#include <ConfChangeMover.hh>

Inheritance diagram for protocols::rbsegment_relax::ConfChangeMover:

[legend]

Public Member Functions
	ConfChangeMover ()
	Constructor. More...

	~ConfChangeMover () override=default

protocols::moves::MoverOP	clone () const override
	Copy function - inherited. More...

void	apply (core::pose::Pose &pose) override
	Pose manipulation for conformational changes. More...

void	stage1_pose_setup (core::pose::Pose &pose)
	SETUP TOPOLOGY FOR RIGID BODY MOVES. More...

void	stage1 (core::pose::Pose &pose)
	APPLY RIGID BODY MOVES. More...

bool	check_gaps (core::pose::Pose &pose)
	Checks that no unbridgeable gaps were introduced during sampling. More...

rbsegment_relax::RBSegment	multi_rb (core::pose::Pose &pose, bool const &multiple_sses)
	Which SSEs to move if more than one is to be moved. More...

utility::vector1< utility::vector1< core::Real > >	sse_contact_strength (core::pose::Pose &pose) const

std::set< core::Size >	get_residues_in_rbsegment (rbsegment_relax::RBSegment const &rbseg) const

void	recursive_residues_from_rbsegs (rbsegment_relax::RBSegment const &rbseg, std::set< core::Size > &residues) const

void	check_or_create_fragments (core::pose::Pose &pose)
	check if fragments (3 and 9) are presents or pick them More...

void	stage2 (core::pose::Pose &pose, core::pose::Pose const &original_pose)
	fragments insertion from either input structure or from picked More...

void	add_dihedral_csts_to_rb (core::pose::Pose &pose, core::pose::Pose const &original_pose)
	add dihedral constraints to rigid-body moves More...

void	add_dihedral_csts (core::pose::Pose &pose, core::pose::Pose const &original_pose)
	add dihedral constraints to stage2 More...

core::pose::PoseOP	get_additional_output () override
	necessary function to output multiple poses More...

Public Member Functions inherited from protocols::hybridization::CartesianHybridize
	CartesianHybridize ()

	CartesianHybridize (utility::vector1< core::pose::PoseOP > const &templates_in, utility::vector1< core::Real > const &template_wts_in, utility::vector1< protocols::loops::Loops > const &template_chunks_in, utility::vector1< protocols::loops::Loops > const &template_contigs_in, core::fragment::FragSetOP fragments9_in)

void	init ()

void	set_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_min_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_pack_scorefunction (core::scoring::ScoreFunctionOP scorefxn_in)

void	set_increase_cycles (core::Real increase_cycles_in)

void	set_no_global_frame (bool no_global_frame_in)

void	set_linmin_only (bool linmin_only_in)

void	set_cartfrag_overlap (core::Size cartfrag_overlap_in)

void	set_seqfrags_only (bool seqfrags_only_in)

void	set_skip_long_min (bool skip_long_min_in)

void	set_cenrot (bool cenrot_in)

void	set_temperature (core::Real temp_in)

void	set_fragment_probs (core::Real prob, core::Real randprob)

void	set_max_insertion (int max_in)

void	set_per_residue_controls (utility::vector1< bool > const &residue_sample_template_in, utility::vector1< bool > const &residue_sample_abinitio_in)

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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 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...

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...

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

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

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

Private Attributes
utility::vector1< core::Size >	newstart_

utility::vector1< core::Size >	addstart_

utility::vector1< core::Size >	newend_

utility::vector1< core::Size >	addend_

utility::vector1< core::Size >	seg_

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

core::Size	stage1_moves_ = 10000

core::Real	stage1_multi_freq_ = 0.5

core::Real	stage1_frag_freq_ = 0.5

core::Real	stage1_twist_freq_ = 0.2

core::Real	stage1_temp_ = 1.0

core::Size	stage1_move_restore_ = 0

core::Size	stage2_moves_ = 1000

core::Real	stage2_segment_freq_ = 0.25

core::Real	stage2_targgaps_freq_ = 0.25

core::Real	stage2_temp_ = 1.0

core::Size	stage2_models_ = 1

core::Real	rot_ = 10.0

core::Real	transl_ = 1.0

core::scoring::ScoreFunctionOP	stage1_scorefxn_

core::scoring::ScoreFunctionOP	stage2_scorefxn_

rbsegment_relax::GaussianRBSegmentMover	rbmover_

rbsegment_relax::HelicalGaussianMover	helixmover_

core::fragment::FragSetOP	frags3_

core::fragment::FragSetOP	frags9_

std::map< core::Size, core::fragment::Frame >	frames_

utility::vector1< rbsegment_relax::RBSegment >	rbsegs_

utility::vector1< rbsegment_relax::RBSegment >	rbsegs_2_

utility::vector1< rbsegment_relax::RBSegment >	stored_rebsegs_

loops::Loops	loops_

core::pose::PoseOP	template_

std::string	rb_file_ = "AUTO"

std::string const	s1_rb_single_ = "1_RB1"

std::string const	s1_rb_multi_ = "1_RB2+"

std::string const	s1_twist_ = "1_TWIST"

std::string const	s1_frag_move_ = "1_FRAG3"

std::string const	s2_homolog_move_ = "2_TEMPLATE"

std::string const	s2_frame_select_ = "2_FRAG9T"

std::string const	s2_frame_random_ = "2_FRAG9R"

utility::vector1< core::Size >	res_adj_ = {3, 4, 5}

bool	stage1_minimization_ = false

core::select::residue_selector::ResidueSelectorCOP	s1_res_ = nullptr

core::select::residue_selector::ResidueSelectorCOP	s2_res_ = nullptr

core::select::residue_selector::ResidueSelectorCOP	dihed2_res_ = nullptr

core::optimization::CartesianMinimizer	minimizer_

utility::vector1< core::select::residue_selector::ResidueSelectorCOP >	s1_rigid_res_

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

Protected Member Functions inherited from protocols::hybridization::CartesianHybridize
void	apply_frag (core::pose::Pose &pose, core::pose::Pose &templ, protocols::loops::Loop &frag, bool superpose=true)

void	apply_frame (core::pose::Pose &pose, core::fragment::Frame &frame)

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

◆ ConfChangeMover()

protocols::rbsegment_relax::ConfChangeMover::ConfChangeMover ( )

Constructor.

◆ ~ConfChangeMover()

protocols::rbsegment_relax::ConfChangeMover::~ConfChangeMover ( )

overridedefault

Member Function Documentation

◆ add_dihedral_csts()

void protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts	(	core::pose::Pose &	pose,
		core::pose::Pose const &	original_pose
	)

add dihedral constraints to stage2

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), dihed2_res_, core::pose::Pose::fold_tree(), get_residues_in_rbsegment(), core::pose::Pose::phi(), core::pose::Pose::psi(), rbsegs_, core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), protocols::rbsegment_relax::TR(), and core::conformation::Residue::xyz().

Referenced by stage2().

◆ add_dihedral_csts_to_rb()

void protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts_to_rb	(	core::pose::Pose &	pose,
		core::pose::Pose const &	original_pose
	)

add dihedral constraints to rigid-body moves

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), get_residues_in_rbsegment(), core::pose::Pose::phi(), core::pose::Pose::psi(), rbsegs_, core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::rbsegment_relax::TR().

Referenced by apply().

◆ apply()

void protocols::rbsegment_relax::ConfChangeMover::apply ( core::pose::Pose & pose )

overridevirtual

Pose manipulation for conformational changes.

Sets up a "star" topology and obtains rigid body segments to move around. A copy of the pose is then made and its rigid body segments are moved in Cartesian space to observe the effects of a rigid body transform. The loops are then closed

Reimplemented from protocols::hybridization::CartesianHybridize.

References add_dihedral_csts_to_rb(), core::pose::addVirtualResAsRoot(), check_or_create_fragments(), core::pose::Pose::clone(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, core::pose::Pose::fold_tree(), core::util::remove_cutpoint_variants(), core::pose::remove_virtual_residues(), stage1(), stage2(), stage2_models_, stage2_moves_, stage2_scorefxn_, store_poseOPs_, template_, protocols::medal::to_centroid(), and protocols::rbsegment_relax::TR().

◆ check_gaps()

bool protocols::rbsegment_relax::ConfChangeMover::check_gaps ( core::pose::Pose & pose )

Checks that no unbridgeable gaps were introduced during sampling.

References core::conformation::Residue::atom(), get_residues_in_rbsegment(), rbsegs_, core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by stage1().

◆ check_or_create_fragments()

void protocols::rbsegment_relax::ConfChangeMover::check_or_create_fragments ( core::pose::Pose & pose )

check if fragments (3 and 9) are presents or pick them

References protocols::simple_filters::dssp(), frags3_, frags9_, core::fragment::picking_old::vall::pick_fragments_by_ss_plus_aa(), core::pose::Pose::sequence(), and core::pose::Pose::total_residue().

Referenced by apply().

◆ clone()

moves::MoverOP protocols::rbsegment_relax::ConfChangeMover::clone ( ) const

overridevirtual

Copy function - inherited.

Reimplemented from protocols::hybridization::CartesianHybridize.

Referenced by parse_my_tag().

◆ get_additional_output()

core::pose::PoseOP protocols::rbsegment_relax::ConfChangeMover::get_additional_output ( )

overridevirtual

necessary function to output multiple poses

Reimplemented from protocols::moves::Mover.

References store_poseOPs_, and protocols::rbsegment_relax::TR().

◆ get_name()

std::string protocols::rbsegment_relax::ConfChangeMover::get_name ( ) const

overrideprivatevirtual

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

Reimplemented from protocols::hybridization::CartesianHybridize.

References mover_name().

◆ get_residues_in_rbsegment()

std::set< core::Size > protocols::rbsegment_relax::ConfChangeMover::get_residues_in_rbsegment ( rbsegment_relax::RBSegment const & rbseg ) const

References protocols::rbsegment_relax::RBSegment::nContinuousSegments(), and protocols::loops::start.

Referenced by add_dihedral_csts(), add_dihedral_csts_to_rb(), check_gaps(), sse_contact_strength(), and stage1_pose_setup().

◆ mover_name()

std::string protocols::rbsegment_relax::ConfChangeMover::mover_name ( )

static

Referenced by get_name(), protocols::rbsegment_relax::ConfChangeMoverCreator::keyname(), and provide_xml_schema().

◆ multi_rb()

rbsegment_relax::RBSegment protocols::rbsegment_relax::ConfChangeMover::multi_rb	(	core::pose::Pose &	pose,
		bool const &	multiple_sses
	)

Which SSEs to move if more than one is to be moved.

References rbsegs_, protocols::sparta::split(), and sse_contact_strength().

Referenced by stage1().

◆ parse_my_tag()

void protocols::rbsegment_relax::ConfChangeMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overrideprivatevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References protocols::denovo_design::components::add_segment(), addend_, addstart_, clone(), core::scoring::ScoreFunctionFactory::create_score_function(), dihed2_res_, frags3_, frags9_, core::select::residue_selector::get_residue_selector(), helixmover_, newend_, newstart_, core::import_pose::pose_from_file(), rbmover_, core::fragment::FragmentIO::read_data(), rot_, s1_res_, s1_rigid_res_, s2_res_, seg_, protocols::sparta::split(), stage1_frag_freq_, stage1_minimization_, stage1_move_restore_, stage1_moves_, stage1_multi_freq_, stage1_scorefxn_, stage1_temp_, stage1_twist_freq_, stage2_models_, stage2_moves_, stage2_scorefxn_, stage2_segment_freq_, stage2_targgaps_freq_, stage2_temp_, template_, protocols::rbsegment_relax::TR(), and transl_.

◆ provide_xml_schema()

void protocols::rbsegment_relax::ConfChangeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::rbsegment_relax::ConfChangeMoverCreator::provide_xml_schema().

◆ recursive_residues_from_rbsegs()

void protocols::rbsegment_relax::ConfChangeMover::recursive_residues_from_rbsegs	(	rbsegment_relax::RBSegment const &	rbseg,
		std::set< core::Size > &	residues
	)		const

References protocols::rbsegment_relax::RBSegment::nContinuousSegments(), and protocols::loops::start.

Referenced by stage1_pose_setup().

◆ sse_contact_strength()

utility::vector1< utility::vector1< core::Real > > protocols::rbsegment_relax::ConfChangeMover::sse_contact_strength ( core::pose::Pose & pose ) const

References core::pose::Pose::energies(), get_residues_in_rbsegment(), core::conformation::Residue::is_virtual_residue(), rbsegs_, core::pose::Pose::residue(), core::scoring::Energies::tenA_neighbor_graph(), and core::pose::Pose::update_residue_neighbors().

Referenced by multi_rb().

◆ stage1()

void protocols::rbsegment_relax::ConfChangeMover::stage1 ( core::pose::Pose & pose )

APPLY RIGID BODY MOVES.

References protocols::simple_moves::ClassicFragmentMover::apply(), protocols::rbsegment_relax::HelicalGaussianMover::apply(), protocols::rbsegment_relax::GaussianRBSegmentMover::apply(), check_gaps(), core::scoring::ScoreFunctionFactory::create_score_function(), protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check(), frags3_, frags9_, helixmover_, core::optimization::MinimizerOptions::max_iter(), minimizer_, multi_rb(), rbmover_, rbsegs_, core::optimization::CartesianMinimizer::run(), s1_frag_move_, s1_rb_multi_, s1_rb_single_, s1_res_, s1_twist_, protocols::simple_moves::ClassicFragmentMover::set_check_ss(), protocols::rbsegment_relax::RBSegmentMover::set_segment(), stage1_frag_freq_, stage1_minimization_, stage1_move_restore_, stage1_moves_, stage1_multi_freq_, stage1_pose_setup(), stage1_scorefxn_, stage1_temp_, stage1_twist_freq_, stored_rebsegs_, and protocols::rbsegment_relax::TR().

Referenced by apply().

◆ stage1_pose_setup()

void protocols::rbsegment_relax::ConfChangeMover::stage1_pose_setup ( core::pose::Pose & pose )

SETUP TOPOLOGY FOR RIGID BODY MOVES.

References addend_, addstart_, get_residues_in_rbsegment(), protocols::rbsegment_relax::guess_rbsegs_from_pose(), loops_, newend_, newstart_, rb_file_, rbsegs_, rbsegs_2_, protocols::rbsegment_relax::read_RBSegment_file(), recursive_residues_from_rbsegs(), s1_res_, s1_rigid_res_, seg_, protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops(), stage1_multi_freq_, protocols::loops::start, stored_rebsegs_, and protocols::rbsegment_relax::TR().

Referenced by stage1().

◆ stage2()

void protocols::rbsegment_relax::ConfChangeMover::stage2	(	core::pose::Pose &	pose,
		core::pose::Pose const &	original_pose
	)

fragments insertion from either input structure or from picked

References add_dihedral_csts(), protocols::hybridization::CartesianHybridize::apply_frag(), protocols::hybridization::CartesianHybridize::apply_frame(), core::conformation::Residue::atom(), core::scoring::cart_bonded, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::dihedral_constraint, frags9_, frames_, protocols::mean_field::max(), core::optimization::MinimizerOptions::max_iter(), protocols::mean_field::min(), minimizer_, protocols::hybridization::r1, res_adj_, core::pose::Pose::residue(), core::scoring::rg, core::optimization::CartesianMinimizer::run(), s2_frame_random_, s2_frame_select_, s2_homolog_move_, s2_res_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::size(), stage2_models_, stage2_moves_, stage2_scorefxn_, stage2_segment_freq_, stage2_targgaps_freq_, stage2_temp_, protocols::loops::start, protocols::loops::stop, protocols::rbsegment_relax::TR(), and core::conformation::Atom::xyz().

Referenced by apply().

Member Data Documentation

◆ addend_

utility::vector1<core::Size> protocols::rbsegment_relax::ConfChangeMover::addend_

private

Referenced by parse_my_tag(), and stage1_pose_setup().

◆ addstart_

utility::vector1<core::Size> protocols::rbsegment_relax::ConfChangeMover::addstart_

private

Referenced by parse_my_tag(), and stage1_pose_setup().

◆ dihed2_res_

core::select::residue_selector::ResidueSelectorCOP protocols::rbsegment_relax::ConfChangeMover::dihed2_res_ = nullptr

private

Referenced by add_dihedral_csts(), and parse_my_tag().

◆ frags3_

core::fragment::FragSetOP protocols::rbsegment_relax::ConfChangeMover::frags3_

private

Referenced by check_or_create_fragments(), parse_my_tag(), and stage1().

◆ frags9_

core::fragment::FragSetOP protocols::rbsegment_relax::ConfChangeMover::frags9_

private

Referenced by check_or_create_fragments(), parse_my_tag(), stage1(), and stage2().

◆ frames_

std::map<core::Size, core::fragment::Frame> protocols::rbsegment_relax::ConfChangeMover::frames_

private

Referenced by stage2().

◆ helixmover_

rbsegment_relax::HelicalGaussianMover protocols::rbsegment_relax::ConfChangeMover::helixmover_

private

Referenced by parse_my_tag(), and stage1().

◆ loops_

loops::Loops protocols::rbsegment_relax::ConfChangeMover::loops_

private

Referenced by stage1_pose_setup().

◆ minimizer_

core::optimization::CartesianMinimizer protocols::rbsegment_relax::ConfChangeMover::minimizer_

private

Referenced by stage1(), and stage2().

◆ newend_

utility::vector1<core::Size> protocols::rbsegment_relax::ConfChangeMover::newend_

private

Referenced by parse_my_tag(), and stage1_pose_setup().

◆ newstart_

utility::vector1<core::Size> protocols::rbsegment_relax::ConfChangeMover::newstart_

private

Referenced by parse_my_tag(), and stage1_pose_setup().

◆ rb_file_

std::string protocols::rbsegment_relax::ConfChangeMover::rb_file_ = "AUTO"

private

Referenced by stage1_pose_setup().

◆ rbmover_

rbsegment_relax::GaussianRBSegmentMover protocols::rbsegment_relax::ConfChangeMover::rbmover_

private

Referenced by parse_my_tag(), and stage1().

◆ rbsegs_

utility::vector1<rbsegment_relax::RBSegment> protocols::rbsegment_relax::ConfChangeMover::rbsegs_

private

Referenced by add_dihedral_csts(), add_dihedral_csts_to_rb(), check_gaps(), multi_rb(), sse_contact_strength(), stage1(), and stage1_pose_setup().

◆ rbsegs_2_

utility::vector1<rbsegment_relax::RBSegment> protocols::rbsegment_relax::ConfChangeMover::rbsegs_2_

private

Referenced by stage1_pose_setup().

◆ res_adj_

utility::vector1<core::Size> protocols::rbsegment_relax::ConfChangeMover::res_adj_ = {3, 4, 5}

private

Referenced by stage2().

◆ rot_

core::Real protocols::rbsegment_relax::ConfChangeMover::rot_ = 10.0

private

Referenced by parse_my_tag().

◆ s1_frag_move_

std::string const protocols::rbsegment_relax::ConfChangeMover::s1_frag_move_ = "1_FRAG3"

private

Referenced by stage1().

◆ s1_rb_multi_

std::string const protocols::rbsegment_relax::ConfChangeMover::s1_rb_multi_ = "1_RB2+"

private

Referenced by stage1().

◆ s1_rb_single_

std::string const protocols::rbsegment_relax::ConfChangeMover::s1_rb_single_ = "1_RB1"

private

Referenced by stage1().

◆ s1_res_

core::select::residue_selector::ResidueSelectorCOP protocols::rbsegment_relax::ConfChangeMover::s1_res_ = nullptr

private

Referenced by parse_my_tag(), stage1(), and stage1_pose_setup().

◆ s1_rigid_res_

utility::vector1<core::select::residue_selector::ResidueSelectorCOP> protocols::rbsegment_relax::ConfChangeMover::s1_rigid_res_

private

Referenced by parse_my_tag(), and stage1_pose_setup().

◆ s1_twist_

std::string const protocols::rbsegment_relax::ConfChangeMover::s1_twist_ = "1_TWIST"

private

Referenced by stage1().

◆ s2_frame_random_

std::string const protocols::rbsegment_relax::ConfChangeMover::s2_frame_random_ = "2_FRAG9R"

private

Referenced by stage2().

◆ s2_frame_select_

std::string const protocols::rbsegment_relax::ConfChangeMover::s2_frame_select_ = "2_FRAG9T"

private

Referenced by stage2().

◆ s2_homolog_move_

std::string const protocols::rbsegment_relax::ConfChangeMover::s2_homolog_move_ = "2_TEMPLATE"

private

Referenced by stage2().

◆ s2_res_

core::select::residue_selector::ResidueSelectorCOP protocols::rbsegment_relax::ConfChangeMover::s2_res_ = nullptr

private

Referenced by parse_my_tag(), and stage2().

◆ seg_

utility::vector1<core::Size> protocols::rbsegment_relax::ConfChangeMover::seg_

private

Referenced by parse_my_tag(), and stage1_pose_setup().

◆ stage1_frag_freq_

core::Real protocols::rbsegment_relax::ConfChangeMover::stage1_frag_freq_ = 0.5

private

Referenced by parse_my_tag(), and stage1().

◆ stage1_minimization_

bool protocols::rbsegment_relax::ConfChangeMover::stage1_minimization_ = false

private

Referenced by parse_my_tag(), and stage1().

◆ stage1_move_restore_

core::Size protocols::rbsegment_relax::ConfChangeMover::stage1_move_restore_ = 0

private

Referenced by parse_my_tag(), and stage1().

◆ stage1_moves_

core::Size protocols::rbsegment_relax::ConfChangeMover::stage1_moves_ = 10000

private

Referenced by parse_my_tag(), and stage1().

◆ stage1_multi_freq_

core::Real protocols::rbsegment_relax::ConfChangeMover::stage1_multi_freq_ = 0.5

private

Referenced by parse_my_tag(), stage1(), and stage1_pose_setup().

◆ stage1_scorefxn_

core::scoring::ScoreFunctionOP protocols::rbsegment_relax::ConfChangeMover::stage1_scorefxn_

private

Referenced by parse_my_tag(), and stage1().

◆ stage1_temp_

core::Real protocols::rbsegment_relax::ConfChangeMover::stage1_temp_ = 1.0

private

Referenced by parse_my_tag(), and stage1().

◆ stage1_twist_freq_

core::Real protocols::rbsegment_relax::ConfChangeMover::stage1_twist_freq_ = 0.2

private

Referenced by parse_my_tag(), and stage1().

◆ stage2_models_

core::Size protocols::rbsegment_relax::ConfChangeMover::stage2_models_ = 1

private

Referenced by apply(), parse_my_tag(), and stage2().

◆ stage2_moves_

core::Size protocols::rbsegment_relax::ConfChangeMover::stage2_moves_ = 1000

private

Referenced by apply(), parse_my_tag(), and stage2().

◆ stage2_scorefxn_

core::scoring::ScoreFunctionOP protocols::rbsegment_relax::ConfChangeMover::stage2_scorefxn_

private

Referenced by apply(), parse_my_tag(), and stage2().

◆ stage2_segment_freq_

core::Real protocols::rbsegment_relax::ConfChangeMover::stage2_segment_freq_ = 0.25

private

Referenced by parse_my_tag(), and stage2().

◆ stage2_targgaps_freq_

core::Real protocols::rbsegment_relax::ConfChangeMover::stage2_targgaps_freq_ = 0.25

private

Referenced by parse_my_tag(), and stage2().

◆ stage2_temp_

core::Real protocols::rbsegment_relax::ConfChangeMover::stage2_temp_ = 1.0

private

Referenced by parse_my_tag(), and stage2().

◆ store_poseOPs_

utility::vector1<core::pose::PoseOP> protocols::rbsegment_relax::ConfChangeMover::store_poseOPs_

private

Referenced by apply(), and get_additional_output().

◆ stored_rebsegs_

utility::vector1<rbsegment_relax::RBSegment> protocols::rbsegment_relax::ConfChangeMover::stored_rebsegs_

private

Referenced by stage1(), and stage1_pose_setup().

◆ template_

core::pose::PoseOP protocols::rbsegment_relax::ConfChangeMover::template_

private

Referenced by apply(), and parse_my_tag().

◆ transl_

core::Real protocols::rbsegment_relax::ConfChangeMover::transl_ = 1.0

private

Referenced by parse_my_tag().

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

src/protocols/rbsegment_relax/ConfChangeMover.hh
src/protocols/rbsegment_relax/ConfChangeMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ ConfChangeMover()

◆ ~ConfChangeMover()

Member Function Documentation

◆ add_dihedral_csts()

◆ add_dihedral_csts_to_rb()

◆ apply()

◆ check_gaps()

◆ check_or_create_fragments()

◆ clone()

◆ get_additional_output()

◆ get_name()

◆ get_residues_in_rbsegment()

◆ mover_name()

◆ multi_rb()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ recursive_residues_from_rbsegs()

◆ sse_contact_strength()

◆ stage1()

◆ stage1_pose_setup()

◆ stage2()

Member Data Documentation

◆ addend_

◆ addstart_

◆ dihed2_res_

◆ frags3_

◆ frags9_

◆ frames_

◆ helixmover_

◆ loops_

◆ minimizer_

◆ newend_

◆ newstart_

◆ rb_file_

◆ rbmover_

◆ rbsegs_

◆ rbsegs_2_

◆ res_adj_

◆ rot_

◆ s1_frag_move_

◆ s1_rb_multi_

◆ s1_rb_single_

◆ s1_res_

◆ s1_rigid_res_

◆ s1_twist_

◆ s2_frame_random_

◆ s2_frame_select_

◆ s2_homolog_move_

◆ s2_res_

◆ seg_

◆ stage1_frag_freq_

◆ stage1_minimization_

◆ stage1_move_restore_

◆ stage1_moves_

◆ stage1_multi_freq_

◆ stage1_scorefxn_

◆ stage1_temp_

◆ stage1_twist_freq_

◆ stage2_models_

◆ stage2_moves_

◆ stage2_scorefxn_

◆ stage2_segment_freq_

◆ stage2_targgaps_freq_

◆ stage2_temp_

◆ store_poseOPs_

◆ stored_rebsegs_

◆ template_

◆ transl_