#include <StepWiseProteinScreener.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinScreener:

Collaboration diagram for protocols::swa::protein::StepWiseProteinScreener:

Public Member Functions
	StepWiseProteinScreener (protocols::swa::StepWiseJobParametersOP &job_parameters)

	~StepWiseProteinScreener ()

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 &setting)

void	set_rmsd_cutoff (core::Real const &setting)

void	set_n_sample (core::Size const &setting)

void	set_nstruct_centroid (core::Size const &setting)

void	set_filter_native_big_bins (bool const &setting)

void	set_centroid_screen (bool const &setting)

void	set_ghost_loops (bool const &setting)

void	set_apply_vdw_cut (bool const &setting)

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

void	set_centroid_score_diff_cut (core::Real const &setting)

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

utility::vector1 < utility::vector1< core::Real > >	main_chain_torsion_set_lists_real () const

utility::vector1 < core::id::TorsionID >	which_torsions ()

void	setup_centroid_screen (core::Real const &centroid_score_diff_cut, std::string const &centroid_weights, core::Size const nstruct_centroid, bool const ghost_loops)

core::Size	get_big_bin (core::Real const phi, core::Real const psi) const

void	set_moving_residues (utility::vector1< core::Size > const &moving_res)

void	set_fixed_residues (utility::vector1< core::Size > const &fixed_res)

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_torsion_sets ()

void	filter_main_chain_torsion_sets ()

void	prepare_ghost_pose (core::pose::Pose const &pose)

void	initialize_ghost_pose (core::pose::PoseOP &ghost_pose, std::string const &desired_sequence, core::pose::Pose const &template_pose, ResMap const &ghost_map, core::kinematics::FoldTree f)

void	copy_coords (core::pose::Pose &pose, core::pose::Pose const &template_pose, ResMap const &ghost_map) const

core::kinematics::FoldTree	figure_out_fold_tree (ResMap const &ghost_map) const

void	sample_residues_recursively (Size const which_res, Size &count, core::pose::Pose &pose)

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

void	get_main_chain_torsion_set_list (core::Size const &n, core::pose::Pose const &pose, MainChainTorsionSetList &main_chain_torsion_set_list)

void	get_main_chain_torsion_set_list_coarse (core::Size const &n, core::pose::Pose const &pose, MainChainTorsionSetList &main_chain_torsion_set_list)

void	get_main_chain_torsion_set_list_full (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)

void	get_main_chain_torsion_set_list_n_terminus (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)

void	get_main_chain_torsion_set_list_c_terminus (core::Size const &n, core::pose::Pose const &pose, core::Real const &best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)

void	get_main_chain_torsion_set_list_sample_phi_only (core::Size const &n, core::pose::Pose const &pose, core::Real const best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)

void	get_main_chain_torsion_set_list_sample_psi_only (core::Size const &n, core::pose::Pose const &pose, core::Real const best_energy_cutoff, MainChainTorsionSetList &main_chain_torsion_set_list)

void	filter_native_BIG_BINS (core::Size const &n, MainChainTorsionSetList &main_chain_torsion_set_list)

void	filter_based_on_desired_secstruct (char const &secstruct, MainChainTorsionSetList &main_chain_torsion_set_list)

void	filter_big_bin (Size const big_bin, MainChainTorsionSetList &main_chain_torsion_set_list)

void	output_centroid_silent_struct (core::pose::Pose const &pose, core::pose::PoseCOP const &native_pose_op, std::string const silent_file, std::string const &tag)

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

void	sample_cis_omega (MainChainTorsionSetList &main_chain_torsion_set_list)

void	initialize_is_fixed_res ()

Private Attributes
protocols::swa::StepWiseJobParametersOP	job_parameters_

utility::vector1< Size >	moving_residues_

core::Size	n_sample_

core::Real	rmsd_cutoff_

core::scoring::ScoreFunctionOP	centroid_scorefxn_

std::string	silent_file_

bool	filter_native_big_bins_

bool	centroid_screen_

core::Real	centroid_score_ref_

core::Real	centroid_score_diff_cut_

bool	apply_vdw_cut_

core::Real	centroid_vdw_ref_

Size	nstruct_centroid_

core::scoring::Ramachandran	ramachandran_

MainChainTorsionSetList	main_chain_torsion_set_for_moving_residues_

utility::vector1 < MainChainTorsionSetList >	main_chain_torsion_sets_for_moving_residues_

utility::vector1< core::Real >	centroid_scores_

bool	ghost_loops_

ResMap	ghost_map_

core::pose::PoseOP	ghost_pose_

core::pose::PoseOP	ghost_native_pose_

utility::vector1< bool >	is_pre_proline_

utility::vector1< bool >	is_fixed_res_

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 42 of file StepWiseProteinScreener.hh.

Constructor & Destructor Documentation

protocols::swa::protein::StepWiseProteinScreener::StepWiseProteinScreener ( protocols::swa::StepWiseJobParametersOP & job_parameters)

Definition at line 86 of file StepWiseProteinScreener.cc.

References initialize_is_fixed_res().

protocols::swa::protein::StepWiseProteinScreener::~StepWiseProteinScreener ( )

Definition at line 108 of file StepWiseProteinScreener.cc.

Member Function Documentation

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

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 120 of file StepWiseProteinScreener.cc.

References centroid_scores_, centroid_screen_, convert_to_centroid(), filter_main_chain_torsion_sets(), ghost_loops_, nstruct_centroid_, prepare_ghost_pose(), sample_residues_recursively(), and setup_torsion_sets().

void protocols::swa::protein::StepWiseProteinScreener::convert_to_centroid ( core::pose::Pose & pose)

private

Definition at line 871 of file StepWiseProteinScreener.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CENTROID, core::scoring::dssp::Dssp::insert_ss_into_pose(), core::pose::remove_variant_type_from_pose_residue(), core::util::switch_to_residue_type_set(), and core::pose::Pose::total_residue().

Referenced by apply(), and prepare_ghost_pose().

void protocols::swa::protein::StepWiseProteinScreener::copy_coords	(	core::pose::Pose &	pose,
		core::pose::Pose const &	template_pose,
		ResMap const &	ghost_map
	)		const

private

Definition at line 163 of file StepWiseProteinScreener.cc.

References core::chemical::ResidueType::atom_name(), core::conformation::Residue::atom_name(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by filter_and_output(), and initialize_ghost_pose().

core::kinematics::FoldTree protocols::swa::protein::StepWiseProteinScreener::figure_out_fold_tree ( ResMap const & ghost_map) const

private

Definition at line 193 of file StepWiseProteinScreener.cc.

References core::kinematics::FoldTree::new_jump().

Referenced by prepare_ghost_pose().

void protocols::swa::protein::StepWiseProteinScreener::filter_and_output	(	core::pose::Pose &	pose,
		std::string const &	tag
	)

private

void protocols::swa::protein::StepWiseProteinScreener::filter_based_on_desired_secstruct	(	char const &	secstruct,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 551 of file StepWiseProteinScreener.cc.

References filter_big_bin().

Referenced by get_main_chain_torsion_set_list().

void protocols::swa::protein::StepWiseProteinScreener::filter_big_bin	(	Size const	big_bin,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 569 of file StepWiseProteinScreener.cc.

References get_big_bin(), protocols::swa::protein::phi(), and protocols::swa::protein::psi().

Referenced by filter_based_on_desired_secstruct(), and filter_native_BIG_BINS().

void protocols::swa::protein::StepWiseProteinScreener::filter_main_chain_torsion_sets ( )

private

Definition at line 588 of file StepWiseProteinScreener.cc.

References centroid_scores_, main_chain_torsion_sets_for_moving_residues_, and nstruct_centroid_.

Referenced by apply().

void protocols::swa::protein::StepWiseProteinScreener::filter_native_BIG_BINS	(	core::Size const &	n,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 527 of file StepWiseProteinScreener.cc.

References filter_big_bin(), get_big_bin(), protocols::moves::Mover::get_native_pose(), core::pose::Pose::phi(), core::pose::Pose::psi(), and core::pose::Pose::total_residue().

Referenced by get_main_chain_torsion_set_list().

Size protocols::swa::protein::StepWiseProteinScreener::get_big_bin	(	core::Real const	phi,
		core::Real const	psi
	)		const

Definition at line 510 of file StepWiseProteinScreener.cc.

Referenced by filter_big_bin(), and filter_native_BIG_BINS().

void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list	(	core::Size const &	n,
		core::pose::Pose const &	pose,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_c_terminus	(	core::Size const &	n,
		core::pose::Pose const &	pose,
		core::Real const &	best_energy_cutoff,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 426 of file StepWiseProteinScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::protein::MainChainTorsionSet(), n_sample_, protocols::swa::protein::phi(), protocols::swa::protein::psi(), and ramachandran_.

Referenced by get_main_chain_torsion_set_list().

void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_coarse	(	core::Size const &	n,
		core::pose::Pose const &	pose,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 346 of file StepWiseProteinScreener.cc.

References core::pose::Pose::aa(), core::chemical::aa_gly, core::chemical::aa_pro, and protocols::swa::protein::MainChainTorsionSet().

Referenced by get_main_chain_torsion_set_list().

void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_full	(	core::Size const &	n,
		core::pose::Pose const &	pose,
		core::Real const &	best_energy_cutoff,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 380 of file StepWiseProteinScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::protein::MainChainTorsionSet(), n_sample_, protocols::swa::protein::phi(), protocols::swa::protein::psi(), and ramachandran_.

Referenced by get_main_chain_torsion_set_list().

void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_n_terminus	(	core::Size const &	n,
		core::pose::Pose const &	pose,
		core::Real const &	best_energy_cutoff,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 402 of file StepWiseProteinScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::protein::MainChainTorsionSet(), n_sample_, protocols::swa::protein::phi(), protocols::swa::protein::psi(), and ramachandran_.

Referenced by get_main_chain_torsion_set_list().

void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_phi_only	(	core::Size const &	n,
		core::pose::Pose const &	pose,
		core::Real const	best_energy_cutoff,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 452 of file StepWiseProteinScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::protein::MainChainTorsionSet(), n_sample_, protocols::swa::protein::phi(), protocols::swa::protein::psi(), core::pose::Pose::psi(), ramachandran_, and protocols::TR().

Referenced by get_main_chain_torsion_set_list().

void protocols::swa::protein::StepWiseProteinScreener::get_main_chain_torsion_set_list_sample_psi_only	(	core::Size const &	n,
		core::pose::Pose const &	pose,
		core::Real const	best_energy_cutoff,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

Definition at line 480 of file StepWiseProteinScreener.cc.

References core::pose::Pose::aa(), core::scoring::Ramachandran::eval_rama_score_residue(), protocols::swa::protein::get_rotamer_angle(), protocols::swa::protein::MainChainTorsionSet(), n_sample_, protocols::swa::protein::phi(), core::pose::Pose::phi(), protocols::swa::protein::psi(), ramachandran_, and protocols::TR().

Referenced by get_main_chain_torsion_set_list().

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

virtual

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

Implements protocols::moves::Mover.

Definition at line 112 of file StepWiseProteinScreener.cc.

void protocols::swa::protein::StepWiseProteinScreener::initialize_ghost_pose	(	core::pose::PoseOP &	ghost_pose,
		std::string const &	desired_sequence,
		core::pose::Pose const &	template_pose,
		ResMap const &	ghost_map,
		core::kinematics::FoldTree	f
	)

private

Definition at line 851 of file StepWiseProteinScreener.cc.

References core::chemical::CENTROID, copy_coords(), core::chemical::ChemicalManager::get_instance(), core::pose::make_pose_from_sequence(), and core::chemical::ChemicalManager::residue_type_set().

Referenced by prepare_ghost_pose().

void protocols::swa::protein::StepWiseProteinScreener::initialize_is_fixed_res ( )

private

Definition at line 726 of file StepWiseProteinScreener.cc.

References is_fixed_res_, and job_parameters_.

Referenced by StepWiseProteinScreener().

utility::vector1< MainChainTorsionSetList > const & protocols::swa::protein::StepWiseProteinScreener::main_chain_torsion_set_lists ( ) const

Definition at line 686 of file StepWiseProteinScreener.cc.

References main_chain_torsion_sets_for_moving_residues_.

utility::vector1< utility::vector1< core::Real > > protocols::swa::protein::StepWiseProteinScreener::main_chain_torsion_set_lists_real ( ) const

Definition at line 693 of file StepWiseProteinScreener.cc.

References main_chain_torsion_sets_for_moving_residues_, protocols::swa::protein::omega(), protocols::swa::protein::phi(), and protocols::swa::protein::psi().

void protocols::swa::protein::StepWiseProteinScreener::output_centroid_silent_struct	(	core::pose::Pose const &	pose,
		core::pose::PoseCOP const &	native_pose_op,
		std::string const	silent_file,
		std::string const &	tag
	)

private

void protocols::swa::protein::StepWiseProteinScreener::prepare_ghost_pose ( core::pose::Pose const & pose)

private

Definition at line 798 of file StepWiseProteinScreener.cc.

References centroid_score_ref_, centroid_scorefxn_, centroid_vdw_ref_, convert_to_centroid(), figure_out_fold_tree(), protocols::moves::Mover::get_native_pose(), ghost_map_, ghost_native_pose_, ghost_pose_, initialize_ghost_pose(), moving_residues_, core::pose::Pose::sequence(), core::kinematics::Jump::set_translation(), protocols::TR(), and core::scoring::vdw.

Referenced by apply().

void protocols::swa::protein::StepWiseProteinScreener::sample_cis_omega ( MainChainTorsionSetList & main_chain_torsion_set_list)

private

Definition at line 609 of file StepWiseProteinScreener.cc.

References protocols::swa::protein::MainChainTorsionSet(), protocols::swa::protein::phi(), and protocols::swa::protein::psi().

Referenced by get_main_chain_torsion_set_list().

void protocols::swa::protein::StepWiseProteinScreener::sample_residues_recursively	(	Size const	which_res,
		Size &	count,
		core::pose::Pose &	pose
	)

private

Definition at line 224 of file StepWiseProteinScreener.cc.

References filter_and_output(), get_main_chain_torsion_set_list(), main_chain_torsion_set_for_moving_residues_, moving_residues_, protocols::swa::protein::MainChainTorsionSet::omega(), protocols::swa::protein::MainChainTorsionSet::phi(), protocols::swa::protein::MainChainTorsionSet::psi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by apply().

void protocols::swa::protein::StepWiseProteinScreener::set_apply_vdw_cut ( bool const & setting)

Definition at line 674 of file StepWiseProteinScreener.cc.

References apply_vdw_cut_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_centroid_score_diff_cut ( core::Real const & setting)

Definition at line 680 of file StepWiseProteinScreener.cc.

References centroid_score_diff_cut_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_centroid_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn)

Definition at line 649 of file StepWiseProteinScreener.cc.

References centroid_scorefxn_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_centroid_screen ( bool const & setting)

Definition at line 662 of file StepWiseProteinScreener.cc.

References centroid_screen_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_filter_native_big_bins ( bool const & setting)

Definition at line 656 of file StepWiseProteinScreener.cc.

References filter_native_big_bins_.

void protocols::swa::protein::StepWiseProteinScreener::set_fixed_residues ( utility::vector1< core::Size > const & fixed_res)

Definition at line 746 of file StepWiseProteinScreener.cc.

References is_fixed_res_, and job_parameters_.

void protocols::swa::protein::StepWiseProteinScreener::set_ghost_loops ( bool const & setting)

Definition at line 668 of file StepWiseProteinScreener.cc.

References ghost_loops_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_moving_residues ( utility::vector1< core::Size > const & moving_res)

Definition at line 740 of file StepWiseProteinScreener.cc.

References moving_residues_.

void protocols::swa::protein::StepWiseProteinScreener::set_n_sample ( core::Size const & setting)

Definition at line 637 of file StepWiseProteinScreener.cc.

References n_sample_.

void protocols::swa::protein::StepWiseProteinScreener::set_nstruct_centroid ( core::Size const & setting)

Definition at line 643 of file StepWiseProteinScreener.cc.

References nstruct_centroid_.

Referenced by setup_centroid_screen().

void protocols::swa::protein::StepWiseProteinScreener::set_rmsd_cutoff ( core::Real const & setting)

Definition at line 631 of file StepWiseProteinScreener.cc.

References rmsd_cutoff_.

void protocols::swa::protein::StepWiseProteinScreener::set_silent_file ( std::string const & setting)

Definition at line 625 of file StepWiseProteinScreener.cc.

References silent_file_.

void protocols::swa::protein::StepWiseProteinScreener::setup_centroid_screen	(	core::Real const &	centroid_score_diff_cut,
		std::string const &	centroid_weights,
		core::Size const	nstruct_centroid,
		bool const	ghost_loops
	)