The RNA de novo structure modeling protocol. More...

#include <MultipleDomainMover.hh>

Inheritance diagram for protocols::rna::denovo::coarse::MultipleDomainMover:

[legend]

Public Member Functions
	MultipleDomainMover (core::pose::Pose const &pose, protocols::rna::denovo::coarse::CoarseRNA_LoopCloserOP rna_loop_closer)
	Construct the protocol object. More...

protocols::moves::MoverOP	clone () const override
	Clone this object. More...

void	apply (core::pose::Pose &pose) override
	Apply the loop-rebuild protocol to the input pose. More...

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

core::Size	apply_and_return_jump (core::pose::Pose &pose)

core::Size	apply_at_domain (core::pose::Pose &pose, core::Size const &n)

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

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

core::Size	num_domains ()

void	update_rot_trans_mag (core::Real const &rot_mag, core::Real const &trans_mag)

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...

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	initialize (core::pose::Pose const &pose, core::pose::toolbox::AtomLevelDomainMapOP atom_level_domain_map)

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

void	setup_ok_for_centroid_calculation (core::pose::toolbox::AtomLevelDomainMapOP &atom_level_domain_map)

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

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

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

void	initialize_rigid_body_movers ()

numeric::xyzVector< core::Real >	get_centroid (core::pose::Pose const &pose)

Private Attributes
bool	verbose_

core::Real	rot_mag_

core::Real	trans_mag_

core::Size	num_domains_

protocols::rna::denovo::coarse::CoarseRNA_LoopCloserOP	rna_loop_closer_

utility::vector1< int >	jump_numbers_

utility::vector1< protocols::rigid::Partner >	partner_

utility::vector1< bool >	ok_for_centroid_calculation_

utility::vector1< protocols::rigid::RigidBodyPerturbMoverOP >	rb_movers_

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...

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

◆ MultipleDomainMover()

protocols::rna::denovo::coarse::MultipleDomainMover::MultipleDomainMover	(	core::pose::Pose const &	pose,
		protocols::rna::denovo::coarse::CoarseRNA_LoopCloserOP	rna_loop_closer
	)

Construct the protocol object.

References initialize(), and rna_loop_closer_.

Member Function Documentation

◆ apply()

void protocols::rna::denovo::coarse::MultipleDomainMover::apply ( core::pose::Pose & pose )

overridevirtual

Apply the loop-rebuild protocol to the input pose.

Implements protocols::moves::Mover.

References apply_and_return_jump().

◆ apply_and_return_jump()

Size protocols::rna::denovo::coarse::MultipleDomainMover::apply_and_return_jump ( core::pose::Pose & pose )

References apply_at_domain(), num_domains_, and core::scoring::rg.

Referenced by apply().

◆ apply_at_domain()

Size protocols::rna::denovo::coarse::MultipleDomainMover::apply_at_domain	(	core::pose::Pose &	pose,
		core::Size const &	n
	)

References jump_numbers_, rb_movers_, and slide_back_to_origin().

Referenced by apply_and_return_jump().

◆ clone()

protocols::moves::MoverOP protocols::rna::denovo::coarse::MultipleDomainMover::clone ( ) const

inlineoverridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

◆ close_all_loops()

void protocols::rna::denovo::coarse::MultipleDomainMover::close_all_loops ( core::pose::Pose & pose )

private

References core::pose::Pose::dump_pdb(), num_domains_, rna_loop_closer_, and verbose_.

Referenced by randomize_pose_rigid_bodies().

◆ get_centroid()

Vector protocols::rna::denovo::coarse::MultipleDomainMover::get_centroid ( core::pose::Pose const & pose )

private

References ok_for_centroid_calculation_, core::pose::Pose::size(), and core::pose::Pose::xyz().

Referenced by slide_back_to_origin().

◆ get_name()

std::string protocols::rna::denovo::coarse::MultipleDomainMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ initialize()

void protocols::rna::denovo::coarse::MultipleDomainMover::initialize	(	core::pose::Pose const &	pose,
		core::pose::toolbox::AtomLevelDomainMapOP	atom_level_domain_map
	)

private

References initialize_rigid_body_movers(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), setup_jump_numbers_and_partner(), setup_ok_for_centroid_calculation(), and core::pose::Pose::size().

Referenced by MultipleDomainMover().

◆ initialize_rigid_body_movers()

void protocols::rna::denovo::coarse::MultipleDomainMover::initialize_rigid_body_movers ( )

private

References jump_numbers_, num_domains_, ok_for_centroid_calculation_, partner_, rb_movers_, rot_mag_, and trans_mag_.

Referenced by initialize().

◆ num_domains()

core::Size protocols::rna::denovo::coarse::MultipleDomainMover::num_domains ( )

inline

References num_domains_.

◆ randomize_orientations()

void protocols::rna::denovo::coarse::MultipleDomainMover::randomize_orientations ( core::pose::Pose & pose )

private

References protocols::rigid::RigidBodyRandomizeMover::apply(), core::pose::Pose::dump_pdb(), jump_numbers_, num_domains_, partner_, and verbose_.

Referenced by randomize_pose_rigid_bodies().

◆ randomize_pose_rigid_bodies()

void protocols::rna::denovo::coarse::MultipleDomainMover::randomize_pose_rigid_bodies ( core::pose::Pose & pose )

References close_all_loops(), randomize_orientations(), slide_back_to_origin(), and try_to_slide_into_contact().

◆ setup_jump_numbers_and_partner()

void protocols::rna::denovo::coarse::MultipleDomainMover::setup_jump_numbers_and_partner ( core::pose::Pose const & pose )

private

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), jump_numbers_, num_domains_, partner_, protocols::rigid::partner_downstream, protocols::rigid::partner_upstream, core::pose::Pose::size(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by initialize().

◆ setup_ok_for_centroid_calculation()

void protocols::rna::denovo::coarse::MultipleDomainMover::setup_ok_for_centroid_calculation ( core::pose::toolbox::AtomLevelDomainMapOP & atom_level_domain_map )

private

References ok_for_centroid_calculation_, and verbose_.

Referenced by initialize().