#include <StepWiseProteinBackboneSampler.hh>

Inheritance diagram for protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler:

[legend]

Public Member Functions
	StepWiseProteinBackboneSampler (protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters)

	~StepWiseProteinBackboneSampler () override

void	apply (core::pose::Pose &pose_to_visualize) override
	Apply the minimizer to one pose. More...

std::string	get_name () const override
	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 (core::pose::Pose const &pose) const

utility::vector1< core::id::TorsionID >	which_torsions (core::pose::Pose const &pose)

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)

void	set_expand_loop_takeoff (bool const setting)

bool	expand_loop_takeoff () const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

virtual MoverOP	clone () const
	Return a clone of the Mover object. 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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	define_moving_res (core::pose::Pose const &pose)

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

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

void	filter_and_save (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 (core::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 ()

core::Real	get_rotamer_angle (core::Size const i, core::Size const N_SAMPLE)

core::Real	rama_energy (core::Size const n, core::pose::Pose const &pose, utility::vector1< core::Real > const &mainchain_torsions)

Private Attributes
protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP	working_parameters_

utility::vector1< core::Size > const	moving_residues_input_

utility::vector1< core::Size >	moving_residues_

core::Size	n_sample_

core::Size	n_sample_beta_

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_

core::Size	nstruct_centroid_

core::scoring::Ramachandran const &	ramachandran_

core::scoring::RamaPrePro const &	rama_pre_pro_

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_

utility::vector1< bool >	is_fixed_res_input_

bool	expand_loop_takeoff_

bool	use_rama_pre_pro_

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 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

◆ StepWiseProteinBackboneSampler()

protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::StepWiseProteinBackboneSampler ( protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP working_parameters )

References initialize_is_fixed_res().

◆ ~StepWiseProteinBackboneSampler()

protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::~StepWiseProteinBackboneSampler ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::apply ( core::pose::Pose & pose_to_visualize )

overridevirtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References centroid_scores_, centroid_screen_, convert_to_centroid(), define_moving_res(), filter_main_chain_torsion_sets(), ghost_loops_, nstruct_centroid_, prepare_ghost_pose(), sample_residues_recursively(), setup_torsion_sets(), and protocols::TR().

Referenced by protocols::stepwise::modeler::protein::loop_close::enable_sampling_of_loop_takeoff(), and protocols::stepwise::sampler::protein::get_basic_protein_sampler().

◆ convert_to_centroid()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::convert_to_centroid ( core::pose::Pose & pose )

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::C_METHYLAMIDATION, core::chemical::CENTROID_t, core::scoring::dssp::Dssp::insert_ss_into_pose(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by apply(), and prepare_ghost_pose().

◆ copy_coords()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::copy_coords	(	core::pose::Pose &	pose,
		core::pose::Pose const &	template_pose,
		ResMap const &	ghost_map
	)		const

private

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

Referenced by filter_and_save(), and initialize_ghost_pose().

◆ define_moving_res()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::define_moving_res ( core::pose::Pose const & pose )

private

References expand_loop_takeoff_, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), is_fixed_res_, is_fixed_res_input_, core::kinematics::FoldTree::jump_nr(), moving_residues_, moving_residues_input_, and core::pose::Pose::size().

Referenced by apply().

◆ expand_loop_takeoff()

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::expand_loop_takeoff ( ) const

inline

References expand_loop_takeoff_.

◆ figure_out_fold_tree()

core::kinematics::FoldTree protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::figure_out_fold_tree ( ResMap const & ghost_map ) const

private

References core::kinematics::FoldTree::new_jump(), and protocols::TR().

Referenced by prepare_ghost_pose().

◆ filter_and_save()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_and_save	(	core::pose::Pose &	pose,
		std::string const &	tag
	)

private

References apply_vdw_cut_, centroid_score_diff_cut_, centroid_score_ref_, centroid_scores_, centroid_screen_, centroid_vdw_ref_, copy_coords(), protocols::moves::Mover::get_native_pose(), ghost_loops_, ghost_map_, ghost_pose_, core::scoring::is_protein_backbone_including_O(), main_chain_torsion_set_for_moving_residues_, main_chain_torsion_sets_for_moving_residues_, rmsd_cutoff_, core::scoring::rmsd_with_super(), protocols::TR(), and core::scoring::vdw.

Referenced by sample_residues_recursively().

◆ filter_based_on_desired_secstruct()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_based_on_desired_secstruct	(	char const	secstruct,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

References filter_big_bin().

Referenced by get_main_chain_torsion_set_list().

◆ filter_big_bin()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_big_bin	(	core::Size const	big_bin,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

References get_big_bin().

Referenced by filter_based_on_desired_secstruct(), and filter_native_BIG_BINS().

◆ filter_main_chain_torsion_sets()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_main_chain_torsion_sets ( )

private

References centroid_scores_, main_chain_torsion_sets_for_moving_residues_, and nstruct_centroid_.

Referenced by apply().

◆ filter_native_BIG_BINS()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_native_BIG_BINS	(	core::Size const	n,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

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::size().

Referenced by get_main_chain_torsion_set_list().

◆ get_big_bin()

Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_big_bin	(	core::Real const	phi,
		core::Real const	psi
	)		const

Referenced by filter_big_bin(), and filter_native_BIG_BINS().

◆ get_main_chain_torsion_set_list()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list	(	core::Size const	n,
		core::pose::Pose const &	pose,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

References core::chemical::C_METHYLAMIDATION, expand_loop_takeoff_, filter_based_on_desired_secstruct(), filter_native_BIG_BINS(), filter_native_big_bins_, core::pose::full_model_info::get_fixed_domain_from_full_model_info_const(), get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_coarse(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), get_main_chain_torsion_set_list_sample_psi_only(), core::conformation::Residue::has_variant_type(), is_fixed_res_, is_pre_proline_, moving_residues_, core::chemical::N_ACETYLATION, core::pose::Pose::residue(), sample_cis_omega(), core::pose::Pose::secstruct(), core::pose::Pose::size(), protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by sample_residues_recursively().

◆ get_main_chain_torsion_set_list_c_terminus()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::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

References get_rotamer_angle(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), n_sample_, n_sample_beta_, rama_energy(), and core::pose::Pose::residue_type().

Referenced by get_main_chain_torsion_set_list().

◆ get_main_chain_torsion_set_list_coarse()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_main_chain_torsion_set_list_coarse	(	core::Size const	n,
		core::pose::Pose const &	pose,
		MainChainTorsionSetList &	main_chain_torsion_set_list
	)

private

References core::pose::Pose::aa(), core::chemical::aa_gly, core::chemical::aa_pro, core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), and core::pose::Pose::residue_type().

Referenced by get_main_chain_torsion_set_list().

◆ get_main_chain_torsion_set_list_full()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::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

References get_rotamer_angle(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), n_sample_, n_sample_beta_, rama_energy(), and core::pose::Pose::residue_type().

Referenced by get_main_chain_torsion_set_list().

◆ get_main_chain_torsion_set_list_n_terminus()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::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

References get_rotamer_angle(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), n_sample_, n_sample_beta_, rama_energy(), and core::pose::Pose::residue_type().

Referenced by get_main_chain_torsion_set_list().

◆ get_main_chain_torsion_set_list_sample_phi_only()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::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

References get_rotamer_angle(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), n_sample_, n_sample_beta_, core::pose::Pose::omega(), core::scoring::omega, core::pose::Pose::psi(), rama_energy(), core::pose::Pose::residue_type(), and core::pose::Pose::theta().

Referenced by get_main_chain_torsion_set_list().

◆ get_main_chain_torsion_set_list_sample_psi_only()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::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

References get_rotamer_angle(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), n_sample_, n_sample_beta_, core::pose::Pose::phi(), rama_energy(), core::pose::Pose::residue_type(), and core::pose::Pose::theta().

Referenced by get_main_chain_torsion_set_list().

◆ get_name()

std::string protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_rotamer_angle()

Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::get_rotamer_angle	(	core::Size const	i,
		core::Size const	N_SAMPLE
	)

private

Referenced by get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), and get_main_chain_torsion_set_list_sample_psi_only().

◆ initialize_ghost_pose()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::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

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

Referenced by prepare_ghost_pose().

◆ initialize_is_fixed_res()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::initialize_is_fixed_res ( )

private

References set_fixed_residues(), and working_parameters_.

Referenced by StepWiseProteinBackboneSampler().

◆ main_chain_torsion_set_lists()

utility::vector1< MainChainTorsionSetList > const & protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists ( ) const

References main_chain_torsion_sets_for_moving_residues_.

◆ main_chain_torsion_set_lists_real()

utility::vector1< utility::vector1< core::Real > > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_lists_real ( core::pose::Pose const & pose ) const

References core::chemical::ResidueType::is_beta_aa(), main_chain_torsion_sets_for_moving_residues_, moving_residues_, and core::pose::Pose::residue_type().

Referenced by protocols::stepwise::modeler::protein::loop_close::enable_sampling_of_loop_takeoff(), and protocols::stepwise::sampler::protein::get_basic_protein_sampler().

◆ output_centroid_silent_struct()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::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

◆ prepare_ghost_pose()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::prepare_ghost_pose ( core::pose::Pose const & pose )

private

◆ rama_energy()

Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy	(	core::Size const	n,
		core::pose::Pose const &	pose,
		utility::vector1< core::Real > const &	mainchain_torsions
	)

private

References core::pose::Pose::aa(), core::pose::Pose::conformation(), core::conformation::Residue::connection_incomplete(), core::scoring::Ramachandran::eval_rama_score_residue(), core::scoring::RamaPrePro::eval_rpp_rama_score(), core::chemical::ResidueType::get_self_ptr(), core::conformation::Residue::has_upper_connect(), rama_pre_pro_, ramachandran_, core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), core::pose::Pose::residue_type(), core::conformation::Residue::type(), core::chemical::ResidueType::upper_connect_id(), and use_rama_pre_pro_.

Referenced by get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), and get_main_chain_torsion_set_list_sample_psi_only().

◆ sample_cis_omega()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_cis_omega ( MainChainTorsionSetList & main_chain_torsion_set_list )

private

Referenced by get_main_chain_torsion_set_list().

◆ sample_residues_recursively()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::sample_residues_recursively	(	core::Size const	which_res,
		core::Size &	count,
		core::pose::Pose &	pose
	)

private

References core::id::BB, filter_and_save(), get_main_chain_torsion_set_list(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), main_chain_torsion_set_for_moving_residues_, moving_residues_, core::pose::Pose::residue_type(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::set_torsion().

Referenced by apply().

◆ set_apply_vdw_cut()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_apply_vdw_cut ( bool const setting )

References apply_vdw_cut_.

Referenced by setup_centroid_screen().

◆ set_centroid_score_diff_cut()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_score_diff_cut ( core::Real const setting )

References centroid_score_diff_cut_.

Referenced by setup_centroid_screen().

◆ set_centroid_scorefxn()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn )

References centroid_scorefxn_.

Referenced by setup_centroid_screen().

◆ set_centroid_screen()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_centroid_screen ( bool const setting )

References centroid_screen_.

Referenced by setup_centroid_screen().

◆ set_expand_loop_takeoff()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_expand_loop_takeoff ( bool const setting )

inline

References expand_loop_takeoff_.

Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().

◆ set_filter_native_big_bins()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_filter_native_big_bins ( bool const setting )

References filter_native_big_bins_.

Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().

◆ set_fixed_residues()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_fixed_residues ( utility::vector1< core::Size > const & fixed_res )

References is_fixed_res_input_, core::pose::rna::remove_bracketed(), and working_parameters_.

Referenced by protocols::stepwise::modeler::protein::loop_close::enable_sampling_of_loop_takeoff(), and initialize_is_fixed_res().

◆ set_ghost_loops()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_ghost_loops ( bool const setting )

References ghost_loops_.

Referenced by setup_centroid_screen().

◆ set_moving_residues()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_moving_residues ( utility::vector1< core::Size > const & moving_res )

References moving_residues_.

Referenced by protocols::stepwise::modeler::protein::loop_close::enable_sampling_of_loop_takeoff().

◆ set_n_sample()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_n_sample ( core::Size const setting )

References n_sample_, and n_sample_beta_.

Referenced by protocols::stepwise::modeler::protein::loop_close::enable_sampling_of_loop_takeoff(), and protocols::stepwise::sampler::protein::get_basic_protein_sampler().

◆ set_nstruct_centroid()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_nstruct_centroid ( core::Size const setting )

References nstruct_centroid_.

Referenced by setup_centroid_screen().

◆ set_rmsd_cutoff()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_rmsd_cutoff ( core::Real const setting )

References rmsd_cutoff_.

◆ set_silent_file()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::set_silent_file ( std::string const & setting )

References silent_file_.

Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().

◆ setup_centroid_screen()

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

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::rg, set_apply_vdw_cut(), set_centroid_score_diff_cut(), set_centroid_scorefxn(), set_centroid_screen(), set_ghost_loops(), and set_nstruct_centroid().

Referenced by protocols::stepwise::sampler::protein::get_basic_protein_sampler().

◆ setup_torsion_sets()

void protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::setup_torsion_sets ( core::pose::Pose const & pose )

private

References core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), main_chain_torsion_set_for_moving_residues_, main_chain_torsion_sets_for_moving_residues_, moving_residues_, and core::pose::Pose::residue_type().

Referenced by apply().

◆ which_torsions()

utility::vector1< id::TorsionID > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::which_torsions ( core::pose::Pose const & pose )

References core::id::BB, moving_residues_, and core::pose::Pose::residue().

Referenced by protocols::stepwise::modeler::protein::loop_close::enable_sampling_of_loop_takeoff(), and protocols::stepwise::sampler::protein::get_basic_protein_sampler().

Member Data Documentation

◆ apply_vdw_cut_

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::apply_vdw_cut_

private

Referenced by filter_and_save(), and set_apply_vdw_cut().

◆ centroid_score_diff_cut_

core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_score_diff_cut_

private

Referenced by filter_and_save(), and set_centroid_score_diff_cut().

◆ centroid_score_ref_

core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_score_ref_

private

Referenced by filter_and_save(), and prepare_ghost_pose().

◆ centroid_scorefxn_

core::scoring::ScoreFunctionOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_scorefxn_

private

Referenced by prepare_ghost_pose(), and set_centroid_scorefxn().

◆ centroid_scores_

utility::vector1< core::Real > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_scores_

private

Referenced by apply(), filter_and_save(), and filter_main_chain_torsion_sets().

◆ centroid_screen_

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_screen_

private

Referenced by apply(), filter_and_save(), and set_centroid_screen().

◆ centroid_vdw_ref_

core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::centroid_vdw_ref_

private

Referenced by filter_and_save(), and prepare_ghost_pose().

◆ expand_loop_takeoff_

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::expand_loop_takeoff_

private

Referenced by define_moving_res(), expand_loop_takeoff(), get_main_chain_torsion_set_list(), and set_expand_loop_takeoff().

◆ filter_native_big_bins_

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::filter_native_big_bins_

private

Referenced by get_main_chain_torsion_set_list(), and set_filter_native_big_bins().

◆ ghost_loops_

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_loops_

private

Referenced by apply(), filter_and_save(), and set_ghost_loops().

◆ ghost_map_

ResMap protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_map_

private

Referenced by filter_and_save(), and prepare_ghost_pose().

◆ ghost_native_pose_

core::pose::PoseOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_native_pose_

private

Referenced by prepare_ghost_pose().

◆ ghost_pose_

core::pose::PoseOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ghost_pose_

private

Referenced by filter_and_save(), and prepare_ghost_pose().

◆ is_fixed_res_

utility::vector1< bool > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::is_fixed_res_

private

Referenced by define_moving_res(), and get_main_chain_torsion_set_list().

◆ is_fixed_res_input_

utility::vector1< bool > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::is_fixed_res_input_

private

Referenced by define_moving_res(), and set_fixed_residues().

◆ is_pre_proline_

utility::vector1< bool > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::is_pre_proline_

private

Referenced by get_main_chain_torsion_set_list().

◆ main_chain_torsion_set_for_moving_residues_

MainChainTorsionSetList protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_set_for_moving_residues_

private

Referenced by filter_and_save(), sample_residues_recursively(), and setup_torsion_sets().

◆ main_chain_torsion_sets_for_moving_residues_

utility::vector1< MainChainTorsionSetList > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::main_chain_torsion_sets_for_moving_residues_

private

Referenced by filter_and_save(), filter_main_chain_torsion_sets(), main_chain_torsion_set_lists(), main_chain_torsion_set_lists_real(), and setup_torsion_sets().

◆ moving_residues_

utility::vector1< core::Size > protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::moving_residues_

private

Referenced by define_moving_res(), get_main_chain_torsion_set_list(), main_chain_torsion_set_lists_real(), prepare_ghost_pose(), sample_residues_recursively(), set_moving_residues(), setup_torsion_sets(), and which_torsions().

◆ moving_residues_input_

utility::vector1< core::Size > const protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::moving_residues_input_

private

Referenced by define_moving_res().

◆ n_sample_

core::Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::n_sample_

private

Referenced by get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), get_main_chain_torsion_set_list_sample_psi_only(), and set_n_sample().

◆ n_sample_beta_

core::Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::n_sample_beta_

private

Referenced by get_main_chain_torsion_set_list_c_terminus(), get_main_chain_torsion_set_list_full(), get_main_chain_torsion_set_list_n_terminus(), get_main_chain_torsion_set_list_sample_phi_only(), get_main_chain_torsion_set_list_sample_psi_only(), and set_n_sample().

◆ nstruct_centroid_

core::Size protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::nstruct_centroid_

private

Referenced by apply(), filter_main_chain_torsion_sets(), and set_nstruct_centroid().

◆ rama_pre_pro_

core::scoring::RamaPrePro const& protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_pre_pro_

private

Referenced by rama_energy().

◆ ramachandran_

core::scoring::Ramachandran const& protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::ramachandran_

private

Referenced by rama_energy().

◆ rmsd_cutoff_

core::Real protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rmsd_cutoff_

private

Referenced by filter_and_save(), and set_rmsd_cutoff().

◆ silent_file_

std::string protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::silent_file_

private

Referenced by set_silent_file().

◆ use_rama_pre_pro_

bool protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::use_rama_pre_pro_

private

Referenced by rama_energy().

◆ working_parameters_

protocols::stepwise::modeler::working_parameters::StepWiseWorkingParametersCOP protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::working_parameters_

private

Referenced by initialize_is_fixed_res(), and set_fixed_residues().

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

src/protocols/stepwise/modeler/protein/StepWiseProteinBackboneSampler.hh
src/protocols/stepwise/modeler/protein/StepWiseProteinBackboneSampler.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWiseProteinBackboneSampler()

◆ ~StepWiseProteinBackboneSampler()

Member Function Documentation

◆ apply()

◆ convert_to_centroid()

◆ copy_coords()

◆ define_moving_res()

◆ expand_loop_takeoff()

◆ figure_out_fold_tree()

◆ filter_and_save()

◆ filter_based_on_desired_secstruct()

◆ filter_big_bin()

◆ filter_main_chain_torsion_sets()

◆ filter_native_BIG_BINS()

◆ get_big_bin()

◆ get_main_chain_torsion_set_list()

◆ get_main_chain_torsion_set_list_c_terminus()

◆ get_main_chain_torsion_set_list_coarse()

◆ get_main_chain_torsion_set_list_full()

◆ get_main_chain_torsion_set_list_n_terminus()

◆ get_main_chain_torsion_set_list_sample_phi_only()

◆ get_main_chain_torsion_set_list_sample_psi_only()

◆ get_name()

◆ get_rotamer_angle()

◆ initialize_ghost_pose()

◆ initialize_is_fixed_res()

◆ main_chain_torsion_set_lists()

◆ main_chain_torsion_set_lists_real()

◆ output_centroid_silent_struct()

◆ prepare_ghost_pose()

◆ rama_energy()

◆ sample_cis_omega()

◆ sample_residues_recursively()

◆ set_apply_vdw_cut()

◆ set_centroid_score_diff_cut()

◆ set_centroid_scorefxn()

◆ set_centroid_screen()

◆ set_expand_loop_takeoff()

◆ set_filter_native_big_bins()

◆ set_fixed_residues()

◆ set_ghost_loops()

◆ set_moving_residues()

◆ set_n_sample()

◆ set_nstruct_centroid()

◆ set_rmsd_cutoff()

◆ set_silent_file()

◆ setup_centroid_screen()

◆ setup_torsion_sets()

◆ which_torsions()

Member Data Documentation

◆ apply_vdw_cut_

◆ centroid_score_diff_cut_

◆ centroid_score_ref_

◆ centroid_scorefxn_

◆ centroid_scores_

◆ centroid_screen_

◆ centroid_vdw_ref_

◆ expand_loop_takeoff_

◆ filter_native_big_bins_

◆ ghost_loops_

◆ ghost_map_

◆ ghost_native_pose_

◆ ghost_pose_

◆ is_fixed_res_

◆ is_fixed_res_input_

◆ is_pre_proline_

◆ main_chain_torsion_set_for_moving_residues_

◆ main_chain_torsion_sets_for_moving_residues_

◆ moving_residues_

◆ moving_residues_input_

◆ n_sample_

◆ n_sample_beta_

◆ nstruct_centroid_

◆ rama_pre_pro_

◆ ramachandran_