Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization. More...

#include <RNAIdealizeMover.hh>

Inheritance diagram for protocols::rna::movers::RNAIdealizeMover:

[legend]

Public Member Functions
	RNAIdealizeMover ()

	RNAIdealizeMover (core::Size const iterations, bool const noise, bool const final_minimize, core::Real const ang_significance_threshold, bool const handle_suites)

	~RNAIdealizeMover () override

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

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	parse XML tag (to use this Mover in Rosetta Scripts) More...

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

core::Size	get_iterations () const

void	set_iterations (core::Size const iterations)

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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 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	perturb_pose (core::pose::Pose &pose) const
	Add Gaussian noise to the xyz coordinates of each atom. More...

void	constrain_to_ideal (core::pose::Pose &pose, utility::vector1< core::Size > const &bad_suite_res) const

void	add_bond_angle_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::id::AtomID const &atom_id3, core::pose::Pose &pose) const

void	add_bond_constraint (core::id::AtomID const &atom_id1, core::id::AtomID const &atom_id2, core::pose::Pose &pose) const

Private Attributes
core::pose::Pose	ref_pose_

core::Size	iterations_ = 100
	Number of iterations made (1/n idealization per iteration). More...

bool	noise_ = false

bool	final_minimize_ = false

core::Real	ang_significance_threshold_ = 5

bool	handle_suites_ = false

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::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

Slowly accomodate movement from non-ideal to ideal bond lengths and angles by repeated minimization.

Constructor & Destructor Documentation

◆ RNAIdealizeMover() [1/2]

protocols::rna::movers::RNAIdealizeMover::RNAIdealizeMover ( )

◆ RNAIdealizeMover() [2/2]

protocols::rna::movers::RNAIdealizeMover::RNAIdealizeMover	(	core::Size const	iterations,
		bool const	noise,
		bool const	final_minimize,
		core::Real const	ang_significance_threshold,
		bool const	handle_suites
	)

inline

◆ ~RNAIdealizeMover()

protocols::rna::movers::RNAIdealizeMover::~RNAIdealizeMover ( )

overridedefault

Member Function Documentation

◆ add_bond_angle_constraint()

void protocols::rna::movers::RNAIdealizeMover::add_bond_angle_constraint	(	core::id::AtomID const &	atom_id1,
		core::id::AtomID const &	atom_id2,
		core::id::AtomID const &	atom_id3,
		core::pose::Pose &	pose
	)		const

private

◆ add_bond_constraint()

void protocols::rna::movers::RNAIdealizeMover::add_bond_constraint	(	core::id::AtomID const &	atom_id1,
		core::id::AtomID const &	atom_id2,
		core::pose::Pose &	pose
	)		const

private

◆ apply()

void protocols::rna::movers::RNAIdealizeMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::add_constraint(), core::pose::addVirtualResAsRoot(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::id::BB, core::id::CHI, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::pose::Pose::dump_pdb(), final_minimize_, core::pose::Pose::fold_tree(), core::scoring::get_score_function(), core::conformation::Residue::is_bonded(), iterations_, core::chemical::ResidueType::natoms(), noise_, perturb_pose(), core::pose::remove_virtual_residues(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), core::pose::Pose::torsion(), protocols::rna::movers::TR(), and core::conformation::Residue::xyz().

◆ clone()

protocols::moves::MoverOP protocols::rna::movers::RNAIdealizeMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ constrain_to_ideal()

void protocols::rna::movers::RNAIdealizeMover::constrain_to_ideal	(	core::pose::Pose &	pose,
		utility::vector1< core::Size > const &	bad_suite_res
	)		const

private

◆ fresh_instance()

protocols::moves::MoverOP protocols::rna::movers::RNAIdealizeMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_iterations()

core::Size protocols::rna::movers::RNAIdealizeMover::get_iterations ( ) const

inline

References iterations_.

◆ get_name()

std::string protocols::rna::movers::RNAIdealizeMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::rna::movers::RNAIdealizeMover::mover_name ( )

static

Referenced by get_name(), protocols::rna::movers::RNAIdealizeMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::rna::movers::RNAIdealizeMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References ang_significance_threshold_, final_minimize_, iterations_, and noise_.

◆ perturb_pose()

void protocols::rna::movers::RNAIdealizeMover::perturb_pose ( core::pose::Pose & pose ) const

private

Add Gaussian noise to the xyz coordinates of each atom.

Intentionally uses set_xyz because we don't want changes to propagate

References core::pose::Pose::conformation(), core::pose::Pose::residue_type(), core::scoring::rg, core::conformation::Conformation::set_xyz(), core::pose::Pose::size(), and core::conformation::Conformation::xyz().

Referenced by apply().

◆ provide_xml_schema()

void protocols::rna::movers::RNAIdealizeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

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

Referenced by protocols::rna::movers::RNAIdealizeMoverCreator::provide_xml_schema().

◆ set_iterations()

void protocols::rna::movers::RNAIdealizeMover::set_iterations ( core::Size const iterations )

inline

References iterations_.

◆ show()

void protocols::rna::movers::RNAIdealizeMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::rna::movers::operator<<().

Member Data Documentation

◆ ang_significance_threshold_

core::Real protocols::rna::movers::RNAIdealizeMover::ang_significance_threshold_ = 5

private

Referenced by parse_my_tag().

◆ final_minimize_

bool protocols::rna::movers::RNAIdealizeMover::final_minimize_ = false

private

Referenced by apply(), and parse_my_tag().

◆ handle_suites_

bool protocols::rna::movers::RNAIdealizeMover::handle_suites_ = false

private

◆ iterations_

core::Size protocols::rna::movers::RNAIdealizeMover::iterations_ = 100

private

Number of iterations made (1/n idealization per iteration).

Referenced by apply(), get_iterations(), parse_my_tag(), and set_iterations().

◆ noise_

bool protocols::rna::movers::RNAIdealizeMover::noise_ = false

private

Referenced by apply(), and parse_my_tag().

◆ ref_pose_

core::pose::Pose protocols::rna::movers::RNAIdealizeMover::ref_pose_

private

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

src/protocols/rna/movers/RNAIdealizeMover.hh
src/protocols/rna/movers/RNAIdealizeMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RNAIdealizeMover() [1/2]

◆ RNAIdealizeMover() [2/2]

◆ ~RNAIdealizeMover()

Member Function Documentation

◆ add_bond_angle_constraint()

◆ add_bond_constraint()

◆ apply()

◆ clone()

◆ constrain_to_ideal()

◆ fresh_instance()

◆ get_iterations()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ perturb_pose()

◆ provide_xml_schema()

◆ set_iterations()

◆ show()

Member Data Documentation

◆ ang_significance_threshold_

◆ final_minimize_

◆ handle_suites_

◆ iterations_

◆ noise_

◆ ref_pose_