#include <LegacyRepeatAssemblyMover.hh>

Inheritance diagram for protocols::legacy_sewing::LegacyRepeatAssemblyMover:

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Public Types
typedef LegacyAssemblyMover	parent

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

Public Member Functions
	LegacyRepeatAssemblyMover ()

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

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

std::pair< bool, AssemblyOP >	dfs_cycle_finder (ModelNode const reference_node, utility::vector1< ModelNode const > visited_nodes, AssemblyOP assembly) const
	recursive function. Start with a given reference node and randomly traverse edges in a depth-first-search of a cycle of a given size (number of nodes). More...

AssemblyOP	generate_assembly () override

void	output_base_stats (AssemblyOP const &assembly)
	adds single repeat unit data to score file More...

void	add_repeats (AssemblyOP assembly) const
	adds remaining data to score file More...

utility::vector1< numeric::xyzVector< core::Real > >	get_segment_coords (SewSegment const &segment) const

void	transform_segment_coords (SewSegment &segment, numeric::xyzTransform< core::Real > transformer, numeric::xyzVector< float > com, core::Size n_transformations) const

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

core::pose::Pose	refine_assembly (AssemblyOP &assembly) override

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

Public Member Functions inherited from protocols::legacy_sewing::LegacyAssemblyMover
	LegacyAssemblyMover ()

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

virtual void	add_starting_model (AssemblyOP assembly) const

virtual core::pose::Pose	get_fullatom_pose (AssemblyOP assembly) const

virtual core::pose::Pose	get_centroid_pose (AssemblyOP assembly) const

bool	follow_random_edge_from_node (AssemblyOP assembly, ModelNode const *reference_node) const

bool	reinitialize_for_new_input () const override
	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...

void	append_movie_frame (AssemblyOP assembly, core::Size cycle) const

virtual void	output_stats (AssemblyOP const &assembly, core::pose::Pose &pose, std::string indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover)
	add several outputs to the score file Pose can't be const due to scoring. More...

virtual void	parse_requirements (TagCOP tag, basic::datacache::DataMap &data)

virtual void	parse_global_requirements (TagCOP tag, basic::datacache::DataMap &data)

virtual void	parse_intra_segment_requirements (TagCOP tag, basic::datacache::DataMap &data)

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...

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::legacy_sewing::LegacyAssemblyMover
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static utility::tag::XMLSchemaComplexTypeGeneratorOP	define_assembly_mover_ct_gen (utility::tag::XMLSchemaDefinition &xsd)

static std::string	legacy_assembly_mover_ct_namer (std::string const &)

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 Attributes
core::Size	num_repeating_segments_

core::Real	threshold_score_of_complete_cycle_

core::Size	num_repeats_

core::Size	num_trials_

scoring::LegacyAssemblyScoreFunctionOP	clash_scorefxn_

Additional Inherited Members
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...

Protected Attributes inherited from protocols::legacy_sewing::LegacyAssemblyMover
scoring::LegacyAssemblyScoreFunctionOP	assembly_scorefxn_

SewGraphOP	graph_

std::string	edge_file_

sampling::requirements::LegacyRequirementSetOP	requirement_set_

sampling::requirements::LegacyRequirementFactory *	requirement_factory_

core::scoring::ScoreFunctionOP	cen_scorefxn_

core::scoring::ScoreFunctionOP	fa_scorefxn_

core::Real	base_native_bonus_

core::Size	neighbor_cutoff_

Member Typedef Documentation

◆ parent

typedef LegacyAssemblyMover protocols::legacy_sewing::LegacyRepeatAssemblyMover::parent

Constructor & Destructor Documentation

◆ LegacyRepeatAssemblyMover()

protocols::legacy_sewing::LegacyRepeatAssemblyMover::LegacyRepeatAssemblyMover ( )

References num_repeats_.

Member Function Documentation

◆ add_repeats()

void protocols::legacy_sewing::LegacyRepeatAssemblyMover::add_repeats ( AssemblyOP assembly ) const

adds remaining data to score file

References core::pose::center_of_mass(), get_segment_coords(), num_repeats_, protocols::legacy_sewing::TR(), and transform_segment_coords().

Referenced by generate_assembly().

◆ clone()

protocols::moves::MoverOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::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.

◆ dfs_cycle_finder()

std::pair< bool, AssemblyOP > protocols::legacy_sewing::LegacyRepeatAssemblyMover::dfs_cycle_finder	(	ModelNode const *	reference_node,
		utility::vector1< ModelNode const * >	visited_nodes,
		AssemblyOP	assembly
	)		const

recursive function. Start with a given reference node and randomly traverse edges in a depth-first-search of a cycle of a given size (number of nodes).

References clash_scorefxn_, protocols::legacy_sewing::LegacyAssemblyMover::edge_file_, protocols::legacy_sewing::LegacyAssemblyMover::graph_, protocols::legacy_sewing::ModelNode::model(), protocols::legacy_sewing::Model::model_id_, num_repeating_segments_, core::scoring::rg, protocols::hybridization::score, and protocols::legacy_sewing::TR().

Referenced by generate_assembly().

◆ fresh_instance()

protocols::moves::MoverOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ generate_assembly()

AssemblyOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly ( )

overridevirtual

Implements protocols::legacy_sewing::LegacyAssemblyMover.

References add_repeats(), protocols::legacy_sewing::LegacyAssemblyMover::assembly_scorefxn_, clash_scorefxn_, protocols::legacy_sewing::AssemblyFactory::create_assembly(), dfs_cycle_finder(), protocols::legacy_sewing::LegacyAssemblyMover::edge_file_, core::chemical::FA_STANDARD, protocols::legacy_sewing::LegacyAssemblyMover::graph_, protocols::legacy_sewing::ModelNode::model(), protocols::legacy_sewing::Model::model_id_, num_trials_, output_base_stats(), protocols::hybridization::score, threshold_score_of_complete_cycle_, and protocols::legacy_sewing::TR().

◆ get_name()

std::string protocols::legacy_sewing::LegacyRepeatAssemblyMover::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::legacy_sewing::LegacyAssemblyMover.

References mover_name().

◆ get_segment_coords()

utility::vector1< numeric::xyzVector< core::Real > > protocols::legacy_sewing::LegacyRepeatAssemblyMover::get_segment_coords ( SewSegment const & segment ) const

References protocols::simple_filters::coords().

Referenced by add_repeats().

◆ mover_name()

std::string protocols::legacy_sewing::LegacyRepeatAssemblyMover::mover_name ( )

static

Referenced by get_name(), protocols::legacy_sewing::LegacyRepeatAssemblyMoverCreator::keyname(), and provide_xml_schema().

◆ output_base_stats()

void protocols::legacy_sewing::LegacyRepeatAssemblyMover::output_base_stats ( AssemblyOP const & assembly )

adds single repeat unit data to score file

References protocols::jd2::add_string_real_pair_to_current_job(), and protocols::legacy_sewing::LegacyAssemblyMover::assembly_scorefxn_.

Referenced by generate_assembly().

◆ parse_my_tag()

void protocols::legacy_sewing::LegacyRepeatAssemblyMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::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::legacy_sewing::LegacyAssemblyMover.

References num_repeating_segments_, protocols::legacy_sewing::LegacyAssemblyMover::parse_my_tag(), and threshold_score_of_complete_cycle_.

◆ provide_xml_schema()

void protocols::legacy_sewing::LegacyRepeatAssemblyMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen(), and mover_name().

Referenced by protocols::legacy_sewing::LegacyRepeatAssemblyMoverCreator::provide_xml_schema().

◆ refine_assembly()

core::pose::Pose protocols::legacy_sewing::LegacyRepeatAssemblyMover::refine_assembly ( AssemblyOP & assembly )

overridevirtual

Reimplemented from protocols::legacy_sewing::LegacyAssemblyMover.

References core::scoring::atom_pair_constraint, core::scoring::dihedral_constraint, protocols::legacy_sewing::LegacyAssemblyMover::fa_scorefxn_, and protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose().

◆ transform_segment_coords()

void protocols::legacy_sewing::LegacyRepeatAssemblyMover::transform_segment_coords	(	SewSegment &	segment,
		numeric::xyzTransform< core::Real >	transformer,
		numeric::xyzVector< float >	com,
		core::Size	n_transformations
	)		const

References protocols::membrane::com().

Referenced by add_repeats().

Member Data Documentation

◆ clash_scorefxn_

scoring::LegacyAssemblyScoreFunctionOP protocols::legacy_sewing::LegacyRepeatAssemblyMover::clash_scorefxn_

private

Referenced by dfs_cycle_finder(), and generate_assembly().

◆ num_repeating_segments_

core::Size protocols::legacy_sewing::LegacyRepeatAssemblyMover::num_repeating_segments_

private

Referenced by dfs_cycle_finder(), and parse_my_tag().

◆ num_repeats_

core::Size protocols::legacy_sewing::LegacyRepeatAssemblyMover::num_repeats_

private

Referenced by add_repeats(), and LegacyRepeatAssemblyMover().

◆ num_trials_

core::Size protocols::legacy_sewing::LegacyRepeatAssemblyMover::num_trials_

private

Referenced by generate_assembly().

◆ threshold_score_of_complete_cycle_

core::Real protocols::legacy_sewing::LegacyRepeatAssemblyMover::threshold_score_of_complete_cycle_

private

Referenced by generate_assembly(), and parse_my_tag().

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

src/protocols/legacy_sewing/sampling/LegacyRepeatAssemblyMover.hh
src/protocols/legacy_sewing/sampling/LegacyRepeatAssemblyMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ LegacyRepeatAssemblyMover()

Member Function Documentation

◆ add_repeats()

◆ clone()

◆ dfs_cycle_finder()

◆ fresh_instance()

◆ generate_assembly()

◆ get_name()

◆ get_segment_coords()

◆ mover_name()

◆ output_base_stats()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ refine_assembly()

◆ transform_segment_coords()

Member Data Documentation

◆ clash_scorefxn_

◆ num_repeating_segments_

◆ num_repeats_

◆ num_trials_

◆ threshold_score_of_complete_cycle_