1< utility::vector1< core::Real > > protocols::swa::protein::StepWiseProteinLoopBridger::main_chain_torsion_sets_for_moving_residues_

private

Definition at line 111 of file StepWiseProteinLoopBridger.hh.

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

Size protocols::swa::protein::StepWiseProteinLoopBridger::middle_offset_

private

Definition at line 126 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close().

Size protocols::swa::protein::StepWiseProteinLoopBridger::middle_res_

private

Definition at line 126 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close().

int const protocols::swa::protein::StepWiseProteinLoopBridger::num_perturb_steps_

private

Definition at line 115 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close_with_perturbations().

core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::OMEGA_MEAN_

private

Definition at line 118 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close(), and sample_omega_recursively().

core::Real const protocols::swa::protein::StepWiseProteinLoopBridger::perturb_torsion_

private

Definition at line 116 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close_with_perturbations().

utility::vector1< core::Real > protocols::swa::protein::StepWiseProteinLoopBridger::phi_offsets_

private

Definition at line 123 of file StepWiseProteinLoopBridger.hh.

Size protocols::swa::protein::StepWiseProteinLoopBridger::pose_count_

private

Definition at line 127 of file StepWiseProteinLoopBridger.hh.

Referenced by apply(), and KIC_loop_close_with_perturbations().

utility::vector1< core::Real > protocols::swa::protein::StepWiseProteinLoopBridger::psi_offsets_

private

Definition at line 124 of file StepWiseProteinLoopBridger.hh.

core::scoring::Ramachandran protocols::swa::protein::StepWiseProteinLoopBridger::ramachandran_

private

Definition at line 113 of file StepWiseProteinLoopBridger.hh.

protocols::swa::StepWisePoseSampleGeneratorOP protocols::swa::protein::StepWiseProteinLoopBridger::sample_generator_

private

Definition at line 101 of file StepWiseProteinLoopBridger.hh.

Referenced by apply().

Size protocols::swa::protein::StepWiseProteinLoopBridger::seg_len_

private

Definition at line 126 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close(), and sample_omega_recursively().

Size protocols::swa::protein::StepWiseProteinLoopBridger::start_res_

private

Definition at line 126 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close(), and sample_omega_recursively().

bool const protocols::swa::protein::StepWiseProteinLoopBridger::use_icoor_geometry_

private

Definition at line 119 of file StepWiseProteinLoopBridger.hh.

Referenced by KIC_loop_close().

bool const protocols::swa::protein::StepWiseProteinLoopBridger::verbose_

private

Definition at line 121 of file StepWiseProteinLoopBridger.hh.

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

utility::vector1< core::id::TorsionID > protocols::swa::protein::StepWiseProteinLoopBridger::which_torsions_

private

Definition at line 109 of file StepWiseProteinLoopBridger.hh.

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

utility::vector1< Size > protocols::swa::protein::StepWiseProteinLoopBridger::working_bridge_res_

private

Definition at line 103 of file StepWiseProteinLoopBridger.hh.

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

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

src/protocols/swa/protein/StepWiseProteinLoopBridger.hh
src/protocols/swa/protein/StepWiseProteinLoopBridger.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation