#include <StepWiseRNA_Minimizer.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_Minimizer:

Collaboration diagram for protocols::swa::rna::StepWiseRNA_Minimizer:

Public Member Functions
	StepWiseRNA_Minimizer (utility::vector1< pose_data_struct2 > const &pose_data_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_list (utility::vector1< core::kinematics::MoveMap > const &move_map_list)

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

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

void	set_base_centroid_screener (StepWiseRNA_BaseCentroidScreenerOP &screener)

void	set_native_edensity_score_cutoff (core::Real const &setting)

void	set_verbose (bool const setting)

void	set_centroid_screen (bool const setting)

void	set_perform_o2star_pack (bool const setting)

void	set_output_before_o2star_pack (bool const setting)

void	set_rm_virt_phosphate (bool const setting)

void	set_perform_minimize (bool const setting)

void	set_num_pose_minimize (Size const setting)

void	set_minimize_and_score_sugar (bool const setting)

void	set_native_rmsd_screen (bool const setting)

void	set_native_screen_rmsd_cutoff (core::Real const setting)

void	set_user_input_VDW_bin_screener (StepWiseRNA_VDW_Bin_ScreenerOP const &user_input_VDW_bin_screener)

void	set_rename_tag (bool const setting)

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
utility::vector1 < core::kinematics::MoveMap >	Get_default_movemap (core::pose::Pose const &pose) const

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

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_data_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_screener (core::pose::Pose &pose, core::pose::Pose &native_pose) const

Private Attributes
utility::vector1 < pose_data_struct2 > const	pose_data_list_

StepWiseRNA_JobParametersCOP	job_parameters_

core::io::silent::SilentFileDataOP	sfd_

utility::vector1 < core::kinematics::MoveMap >	move_map_list_

core::scoring::ScoreFunctionOP	scorefxn_

std::string	silent_file_

bool	verbose_

bool	screen_verbose_

bool	native_screen_

core::Real	native_screen_rmsd_cutoff_

bool	perform_electron_density_screen_

bool	rm_virt_phosphate_

core::Real	native_edensity_score_cutoff_

bool	centroid_screen_

bool	perform_o2star_pack_

bool	output_before_o2star_pack_

bool	perform_minimize_

core::Size	num_pose_minimize_

bool	minimize_and_score_sugar_

bool	rename_tag_

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

utility::vector1< core::Size >	fixed_res_

StepWiseRNA_BaseCentroidScreenerOP	base_centroid_screener_

StepWiseRNA_VDW_Bin_ScreenerOP	user_input_VDW_bin_screener_

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 45 of file StepWiseRNA_Minimizer.hh.

Constructor & Destructor Documentation

protocols::swa::rna::StepWiseRNA_Minimizer::StepWiseRNA_Minimizer	(	utility::vector1< pose_data_struct2 > const &	pose_data_list,
		StepWiseRNA_JobParametersCOP &	job_parameters
	)

Definition at line 93 of file StepWiseRNA_Minimizer.cc.

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

protocols::swa::rna::StepWiseRNA_Minimizer::~StepWiseRNA_Minimizer ( )

Definition at line 119 of file StepWiseRNA_Minimizer.cc.

Member Function Documentation

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

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 137 of file StepWiseRNA_Minimizer.cc.

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

private

Definition at line 326 of file StepWiseRNA_Minimizer.cc.

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

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_Minimizer::Figure_out_moving_residues	(	core::kinematics::MoveMap &	mm,
		core::pose::Pose const &	pose
	)		const

private

Definition at line 599 of file StepWiseRNA_Minimizer.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::id::BB, core::id::CHI, core::pose::Pose::conformation(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::conformation::Conformation::get_torsion_angle_atom_ids(), job_parameters_, core::kinematics::FoldTree::num_jump(), core::scoring::rna::NUM_RNA_CHI_TORSIONS(), core::scoring::rna::NUM_RNA_MAINCHAIN_TORSIONS(), protocols::swa::rna::Output_boolean(), core::pose::Pose::residue(), core::id::AtomID::rsd(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by Get_default_movemap().

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

private

Definition at line 407 of file StepWiseRNA_Minimizer.cc.

References core::id::BB, core::id::CHI, and core::kinematics::MoveMap::set().

Referenced by apply().

utility::vector1< core::kinematics::MoveMap > protocols::swa::rna::StepWiseRNA_Minimizer::Get_default_movemap ( core::pose::Pose const & pose) const

private

Definition at line 580 of file StepWiseRNA_Minimizer.cc.

References Figure_out_moving_residues().

Referenced by apply().

std::string protocols::swa::rna::StepWiseRNA_Minimizer::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 124 of file StepWiseRNA_Minimizer.cc.

bool protocols::swa::rna::StepWiseRNA_Minimizer::native_edensity_score_screener	(	core::pose::Pose &	pose,
		core::pose::Pose &	native_pose
	)		const

private

Definition at line 556 of file StepWiseRNA_Minimizer.cc.

References core::scoring::elec_dens_atomwise, native_edensity_score_cutoff_, and core::pose::Pose::total_residue().

Referenced by pass_all_pose_screens().

void protocols::swa::rna::StepWiseRNA_Minimizer::output_empty_minimizer_silent_file ( ) const

private

Definition at line 391 of file StepWiseRNA_Minimizer.cc.

References protocols::swa::rna::file_exists(), and silent_file_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_Minimizer::output_pose_data_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

Definition at line 371 of file StepWiseRNA_Minimizer.cc.

References protocols::moves::Mover::get_native_pose(), job_parameters_, and protocols::swa::rna::Output_data().

Referenced by apply(), and pass_all_pose_screens().

bool protocols::swa::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

Definition at line 425 of file StepWiseRNA_Minimizer.cc.

References base_centroid_screener_, centroid_screen_, protocols::swa::rna::Check_chain_closable(), protocols::swa::rna::check_for_messed_up_structure(), core::scoring::dna::DELTA, protocols::moves::Mover::get_native_pose(), core::conformation::Residue::has_variant_type(), job_parameters_, protocols::loops::loop_rmsd(), core::conformation::Residue::mainchain_torsion(), native_edensity_score_screener(), native_screen_, native_screen_rmsd_cutoff_, output_pose_data_wrapper(), perform_electron_density_screen_, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), protocols::swa::rna::rmsd_over_residue_list(), silent_file_, protocols::swa::rna::suite_rmsd(), core::pose::Pose::total_residue(), user_input_VDW_bin_screener_, and verbose_.

Referenced by apply().

void protocols::swa::rna::StepWiseRNA_Minimizer::set_base_centroid_screener ( StepWiseRNA_BaseCentroidScreenerOP & screener)

Definition at line 695 of file StepWiseRNA_Minimizer.cc.

References base_centroid_screener_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_centroid_screen ( bool const setting)

inline

Definition at line 83 of file StepWiseRNA_Minimizer.hh.

References centroid_screen_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_minimize_and_score_sugar ( bool const setting)

inline

Definition at line 101 of file StepWiseRNA_Minimizer.hh.

References minimize_and_score_sugar_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_move_map_list ( utility::vector1< core::kinematics::MoveMap > const & move_map_list)

Definition at line 670 of file StepWiseRNA_Minimizer.cc.

References move_map_list_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_native_edensity_score_cutoff ( core::Real const & setting)

Definition at line 701 of file StepWiseRNA_Minimizer.cc.

References native_edensity_score_cutoff_, and perform_electron_density_screen_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_native_rmsd_screen ( bool const setting)

inline

Definition at line 104 of file StepWiseRNA_Minimizer.hh.

References native_screen_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_native_screen_rmsd_cutoff ( core::Real const setting)

inline

Definition at line 107 of file StepWiseRNA_Minimizer.hh.

References native_screen_rmsd_cutoff_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_num_pose_minimize ( Size const setting)

inline

Definition at line 98 of file StepWiseRNA_Minimizer.hh.

References num_pose_minimize_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_output_before_o2star_pack ( bool const setting)

inline

Definition at line 89 of file StepWiseRNA_Minimizer.hh.

References output_before_o2star_pack_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_perform_minimize ( bool const setting)

inline

Definition at line 95 of file StepWiseRNA_Minimizer.hh.

References perform_minimize_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_perform_o2star_pack ( bool const setting)

inline

Definition at line 86 of file StepWiseRNA_Minimizer.hh.

References perform_o2star_pack_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_rename_tag ( bool const setting)

inline

Definition at line 113 of file StepWiseRNA_Minimizer.hh.

References rename_tag_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_rm_virt_phosphate ( bool const setting)

inline

Definition at line 92 of file StepWiseRNA_Minimizer.hh.

References rm_virt_phosphate_.

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

Definition at line 683 of file StepWiseRNA_Minimizer.cc.

References scorefxn_.

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

Definition at line 677 of file StepWiseRNA_Minimizer.cc.

References silent_file_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_user_input_VDW_bin_screener ( StepWiseRNA_VDW_Bin_ScreenerOP const & user_input_VDW_bin_screener)

inline

Definition at line 110 of file StepWiseRNA_Minimizer.hh.

References user_input_VDW_bin_screener_.

void protocols::swa::rna::StepWiseRNA_Minimizer::set_verbose ( bool const setting)

inline

Definition at line 80 of file StepWiseRNA_Minimizer.hh.

References verbose_.

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

Definition at line 689 of file StepWiseRNA_Minimizer.cc.

References sfd_.

Referenced by apply().