#include <StepWiseRNA_Minimizer.hh>

Public Member Functions
	StepWiseRNA_Minimizer (utility::vector1< core::pose::PoseOP > const &pose_list, StepWiseRNA_JobParametersCOP &job_parameters)

	~StepWiseRNA_Minimizer ()

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...

void	set_silent_file (std::string const &silent_file)

void	set_move_map (core::kinematics::MoveMapOP move_map_)

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

core::io::silent::SilentFileDataOP &	silent_file_data ()

void	set_base_centroid_checker (checker::RNA_BaseCentroidCheckerOP &checker)

void	set_user_input_VDW_bin_checker (checker::RNA_VDW_BinCheckerOP const &user_input_VDW_bin_checker)

void	output_pose_wrapper (std::string const &tag, core::pose::Pose &pose, std::string const &out_silent_file) const

void	set_extra_minimize_res (utility::vector1< core::Size > setting)

void	set_allow_variable_bond_geometry (bool const setting)

void	set_vary_bond_geometry_frequency (core::Real const setting)

void	set_allow_insert (toolbox::AllowInsertOP setting)

void	set_options (StepWiseRNA_ModelerOptionsOP options)

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
utility::vector1< core::Size >	get_working_moving_res (Size const &nres) const

core::kinematics::MoveMapOP	get_default_movemap (core::pose::Pose const &pose)

void	figure_out_moving_residues (core::kinematics::MoveMap &mm, core::pose::Pose const &pose)

bool	pass_all_pose_screens (core::pose::Pose &pose, std::string const in_tag, core::io::silent::SilentFileData &silent_file_data) const

void	Freeze_sugar_torsions (core::kinematics::MoveMap &mm, Size const nres) const

void	output_empty_minimizer_silent_file () const

void	output_pose_wrapper (std::string &tag, char tag_first_char, core::pose::Pose &pose, core::io::silent::SilentFileData &silent_file_data, std::string const out_silent_file) const

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

bool	native_edensity_score_checker (core::pose::Pose &pose, core::pose::Pose &native_pose) const

void	output_minimized_pose_list ()

void	output_parameters ()

Private Attributes
utility::vector1 < core::pose::PoseOP > const	pose_list_

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

StepWiseRNA_JobParametersCOP	job_parameters_

core::io::silent::SilentFileDataOP	sfd_

kinematics::MoveMapOP	move_map_

core::scoring::ScoreFunctionOP	scorefxn_

std::string	silent_file_

bool	perform_electron_density_screen_

StepWiseRNA_ModelerOptionsOP	options_

std::map< core::id::AtomID, core::id::AtomID >	pose_to_native_map_

utility::vector1< core::Size >	fixed_res_

checker::RNA_BaseCentroidCheckerOP	base_centroid_checker_

checker::RNA_VDW_BinCheckerOP	user_input_VDW_bin_checker_

core::Real	vary_bond_geometry_frequency_

bool	allow_variable_bond_geometry_

utility::vector1< core::Size >	extra_minimize_res_

toolbox::AllowInsertOP	allow_insert_

core::Real	original_geometry_weight_

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::rna::StepWiseRNA_Minimizer::StepWiseRNA_Minimizer	(	utility::vector1< core::pose::PoseOP > const &	pose_list,
		StepWiseRNA_JobParametersCOP &	job_parameters
	)

References job_parameters_, and protocols::moves::Mover::set_native_pose().

protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::~StepWiseRNA_Minimizer ( )

Member Function Documentation

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::apply ( core::pose::Pose & pose_to_visualize )

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

core::Size protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::figure_out_actual_five_prime_chain_break_res ( core::pose::Pose const & pose ) const

private

References protocols::pack_daemon::error_message, core::conformation::Residue::has_variant_type(), job_parameters_, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and utility_exit_with_message.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::figure_out_moving_residues	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose
	)

private

References allow_insert_, extra_minimize_res_, protocols::stepwise::sampling::rna::figure_out_stepwise_rna_movemap(), fixed_res, job_parameters_, and protocols::stepwise::sampling::rna::update_allow_insert_with_extra_minimize_res().

Referenced by get_default_movemap().

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::Freeze_sugar_torsions	(	core::kinematics::MoveMap &	mm,
		Size const	nres
	)		const

private

References core::kinematics::MoveMap::set(), and protocols::TR.

Referenced by apply().

core::kinematics::MoveMapOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::get_default_movemap ( core::pose::Pose const & pose )

private

References figure_out_moving_residues().

Referenced by apply().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::get_working_moving_res ( Size const & nres ) const

private

References utility::vector1< T, class >::has_value(), and job_parameters_.

Referenced by apply().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::native_edensity_score_checker	(	core::pose::Pose &	pose,
		core::pose::Pose &	native_pose
	)		const

private

References elec_dens_atomwise, protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::native_edensity_score_cutoff(), nres, options_, core::pose::Pose::total_residue(), and protocols::TR.

Referenced by pass_all_pose_screens().

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_empty_minimizer_silent_file ( ) const

private

References utility::file::file_exists(), silent_file_, and utility_exit_with_message.

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_minimized_pose_list ( )

private

References minimized_pose_list_, protocols::stepwise::sampling::rna::StepWiseRNA_ModelerOptions::minimizer_rename_tag(), options_, output_pose_wrapper(), silent_file_, silent_file_data(), tag, and tag_from_pose().

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_parameters ( )

private

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_pose_wrapper	(	std::string const &	tag,
		core::pose::Pose &	pose,
		std::string const &	out_silent_file
	)		const

References runtime_assert, and silent_file_data().

Referenced by apply(), output_minimized_pose_list(), and pass_all_pose_screens().

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::output_pose_wrapper	(	std::string &	tag,
		char	tag_first_char,
		core::pose::Pose &	pose,
		core::io::silent::SilentFileData &	silent_file_data,
		std::string const	out_silent_file
	)		const

private

References protocols::moves::Mover::get_native_pose(), job_parameters_, protocols::stepwise::sampling::rna::output_data(), and protocols::TR.

bool protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pass_all_pose_screens	(	core::pose::Pose &	pose,
		std::string const	in_tag,
		core::io::silent::SilentFileData &	silent_file_data
	)		const

private

Referenced by apply().

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_allow_insert ( toolbox::AllowInsertOP setting )

inline

References allow_insert_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_allow_variable_bond_geometry ( bool const setting )

inline

References allow_variable_bond_geometry_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_base_centroid_checker ( checker::RNA_BaseCentroidCheckerOP & checker )

References base_centroid_checker_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_extra_minimize_res ( utility::vector1< core::Size > setting )

inline

References extra_minimize_res_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_move_map ( core::kinematics::MoveMapOP move_map_ )

References move_map_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_options ( StepWiseRNA_ModelerOptionsOP options )

References options_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

References scorefxn_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_silent_file ( std::string const & silent_file )

References silent_file_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_user_input_VDW_bin_checker ( checker::RNA_VDW_BinCheckerOP const & user_input_VDW_bin_checker )

inline

References user_input_VDW_bin_checker_.

void protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::set_vary_bond_geometry_frequency ( core::Real const setting )

inline

References vary_bond_geometry_frequency_.

core::io::silent::SilentFileDataOP & protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::silent_file_data ( )

References sfd_.

Referenced by apply(), output_minimized_pose_list(), and output_pose_wrapper().

Member Data Documentation

toolbox::AllowInsertOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::allow_insert_

private

Referenced by apply(), figure_out_moving_residues(), and set_allow_insert().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::allow_variable_bond_geometry_

private

Referenced by apply(), and set_allow_variable_bond_geometry().

checker::RNA_BaseCentroidCheckerOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::base_centroid_checker_

private

Referenced by output_parameters(), pass_all_pose_screens(), and set_base_centroid_checker().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::extra_minimize_res_

private

Referenced by figure_out_moving_residues(), and set_extra_minimize_res().

utility::vector1< core::Size > protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::fixed_res_

private

StepWiseRNA_JobParametersCOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::job_parameters_

private

Referenced by apply(), figure_out_actual_five_prime_chain_break_res(), figure_out_moving_residues(), get_working_moving_res(), output_parameters(), output_pose_wrapper(), pass_all_pose_screens(), and StepWiseRNA_Minimizer().

utility::vector1< core::pose::PoseOP > protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::minimized_pose_list_

private

Referenced by apply(), and output_minimized_pose_list().

kinematics::MoveMapOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::move_map_

private

Referenced by apply(), and set_move_map().

StepWiseRNA_ModelerOptionsOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::options_

private

Referenced by apply(), native_edensity_score_checker(), output_minimized_pose_list(), output_parameters(), pass_all_pose_screens(), and set_options().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::original_geometry_weight_

private

Referenced by apply().

bool protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::perform_electron_density_screen_

private

Referenced by apply(), output_parameters(), and pass_all_pose_screens().

utility::vector1< core::pose::PoseOP > const protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pose_list_

private

Referenced by apply(), and output_parameters().

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::pose_to_native_map_

private

core::scoring::ScoreFunctionOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::scorefxn_

private

Referenced by apply(), and set_scorefxn().

core::io::silent::SilentFileDataOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::sfd_

private

Referenced by silent_file_data().

std::string protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::silent_file_

private

Referenced by apply(), output_empty_minimizer_silent_file(), output_minimized_pose_list(), pass_all_pose_screens(), and set_silent_file().

checker::RNA_VDW_BinCheckerOP protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::user_input_VDW_bin_checker_

private

Referenced by output_parameters(), pass_all_pose_screens(), and set_user_input_VDW_bin_checker().

core::Real protocols::stepwise::sampling::rna::StepWiseRNA_Minimizer::vary_bond_geometry_frequency_

private

Referenced by apply(), and set_vary_bond_geometry_frequency().

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

symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_Minimizer.hh
symlinks/rosetta/src/protocols/stepwise/sampling/rna/StepWiseRNA_Minimizer.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation