#include <RepeatProteinRelax.hh>

Inheritance diagram for protocols::relax::RepeatProteinRelax:

[legend]

Public Member Functions
	RepeatProteinRelax ()

core::Size	get_midpoint_longest_loop (core::pose::Pose const &pose, core::Size const repeat_length)

void	setup_repeat_symminfo (core::Size const repeatlen, core::Size const nrepeat, core::Size const base_repeat, bool const with_jumping, core::conformation::symmetry::SymmetryInfo &symminfo)

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

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

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

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

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

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

void	add_residue_labels_back (core::pose::Pose &pose, std::map< core::Size, utility::vector1< std::string > > res_label_map, int symmetry_resid_offset)

void	apply (core::pose::Pose &pose) override
	Main Method. More...

moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &datamap) 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...

Public Member Functions inherited from protocols::relax::RelaxProtocolBase
	RelaxProtocolBase (core::scoring::ScoreFunctionOP)

	RelaxProtocolBase (std::string const &movername="RelaxProtocol")

	RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)

	~RelaxProtocolBase () override

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

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

void	set_defaults ()

void	set_default_minimization_settings ()

void	set_default_coordinate_settings ()

void	set_default_movemap ()

core::kinematics::MoveMapCOP	get_movemap () const

core::kinematics::MoveMapOP	get_movemap ()

const core::scoring::ScoreFunctionCOP	get_scorefxn () const

core::pack::task::TaskFactoryOP const &	get_task_factory () const

bool	cartesian () const

std::string	min_type () const

core::Size	max_iter () const

bool	dry_run () const

bool	constrain_relax_to_native_coords () const

bool	constrain_relax_to_start_coords () const

bool	constrain_coords () const

bool	coord_constrain_sidechains () const

bool	ramp_down_constraints () const

bool	constrain_relax_segments () const

bool	minimize_bond_lengths () const

bool	minimize_bond_angles () const

void	set_movemap (core::kinematics::MoveMapOP movemap)

void	set_movemap_factory (core::select::movemap::MoveMapFactoryOP mm_factory)

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

void	set_task_factory (core::pack::task::TaskFactoryOP task_factory)

void	cartesian (bool newval)
	Use cartesian (minimization step) More...

void	min_type (std::string min_type)

void	max_iter (core::Size max_iter)

void	dry_run (bool setting)

void	constrain_relax_to_native_coords (bool constrain_relax_to_native_coords)

void	constrain_relax_to_start_coords (bool constrain_relax_to_start_coords)

void	constrain_coords (bool constrain_coords)

void	coord_constrain_sidechains (bool coord_constrain_sidechains)

void	constrain_relax_segments (bool constrain_relax_segments)

void	ramp_down_constraints (bool ramp_down_constraints)

void	minimize_bond_lengths (bool minimize_bond_lengths)

void	minimize_bond_angles (bool minimize_bond_angles)

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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...

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

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...

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::relax::RelaxProtocolBase
static void	register_options ()

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 Attributes
core::Size	numb_repeats_

bool	minimize_

bool	loop_cutpoint_mode_

core::Size	relax_iterations_

bool	cartesian_

bool	ramp_down_constraints_

bool	remove_symm_

bool	modify_symmetry_and_exit_

std::string	min_type_

core::scoring::ScoreFunctionOP	sfxn_

Additional Inherited Members
Public Types inherited from protocols::relax::RelaxProtocolBase
typedef moves::Mover	parent

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::relax::RelaxProtocolBase
core::scoring::ScoreFunctionOP	get_scorefxn ()

bool	fix_omega () const

int	minimize_bondlength_subset () const

int	minimize_bondangle_subset () const

bool	limit_aroma_chi2 () const

std::string	cst_files (core::Size const i) const

void	fix_omega (bool fix_omega)

void	minimize_bondangle_subset (int minimize_bondangle_subset)

void	minimize_bondlength_subset (int minimize_bondlength_subset)

void	initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)

void	set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)

void	output_debug_structure (core::pose::Pose &pose, std::string prefix)

void	add_cst_files (std::string const &cstfile)

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

◆ RepeatProteinRelax()

protocols::relax::RepeatProteinRelax::RepeatProteinRelax ( )

Member Function Documentation

◆ add_residue_labels_back()

void protocols::relax::RepeatProteinRelax::add_residue_labels_back	(	core::pose::Pose &	pose,
		std::map< core::Size, utility::vector1< std::string > >	res_label_map,
		int	symmetry_resid_offset
	)

References core::pose::Pose::pdb_info().

◆ apply()

void protocols::relax::RepeatProteinRelax::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::symmetry::make_asymmetric_pose(), core::scoring::pair, core::pose::Pose::pdb_info(), protocols::relax::relax_pose(), and core::pose::Pose::size().

◆ clone()

moves::MoverOP protocols::relax::RepeatProteinRelax::clone ( ) const

inlineoverridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ get_midpoint_longest_loop()

Size protocols::relax::RepeatProteinRelax::get_midpoint_longest_loop	(	core::pose::Pose const &	pose,
		core::Size const	repeat_length
	)

gets the midpoint of the longest loop

References protocols::loops::Loops::add_loop(), protocols::simple_filters::dssp(), core::pose::Pose::size(), protocols::loops::Loops::size(), and protocols::loops::start.

◆ get_name()

std::string protocols::relax::RepeatProteinRelax::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ minimize_pose()

void protocols::relax::RepeatProteinRelax::minimize_pose ( core::pose::Pose & pose )

◆ mover_name()

std::string protocols::relax::RepeatProteinRelax::mover_name ( )

static

Referenced by protocols::relax::RepeatProteinRelaxCreator::keyname().

◆ parse_my_tag()

void protocols::relax::RepeatProteinRelax::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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 core::scoring::linear_chainbreak, and core::scoring::parse_score_function().

◆ provide_xml_schema()

void protocols::relax::RepeatProteinRelax::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::relax::RepeatProteinRelaxCreator::provide_xml_schema().

◆ relax_pose()

void protocols::relax::RepeatProteinRelax::relax_pose ( core::pose::Pose & pose )

References protocols::relax::FastRelax::apply(), core::scoring::CA_rmsd(), protocols::relax::RelaxProtocolBase::cartesian(), core::pose::Pose::clone(), core::chemical::element::F, protocols::relax::RelaxProtocolBase::set_movemap(), and protocols::relax::TR().

◆ seal_jumps()

void protocols::relax::RepeatProteinRelax::seal_jumps ( core::pose::Pose & pose )

References core::kinematics::FoldTree::add_edge(), core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::delete_residue_slow(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueTypeBase::name(), core::kinematics::Edge::PEPTIDE, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

◆ setup_movemap()

void protocols::relax::RepeatProteinRelax::setup_movemap ( core::pose::Pose & pose )

References core::pose::Pose::size().

◆ setup_repeat_pose()

void protocols::relax::RepeatProteinRelax::setup_repeat_pose ( core::pose::Pose & pose )

sets up a repeat pose, starting from a non-symmetric pdb with nres=repeatlen*nrepeat

References core::pose::Pose::append_residue_by_bond(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::pose::get_restype_for_pose(), core::conformation::Conformation::insert_chain_ending(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_pose(), core::pose::nres_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), and protocols::relax::TR().

◆ setup_repeat_pose_jumping()

void protocols::relax::RepeatProteinRelax::setup_repeat_pose_jumping ( core::pose::Pose & pose )

sets up a repeat pose with jumping

References core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::pose::get_restype_for_pose(), core::conformation::Conformation::insert_chain_ending(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_pose(), core::kinematics::FoldTree::new_jump(), core::pose::nres_protein(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::kinematics::FoldTree::reorder(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::size(), protocols::relax::TR(), and core::conformation::Residue::xyz().

◆ setup_repeat_symminfo()

void protocols::relax::RepeatProteinRelax::setup_repeat_symminfo	(	core::Size const	repeatlen,
		core::Size const	nrepeat,
		core::Size const	base_repeat,
		bool const	with_jumping,
		core::conformation::symmetry::SymmetryInfo &	symminfo
	)

fills in a SymmetryInfo object with the necessary info

Member Data Documentation

◆ cartesian_

bool protocols::relax::RepeatProteinRelax::cartesian_

private

◆ loop_cutpoint_mode_

bool protocols::relax::RepeatProteinRelax::loop_cutpoint_mode_

private

◆ min_type_

std::string protocols::relax::RepeatProteinRelax::min_type_

private

◆ minimize_

bool protocols::relax::RepeatProteinRelax::minimize_

private

◆ modify_symmetry_and_exit_

bool protocols::relax::RepeatProteinRelax::modify_symmetry_and_exit_

private

◆ numb_repeats_

core::Size protocols::relax::RepeatProteinRelax::numb_repeats_

private

◆ ramp_down_constraints_

bool protocols::relax::RepeatProteinRelax::ramp_down_constraints_

private

◆ relax_iterations_

core::Size protocols::relax::RepeatProteinRelax::relax_iterations_

private

◆ remove_symm_

bool protocols::relax::RepeatProteinRelax::remove_symm_

private

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::relax::RepeatProteinRelax::sfxn_

private

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

src/protocols/relax/RepeatProteinRelax.hh
src/protocols/relax/RepeatProteinRelax.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RepeatProteinRelax()

Member Function Documentation

◆ add_residue_labels_back()

◆ apply()

◆ clone()

◆ get_midpoint_longest_loop()

◆ get_name()

◆ minimize_pose()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ relax_pose()

◆ seal_jumps()

◆ setup_movemap()

◆ setup_repeat_pose()

◆ setup_repeat_pose_jumping()

◆ setup_repeat_symminfo()

Member Data Documentation

◆ cartesian_

◆ loop_cutpoint_mode_

◆ min_type_

◆ minimize_

◆ modify_symmetry_and_exit_

◆ numb_repeats_

◆ ramp_down_constraints_

◆ relax_iterations_

◆ remove_symm_

◆ sfxn_