#include <SymDofMover.hh>

Inheritance diagram for protocols::matdes::SymDofMover:

[legend]

Public Member Functions
	SymDofMover ()

void	apply (Pose &pose) override

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

MoverOP	fresh_instance () const override
	create this type of object More...

void	parse_my_tag (TagCOP tag, DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	add_components_to_pose_if_necessary (Pose &pose)

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 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...

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 Types
typedef core::pose::Pose	Pose

typedef core::Real	Real

typedef core::Size	Size

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef protocols::moves::MoverOP	MoverOP

typedef basic::datacache::DataMap	DataMap

typedef utility::tag::TagCOP	TagCOP

Private Member Functions
utility::vector1< std::string >	get_sym_dof_names ()

utility::vector1< Real >	get_radial_disps ()

utility::vector1< Real >	get_angles ()

Private Attributes
bool	set_sampler_

bool	auto_range_

std::string	sampling_mode_

std::string	symm_file_

utility::vector1< std::string >	translation_axes_

utility::vector1< std::string >	rotation_axes_

utility::vector1< std::string >	flip_input_about_axes_

utility::vector1< std::string >	align_input_axes_to_symdof_axes_

utility::vector1< std::string >	sym_dof_names_

utility::vector1< Real >	radial_disps_

utility::vector1< Real >	angles_

utility::vector1< Real >	radial_offsets_

utility::vector1< Real >	radial_disps_range_min_

utility::vector1< Real >	radial_disps_range_max_

utility::vector1< Real >	angles_range_min_

utility::vector1< Real >	angles_range_max_

utility::vector1< Real >	radial_disp_steps_

utility::vector1< Real >	angle_steps_

utility::vector1< Real >	radial_disp_deltas_

utility::vector1< Real >	angle_deltas_

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

WARNING WARNING WARNING THIS IS A THREAD-UNSAFE CLASS SINCE IT USES THE SymDofMoverSampler, A NON-CONSTANT SINGLETON. ANY PROTOCOL THAT RELIES ON THIS MOVER IS THREAD-UNSAFE.

Member Typedef Documentation

◆ DataMap

typedef basic::datacache::DataMap protocols::matdes::SymDofMover::DataMap

private

◆ MoverOP

typedef protocols::moves::MoverOP protocols::matdes::SymDofMover::MoverOP

private

◆ Pose

typedef core::pose::Pose protocols::matdes::SymDofMover::Pose

private

◆ Real

typedef core::Real protocols::matdes::SymDofMover::Real

private

◆ ScoreFunction

typedef core::scoring::ScoreFunction protocols::matdes::SymDofMover::ScoreFunction

private

◆ ScoreFunctionCOP

typedef core::scoring::ScoreFunctionCOP protocols::matdes::SymDofMover::ScoreFunctionCOP

private

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::matdes::SymDofMover::ScoreFunctionOP

private

◆ Size

typedef core::Size protocols::matdes::SymDofMover::Size

private

◆ TagCOP

typedef utility::tag::TagCOP protocols::matdes::SymDofMover::TagCOP

private

Constructor & Destructor Documentation

◆ SymDofMover()

protocols::matdes::SymDofMover::SymDofMover ( )

Member Function Documentation

◆ add_components_to_pose_if_necessary()

void protocols::matdes::SymDofMover::add_components_to_pose_if_necessary ( Pose & pose )

References core::pose::append_pose_to_pose(), protocols::match::upstream::b, core::pose::Pose::conformation(), core::conformation::Conformation::num_chains(), core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), core::pose::Pose::size(), protocols::hybridization::t, protocols::matdes::TR(), and core::pose::Pose::update_pose_chains_from_pdb_chains().

◆ apply()

void protocols::matdes::SymDofMover::apply ( Pose & pose )

overridevirtual

WARNING WARNING WARNING THIS IS A THREAD-UNSAFE FUNCTION SINCE IT USES THE SymDofMoverSampler, A NON-CONSTANT SINGLETON.

Implements protocols::moves::Mover.

References protocols::matdes::alignaxis(), core::scoring::packstat::old::angles, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::simple_filters::coords(), core::membrane::get_angles(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), core::conformation::symmetry::SymmData::get_virtual_connects(), core::conformation::symmetry::SymmData::get_virtual_coordinates(), core::conformation::symmetry::VirtualCoordinate::get_x(), core::pose::symmetry::is_symmetric(), core::pose::Pose::jump(), core::pose::symmetry::make_symmetric_pose(), core::pose::Pose::num_jump(), core::conformation::symmetry::SymmData::read_symmetry_data_from_file(), protocols::matdes::rot_pose(), core::pose::Pose::set_jump(), core::kinematics::Jump::set_rotation(), core::kinematics::Jump::set_translation(), core::pose::Pose::size(), core::pose::symmetry::sym_dof_jump_num(), core::pose::symmetry::sym_dof_names(), protocols::hybridization::t, protocols::matdes::TR(), protocols::matdes::trans_pose(), and core::pose::Pose::xyz().

◆ clone()

protocols::moves::MoverOP protocols::matdes::SymDofMover::clone ( ) const

overridevirtual

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.

◆ fresh_instance()

protocols::moves::MoverOP protocols::matdes::SymDofMover::fresh_instance ( ) const

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

◆ get_angles()

utility::vector1< Real > protocols::matdes::SymDofMover::get_angles ( )

private

WARNING WARNING WARNING THIS IS A THREAD-UNSAFE FUNCTION SINCE IT USES THE SymDofMoverSampler, A NON-CONSTANT SINGLETON.

References angle_deltas_, core::scoring::packstat::old::angles, angles_, angles_range_max_, angles_range_min_, get_sym_dof_names(), core::scoring::rg, sampling_mode_, set_sampler_, and core::pose::symmetry::sym_dof_names().

◆ get_name()

std::string protocols::matdes::SymDofMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_radial_disps()

utility::vector1< Real > protocols::matdes::SymDofMover::get_radial_disps ( )

private

WARNING WARNING WARNING THIS IS A THREAD-UNSAFE FUNCTION SINCE IT USES THE SymDofMoverSampler, A NON-CONSTANT SINGLETON.

References get_sym_dof_names(), radial_disp_deltas_, radial_disps_, radial_disps_range_max_, radial_disps_range_min_, radial_offsets_, core::scoring::rg, sampling_mode_, set_sampler_, and core::pose::symmetry::sym_dof_names().

◆ get_sym_dof_names()

utility::vector1< std::string > protocols::matdes::SymDofMover::get_sym_dof_names ( )

private

References sym_dof_names_.

Referenced by get_angles(), and get_radial_disps().

◆ mover_name()

std::string protocols::matdes::SymDofMover::mover_name ( )

static

Referenced by protocols::matdes::SymDofMoverCreator::keyname().

◆ parse_my_tag()

void protocols::matdes::SymDofMover::parse_my_tag	(	TagCOP	tag,
		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::packstat::old::angles, and protocols::matdes::TR().

◆ provide_xml_schema()

void protocols::matdes::SymDofMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::matdes::SymDofMoverCreator::provide_xml_schema().

Member Data Documentation

◆ align_input_axes_to_symdof_axes_

utility::vector1<std::string> protocols::matdes::SymDofMover::align_input_axes_to_symdof_axes_

private

◆ angle_deltas_

utility::vector1<Real> protocols::matdes::SymDofMover::angle_deltas_

private

Referenced by get_angles().

◆ angle_steps_

utility::vector1<Real> protocols::matdes::SymDofMover::angle_steps_

private

◆ angles_

utility::vector1<Real> protocols::matdes::SymDofMover::angles_

private

Referenced by get_angles().

◆ angles_range_max_

utility::vector1<Real> protocols::matdes::SymDofMover::angles_range_max_

private

Referenced by get_angles().

◆ angles_range_min_

utility::vector1<Real> protocols::matdes::SymDofMover::angles_range_min_

private

Referenced by get_angles().

◆ auto_range_

bool protocols::matdes::SymDofMover::auto_range_

private

◆ flip_input_about_axes_

utility::vector1<std::string> protocols::matdes::SymDofMover::flip_input_about_axes_

private

◆ radial_disp_deltas_

utility::vector1<Real> protocols::matdes::SymDofMover::radial_disp_deltas_

private

Referenced by get_radial_disps().

◆ radial_disp_steps_

utility::vector1<Real> protocols::matdes::SymDofMover::radial_disp_steps_

private

◆ radial_disps_

utility::vector1<Real> protocols::matdes::SymDofMover::radial_disps_

private

Referenced by get_radial_disps().

◆ radial_disps_range_max_

utility::vector1<Real> protocols::matdes::SymDofMover::radial_disps_range_max_

private

Referenced by get_radial_disps().

◆ radial_disps_range_min_

utility::vector1<Real> protocols::matdes::SymDofMover::radial_disps_range_min_

private

Referenced by get_radial_disps().

◆ radial_offsets_

utility::vector1<Real> protocols::matdes::SymDofMover::radial_offsets_

private

Referenced by get_radial_disps().

◆ rotation_axes_

utility::vector1<std::string> protocols::matdes::SymDofMover::rotation_axes_

private

◆ sampling_mode_

std::string protocols::matdes::SymDofMover::sampling_mode_

private

Referenced by get_angles(), and get_radial_disps().

◆ set_sampler_

bool protocols::matdes::SymDofMover::set_sampler_

private

Referenced by get_angles(), and get_radial_disps().

◆ sym_dof_names_

utility::vector1<std::string> protocols::matdes::SymDofMover::sym_dof_names_

private

Referenced by get_sym_dof_names().

◆ symm_file_

std::string protocols::matdes::SymDofMover::symm_file_

private

◆ translation_axes_

utility::vector1<std::string> protocols::matdes::SymDofMover::translation_axes_

private

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

src/protocols/matdes/SymDofMover.hh
src/protocols/matdes/SymDofMover.cc

Public Member Functions

Static Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ DataMap

◆ MoverOP

◆ Pose

◆ Real

◆ ScoreFunction

◆ ScoreFunctionCOP

◆ ScoreFunctionOP

◆ Size

◆ TagCOP

Constructor & Destructor Documentation

◆ SymDofMover()

Member Function Documentation

◆ add_components_to_pose_if_necessary()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_angles()

◆ get_name()

◆ get_radial_disps()

◆ get_sym_dof_names()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

Member Data Documentation

◆ align_input_axes_to_symdof_axes_

◆ angle_deltas_

◆ angle_steps_

◆ angles_

◆ angles_range_max_

◆ angles_range_min_

◆ auto_range_

◆ flip_input_about_axes_

◆ radial_disp_deltas_

◆ radial_disp_steps_

◆ radial_disps_

◆ radial_disps_range_max_

◆ radial_disps_range_min_

◆ radial_offsets_

◆ rotation_axes_

◆ sampling_mode_

◆ set_sampler_

◆ sym_dof_names_

◆ symm_file_

◆ translation_axes_