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

#include <MultipleDomainMover.hh>

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

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

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

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

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

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

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

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

Size	num_domains ()

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

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Private Member Functions
void	initialize (core::pose::Pose const &pose, protocols::toolbox::AllowInsertOP allow_insert)

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

void	setup_ok_for_centroid_calculation (protocols::toolbox::AllowInsertOP &allow_insert)

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)

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 protocols::filters::Filters_map	Filters_map

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

protocols::farna::MultipleDomainMover::MultipleDomainMover	(	core::pose::Pose const &	pose,
		protocols::coarse_rna::CoarseRNA_LoopCloserOP	rna_loop_closer
	)

Construct the protocol object.

References initialize(), and rna_loop_closer_.

Referenced by clone().

Member Function Documentation

void protocols::farna::MultipleDomainMover::apply ( core::pose::Pose & pose )

virtual

Apply the loop-rebuild protocol to the input pose.

Implements protocols::moves::Mover.

References apply_and_return_jump().

Size protocols::farna::MultipleDomainMover::apply_and_return_jump ( core::pose::Pose & pose )

References apply_at_domain(), num_domains_, protocols::farna::RG, and numeric::random::RandomGenerator::uniform().

Referenced by apply().

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

References jump_numbers_, rb_movers_, and slide_back_to_origin().

Referenced by apply_and_return_jump().

virtual protocols::moves::MoverOP protocols::farna::MultipleDomainMover::clone ( ) const

inlinevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References MultipleDomainMover().

void protocols::farna::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().

Vector protocols::farna::MultipleDomainMover::get_centroid ( core::pose::Pose const & pose )

private

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

Referenced by slide_back_to_origin().

std::string protocols::farna::MultipleDomainMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::farna::MultipleDomainMover::initialize	(	core::pose::Pose const &	pose,
		protocols::toolbox::AllowInsertOP	allow_insert
	)

private

References initialize_rigid_body_movers(), core::pose::Pose::residue_type(), setup_jump_numbers_and_partner(), setup_ok_for_centroid_calculation(), and core::pose::Pose::total_residue().

Referenced by MultipleDomainMover().

void protocols::farna::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().

Size protocols::farna::MultipleDomainMover::num_domains ( )

inline

References num_domains_.

void protocols::farna::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().

void protocols::farna::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().

void protocols::farna::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_, core::kinematics::FoldTree::num_jump(), partner_, protocols::rigid::partner_downstream, protocols::rigid::partner_upstream, core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by initialize().

void protocols::farna::MultipleDomainMover::setup_ok_for_centroid_calculation ( protocols::toolbox::AllowInsertOP & allow_insert )

private

References utility::pointer::owning_ptr< T >::get(), ok_for_centroid_calculation_, and verbose_.

Referenced by initialize().

void protocols::farna::MultipleDomainMover::slide_back_to_origin ( core::pose::Pose & pose )

References core::pose::Pose::conformation(), get_centroid(), core::pose::Pose::jump(), jump_numbers_, num_domains_, core::pose::Pose::set_jump(), and core::conformation::Conformation::upstream_jump_stub().

Referenced by apply_at_domain(), and randomize_pose_rigid_bodies().

void protocols::farna::MultipleDomainMover::try_to_slide_into_contact ( core::pose::Pose & pose )

private

void protocols::farna::MultipleDomainMover::update_rot_trans_mag	(	Real const &	rot_mag,
		Real const &	trans_mag
	)

References num_domains_, rb_movers_, rot_mag_, and trans_mag_.

Member Data Documentation

utility::vector1< int > protocols::farna::MultipleDomainMover::jump_numbers_

private

Referenced by apply_at_domain(), initialize_rigid_body_movers(), randomize_orientations(), setup_jump_numbers_and_partner(), slide_back_to_origin(), and try_to_slide_into_contact().

Size protocols::farna::MultipleDomainMover::num_domains_

private

Referenced by apply_and_return_jump(), close_all_loops(), initialize_rigid_body_movers(), num_domains(), randomize_orientations(), setup_jump_numbers_and_partner(), slide_back_to_origin(), try_to_slide_into_contact(), and update_rot_trans_mag().

utility::vector1< bool > protocols::farna::MultipleDomainMover::ok_for_centroid_calculation_

private

Referenced by get_centroid(), initialize_rigid_body_movers(), and setup_ok_for_centroid_calculation().

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

private

Referenced by initialize_rigid_body_movers(), randomize_orientations(), and setup_jump_numbers_and_partner().

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

private

Referenced by apply_at_domain(), initialize_rigid_body_movers(), and update_rot_trans_mag().

protocols::coarse_rna::CoarseRNA_LoopCloserOP protocols::farna::MultipleDomainMover::rna_loop_closer_

private

Referenced by close_all_loops(), MultipleDomainMover(), and try_to_slide_into_contact().

Real protocols::farna::MultipleDomainMover::rot_mag_

private

Referenced by initialize_rigid_body_movers(), and update_rot_trans_mag().

Real protocols::farna::MultipleDomainMover::trans_mag_

private

Referenced by initialize_rigid_body_movers(), and update_rot_trans_mag().

bool protocols::farna::MultipleDomainMover::verbose_

private

Referenced by close_all_loops(), randomize_orientations(), setup_ok_for_centroid_calculation(), and try_to_slide_into_contact().

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

src/protocols/farna/MultipleDomainMover.hh
src/protocols/farna/MultipleDomainMover.cc

Private Attributes
bool	verbose_

Real	rot_mag_

Real	trans_mag_

Size	num_domains_

protocols::coarse_rna::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_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation