#include <StepWiseProteinResidueSampler.hh>

Public Member Functions
	StepWiseProteinResidueSampler (StepWiseProteinJobParametersCOP &job_parameters)

	~StepWiseProteinResidueSampler ()

virtual void	apply (core::pose::Pose &pose_to_visualize)

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

void	set_scorefxn (core::scoring::ScoreFunctionOP const &scorefxn)

utility::vector1 < core::pose::PoseOP > const &	get_pose_list ()

void	set_options (StepWiseProteinModelerOptionsCOP options)

void	set_frag_files (utility::vector1< std::string > const &frag_files)

void	set_input_streams (utility::vector1< InputStreamWithResidueInfoOP > const &input_streams)

void	set_do_ccd (bool const setting)

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

utility::vector1< Size >	moving_res_list () const

bool	full_optimize () 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
void	initialize_sampler (core::pose::Pose &pose)

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

rotamer_sampler::RotamerSizedOP	get_basic_sampler (core::pose::Pose &pose)

rotamer_sampler::RotamerSizedOP	close_loops_in_samples (core::pose::Pose &pose, rotamer_sampler::RotamerSizedOP sampler)

StepWiseProteinPackerOP	get_packer (core::pose::Pose &pose)

void	enable_sampling_of_loop_takeoff (core::pose::Pose &pose, rotamer_sampler::RotamerSizedOP sampler)

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::StepWiseProteinResidueSampler::StepWiseProteinResidueSampler ( StepWiseProteinJobParametersCOP & job_parameters )

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

Member Function Documentation

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

virtual

Implements protocols::moves::Mover.

References initialize_sampler(), initialize_screeners(), options_, pose_list_, pose_selection_, protocols::stepwise::StepWiseSampleAndScreen::run(), sampler_, screeners_, protocols::stepwise::StepWiseSampleAndScreen::set_max_ntries(), and protocols::stepwise::StepWiseSampleAndScreen::set_num_random_samples().

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

rotamer_sampler::RotamerSizedOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_in_samples	(	core::pose::Pose &	pose,
		rotamer_sampler::RotamerSizedOP	sampler
	)

private

Referenced by initialize_sampler().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::enable_sampling_of_loop_takeoff	(	core::pose::Pose &	pose,
		rotamer_sampler::RotamerSizedOP	sampler
	)

private

References job_parameters_, moving_res_list_, options_, runtime_assert, core::pose::Pose::total_residue(), and protocols::TR.

Referenced by close_loops_in_samples().

bool protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::full_optimize ( ) const

inline

References full_optimize_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

rotamer_sampler::RotamerSizedOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::get_basic_sampler ( core::pose::Pose & pose )

private

Referenced by initialize_sampler().

virtual std::string protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::get_name ( ) const

inlinevirtual

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

Implements protocols::moves::Mover.

StepWiseProteinPackerOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::get_packer ( core::pose::Pose & pose )

private

References protocols::stepwise::check_scorefxn_has_constraint_terms_if_pose_has_constraints(), elec_dens_atomwise, job_parameters_, linear_chainbreak, moving_res_list_, options_, and scorefxn_.

Referenced by initialize_screeners().

utility::vector1< core::pose::PoseOP > const& protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::get_pose_list ( )

inline

References pose_list_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::initialize_sampler ( core::pose::Pose & pose )

private

References close_loops_, close_loops_in_samples(), do_ccd_, get_basic_sampler(), job_parameters_, moving_res_list_, options_, and sampler_.

Referenced by apply().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::initialize_screeners ( core::pose::Pose & pose )

private

References core::pose::Pose::clone(), close_loops_, protocols::stepwise::figure_out_moving_partition_res(), full_optimize_, get_packer(), job_parameters_, moving_res_list_, options_, pose_selection_, runtime_assert, screeners_, and screening_pose_.

Referenced by apply().

utility::vector1< Size > protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::moving_res_list ( ) const

inline

References moving_res_list_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::set_do_ccd ( bool const setting )

inline

References do_ccd_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::set_frag_files ( utility::vector1< std::string > const & frag_files )

inline

References frag_files_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::set_input_streams ( utility::vector1< InputStreamWithResidueInfoOP > const & input_streams )

inline

References input_streams_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

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

inline

References moving_res_list_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::set_options ( StepWiseProteinModelerOptionsCOP options )

inline

References options_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

void protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

inline

References scorefxn_.

Referenced by protocols::stepwise::sampling::protein::StepWiseProteinModeler::do_residue_sampling().

Member Data Documentation

bool protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::close_loops_

private

Referenced by close_loops_in_samples(), initialize_sampler(), and initialize_screeners().

bool protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::do_ccd_

private

Referenced by close_loops_in_samples(), initialize_sampler(), and set_do_ccd().

utility::vector1< std::string > protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::frag_files_

private

Referenced by get_basic_sampler(), and set_frag_files().

bool protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::full_optimize_

private

Referenced by full_optimize(), get_basic_sampler(), and initialize_screeners().

utility::vector1< InputStreamWithResidueInfoOP > protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::input_streams_

private

Referenced by get_basic_sampler(), and set_input_streams().

StepWiseProteinJobParametersCOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::job_parameters_

private

Referenced by close_loops_in_samples(), enable_sampling_of_loop_takeoff(), get_basic_sampler(), get_packer(), initialize_sampler(), and initialize_screeners().

utility::vector1< Size > protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::moving_res_list_

private

Referenced by close_loops_in_samples(), enable_sampling_of_loop_takeoff(), get_basic_sampler(), get_packer(), initialize_sampler(), initialize_screeners(), moving_res_list(), and set_moving_res_list().

StepWiseProteinModelerOptionsCOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::options_

private

Referenced by apply(), close_loops_in_samples(), enable_sampling_of_loop_takeoff(), get_basic_sampler(), get_packer(), initialize_sampler(), initialize_screeners(), and set_options().

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::pose_list_

private

Referenced by apply(), and get_pose_list().

screener::SimplePoseSelectionOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::pose_selection_

private

Referenced by apply(), and initialize_screeners().

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

private

Referenced by apply(), and initialize_sampler().

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::scorefxn_

private

Referenced by get_packer(), and set_scorefxn().

utility::vector1< screener::StepWiseScreenerOP > protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::screeners_

private

Referenced by apply(), and initialize_screeners().

core::pose::PoseOP protocols::stepwise::sampling::protein::StepWiseProteinResidueSampler::screening_pose_

private

Referenced by initialize_screeners().

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

symlinks/rosetta/src/protocols/stepwise/sampling/protein/StepWiseProteinResidueSampler.hh
symlinks/rosetta/src/protocols/stepwise/sampling/protein/StepWiseProteinResidueSampler.cc

Private Attributes
StepWiseProteinJobParametersCOP	job_parameters_

utility::vector1 < core::pose::PoseOP >	pose_list_

core::scoring::ScoreFunctionOP	scorefxn_

StepWiseProteinModelerOptionsCOP	options_

utility::vector1< Size >	moving_res_list_

core::pose::PoseOP	screening_pose_

rotamer_sampler::RotamerSizedOP	sampler_

utility::vector1 < screener::StepWiseScreenerOP >	screeners_

screener::SimplePoseSelectionOP	pose_selection_

bool	do_ccd_

bool	close_loops_

bool	full_optimize_

utility::vector1< std::string >	frag_files_

utility::vector1 < InputStreamWithResidueInfoOP >	input_streams_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation