rotations and translations of helix along helical axis More...

#include <RNA_HelixMover.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_HelixMover:

[legend]

Public Member Functions
	RNA_HelixMover (utility::vector1< utility::vector1< core::Size > > const &helix_regions, core::import_pose::RNA_BasePairHandlerCOP rna_base_pair_handler, bool const &move_first_rigid_body)
	Construct the mover object. More...

	~RNA_HelixMover () override

void	apply (core::pose::Pose &pose) override

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

void	get_helix_ends ()

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

void	set_rot_magnitude (core::Real const &rot_mag)

void	set_trans_magnitude (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 MoverOP	clone () const
	Return a clone of the Mover object. 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
std::pair< core::Vector, core::Vector >	get_helical_axis_and_center (core::pose::Pose const &pose, core::Size const &region) const

core::Vector	get_bp_center (core::pose::Pose const &pose, std::pair< core::Size, core::Size > const &bp_res) const

core::Vector	get_bb_pos (core::pose::Pose const &pose, core::Size const &res) const

core::Vector	get_backbone_centroid (core::pose::Pose const &pose, core::Size const &res) const

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

utility::vector1< utility::vector1< core::Size > >	helix_regions_with_jumps_and_ends_

utility::vector1< core::Size >	helix_regions_jumps_

utility::vector1< core::Size >	helix_regions_jumps_final_

core::import_pose::RNA_BasePairHandlerCOP	rna_base_pair_handler_

utility::vector1< std::pair< std::pair< core::Size, core::Size >, std::pair< core::Size, core::Size > > >	helix_ends_

utility::vector1< std::pair< std::pair< core::Size, core::Size >, std::pair< core::Size, core::Size > > >	helix_ends_final_

core::kinematics::FoldTree	pose_fold_tree_

bool	pose_is_set_

bool	move_first_rigid_body_

utility::vector1< protocols::rigid::RigidBodySpinMoverOP >	spin_movers_

utility::vector1< protocols::rigid::RigidBodyTransMoverOP >	trans_movers_

core::Real	rot_mag_

core::Real	trans_mag_

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

rotations and translations of helix along helical axis

Constructor & Destructor Documentation

◆ RNA_HelixMover()

protocols::rna::denovo::movers::RNA_HelixMover::RNA_HelixMover	(	utility::vector1< utility::vector1< core::Size > > const &	helix_regions,
		core::import_pose::RNA_BasePairHandlerCOP	rna_base_pair_handler,
		bool const &	move_first_rigid_body
	)

Construct the mover object.

References get_helix_ends().

◆ ~RNA_HelixMover()

protocols::rna::denovo::movers::RNA_HelixMover::~RNA_HelixMover ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Apply the RNA helix mover

Implements protocols::moves::Mover.

References core::pose::Pose::fold_tree(), get_helical_axis_and_center(), helix_regions_with_jumps_and_ends_, pose_fold_tree_, pose_is_set_, core::scoring::rg, rot_mag_, protocols::cluster::calibur::rotate(), set_pose(), spin_movers_, protocols::rna::denovo::TR(), trans_mag_, and trans_movers_.

◆ get_backbone_centroid()

core::Vector protocols::rna::denovo::movers::RNA_HelixMover::get_backbone_centroid	(	core::pose::Pose const &	pose,
		core::Size const &	res
	)		const

private

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

Referenced by get_bb_pos().

◆ get_bb_pos()

core::Vector protocols::rna::denovo::movers::RNA_HelixMover::get_bb_pos	(	core::pose::Pose const &	pose,
		core::Size const &	res
	)		const

private

References get_backbone_centroid(), core::conformation::Residue::has(), core::conformation::Residue::is_purine(), core::conformation::Residue::is_pyrimidine(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by get_bp_center().

◆ get_bp_center()

core::Vector protocols::rna::denovo::movers::RNA_HelixMover::get_bp_center	(	core::pose::Pose const &	pose,
		std::pair< core::Size, core::Size > const &	bp_res
	)		const

private

References get_bb_pos().

Referenced by get_helical_axis_and_center().

◆ get_helical_axis_and_center()

std::pair< core::Vector, core::Vector > protocols::rna::denovo::movers::RNA_HelixMover::get_helical_axis_and_center	(	core::pose::Pose const &	pose,
		core::Size const &	region
	)		const

private

References get_bp_center(), and helix_ends_final_.

Referenced by apply().

◆ get_helix_ends()

void protocols::rna::denovo::movers::RNA_HelixMover::get_helix_ends ( )

References core::sequence::end, helix_ends_, helix_regions_, and rna_base_pair_handler_.

Referenced by RNA_HelixMover().

◆ get_name()

std::string protocols::rna::denovo::movers::RNA_HelixMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ set_pose()

void protocols::rna::denovo::movers::RNA_HelixMover::set_pose ( core::pose::Pose const & pose )

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::pose::rna::get_rigid_body_jumps(), helix_ends_, helix_ends_final_, helix_regions_, helix_regions_jumps_, helix_regions_jumps_final_, helix_regions_with_jumps_and_ends_, move_first_rigid_body_, pose_fold_tree_, pose_is_set_, core::pose::Pose::size(), spin_movers_, trans_movers_, and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by apply().

◆ set_rot_magnitude()

void protocols::rna::denovo::movers::RNA_HelixMover::set_rot_magnitude ( core::Real const & rot_mag )

inline

References rot_mag_.

◆ set_trans_magnitude()

void protocols::rna::denovo::movers::RNA_HelixMover::set_trans_magnitude ( core::Real const & trans_mag )

inline

References trans_mag_.

Member Data Documentation

◆ helix_ends_

utility::vector1< std::pair< std::pair< core::Size, core::Size>, std::pair< core::Size, core::Size > > > protocols::rna::denovo::movers::RNA_HelixMover::helix_ends_

private

Referenced by get_helix_ends(), and set_pose().

◆ helix_ends_final_

utility::vector1< std::pair< std::pair< core::Size, core::Size>, std::pair< core::Size, core::Size > > > protocols::rna::denovo::movers::RNA_HelixMover::helix_ends_final_

private

Referenced by get_helical_axis_and_center(), and set_pose().

◆ helix_regions_

utility::vector1< utility::vector1< core::Size > > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_

private

Referenced by get_helix_ends(), and set_pose().

◆ helix_regions_jumps_

utility::vector1< core::Size > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_jumps_

private

Referenced by set_pose().

◆ helix_regions_jumps_final_

utility::vector1< core::Size > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_jumps_final_

private

Referenced by set_pose().

◆ helix_regions_with_jumps_and_ends_

utility::vector1< utility::vector1< core::Size > > protocols::rna::denovo::movers::RNA_HelixMover::helix_regions_with_jumps_and_ends_

private

Referenced by apply(), and set_pose().

◆ move_first_rigid_body_

bool protocols::rna::denovo::movers::RNA_HelixMover::move_first_rigid_body_

private

Referenced by set_pose().

◆ pose_fold_tree_

core::kinematics::FoldTree protocols::rna::denovo::movers::RNA_HelixMover::pose_fold_tree_

private

Referenced by apply(), and set_pose().

◆ pose_is_set_

bool protocols::rna::denovo::movers::RNA_HelixMover::pose_is_set_

private

Referenced by apply(), and set_pose().

◆ rna_base_pair_handler_

core::import_pose::RNA_BasePairHandlerCOP protocols::rna::denovo::movers::RNA_HelixMover::rna_base_pair_handler_

private

Referenced by get_helix_ends().

◆ rot_mag_

core::Real protocols::rna::denovo::movers::RNA_HelixMover::rot_mag_

private

Referenced by apply(), and set_rot_magnitude().

◆ spin_movers_

utility::vector1< protocols::rigid::RigidBodySpinMoverOP > protocols::rna::denovo::movers::RNA_HelixMover::spin_movers_

private

Referenced by apply(), and set_pose().

◆ trans_mag_

core::Real protocols::rna::denovo::movers::RNA_HelixMover::trans_mag_

private

Referenced by apply(), and set_trans_magnitude().

◆ trans_movers_

utility::vector1< protocols::rigid::RigidBodyTransMoverOP > protocols::rna::denovo::movers::RNA_HelixMover::trans_movers_

private

Referenced by apply(), and set_pose().

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

src/protocols/rna/denovo/movers/RNA_HelixMover.hh
src/protocols/rna/denovo/movers/RNA_HelixMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ RNA_HelixMover()

◆ ~RNA_HelixMover()

Member Function Documentation

◆ apply()

◆ get_backbone_centroid()

◆ get_bb_pos()

◆ get_bp_center()

◆ get_helical_axis_and_center()

◆ get_helix_ends()

◆ get_name()

◆ set_pose()

◆ set_rot_magnitude()

◆ set_trans_magnitude()

Member Data Documentation

◆ helix_ends_

◆ helix_ends_final_

◆ helix_regions_

◆ helix_regions_jumps_

◆ helix_regions_jumps_final_

◆ helix_regions_with_jumps_and_ends_

◆ move_first_rigid_body_

◆ pose_fold_tree_

◆ pose_is_set_

◆ rna_base_pair_handler_

◆ rot_mag_

◆ spin_movers_

◆ trans_mag_

◆ trans_movers_