#include <LegacyAssemblyMover.hh>

Inheritance diagram for protocols::legacy_sewing::LegacyAssemblyMover:

[legend]

Public Member Functions
	LegacyAssemblyMover ()

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

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

virtual AssemblyOP	generate_assembly ()=0

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

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...

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...

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 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 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

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 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...

Protected Attributes
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_

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...

Constructor & Destructor Documentation

◆ LegacyAssemblyMover()

protocols::legacy_sewing::LegacyAssemblyMover::LegacyAssemblyMover ( )

References requirement_set_.

Member Function Documentation

◆ add_starting_model()

void protocols::legacy_sewing::LegacyAssemblyMover::add_starting_model ( AssemblyOP assembly ) const

virtual

Reimplemented in protocols::legacy_sewing::LegacyAppendAssemblyMover.

References graph_, protocols::legacy_sewing::ModelNode::model(), requirement_set_, and core::scoring::rg.

Referenced by protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::add_edge(), and protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly().

◆ append_movie_frame()

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

References core::chemical::element::F, core::chemical::element::I, and core::conformation::membrane::out.

Referenced by protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), and protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::generate_assembly().

◆ apply()

void protocols::legacy_sewing::LegacyAssemblyMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References assembly_scorefxn_, cen_scorefxn_, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), fa_scorefxn_, protocols::moves::FAIL_RETRY, generate_assembly(), get_fullatom_pose(), protocols::moves::MS_SUCCESS, output_stats(), refine_assembly(), requirement_set_, core::scoring::res_type_constraint, core::scoring::SCORE4_SMOOTH_CART, protocols::moves::Mover::set_last_move_status(), core::scoring::TALARIS_2013_CART, and protocols::legacy_sewing::TR().

Referenced by protocols::legacy_sewing::LegacyAppendAssemblyMover::apply().

◆ define_assembly_mover_ct_gen()

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::legacy_sewing::LegacyAssemblyMover::define_assembly_mover_ct_gen ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::moves::complex_type_name_for_mover(), and legacy_assembly_mover_ct_namer().

Referenced by protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::define_mc_assembly_mover_ct_gen(), provide_xml_schema(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::provide_xml_schema(), protocols::legacy_sewing::LegacyGivenPathAssemblyMover::provide_xml_schema(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::provide_xml_schema(), and protocols::legacy_sewing::LegacyRepeatAssemblyMover::provide_xml_schema().

◆ follow_random_edge_from_node()

bool protocols::legacy_sewing::LegacyAssemblyMover::follow_random_edge_from_node	(	AssemblyOP	assembly,
		ModelNode const *	reference_node
	)		const

References graph_, requirement_set_, core::scoring::rg, and protocols::legacy_sewing::TR().

◆ generate_assembly()

virtual AssemblyOP protocols::legacy_sewing::LegacyAssemblyMover::generate_assembly ( )

pure virtual

Implemented in protocols::legacy_sewing::LegacyRepeatAssemblyMover, protocols::legacy_sewing::LegacyMonteCarloAssemblyMover, protocols::legacy_sewing::LegacyGreedyAssemblyMover, protocols::legacy_sewing::LegacyGivenPathAssemblyMover, and protocols::legacy_sewing::LegacyEnumerateAssemblyMover.

Referenced by apply().

◆ get_centroid_pose()

core::pose::Pose protocols::legacy_sewing::LegacyAssemblyMover::get_centroid_pose ( AssemblyOP assembly ) const

virtual

References core::chemical::CENTROID.

Referenced by output_stats().

◆ get_fullatom_pose()

core::pose::Pose protocols::legacy_sewing::LegacyAssemblyMover::get_fullatom_pose ( AssemblyOP assembly ) const

virtual

References core::chemical::FA_STANDARD.

Referenced by apply(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), output_stats(), refine_assembly(), protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly(), and protocols::legacy_sewing::LegacyRepeatAssemblyMover::refine_assembly().

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::legacy_sewing::LegacyRepeatAssemblyMover, protocols::legacy_sewing::LegacyMonteCarloAssemblyMover, protocols::legacy_sewing::LegacyGreedyAssemblyMover, protocols::legacy_sewing::LegacyGivenPathAssemblyMover, and protocols::legacy_sewing::LegacyEnumerateAssemblyMover.

References mover_name().

◆ legacy_assembly_mover_ct_namer()

std::string protocols::legacy_sewing::LegacyAssemblyMover::legacy_assembly_mover_ct_namer ( std::string const & input )

static

Referenced by define_assembly_mover_ct_gen(), protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory::define_global_requirements_subelement(), and protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory::define_intra_segment_requirements_subelement().

◆ mover_name()

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

static

Referenced by get_name(), and provide_xml_schema().

◆ output_stats()

void protocols::legacy_sewing::LegacyAssemblyMover::output_stats	(	AssemblyOP const &	assembly,
		core::pose::Pose &	pose,
		std::string	indicator_whether_from_LegacyMonteCarloAssemblyMover_or_LegacyExhaustiveAssemblyMover
	)

virtual

add several outputs to the score file Pose can't be const due to scoring.

References protocols::jd2::add_string_real_pair_to_current_job(), protocols::jd2::add_string_string_pair_to_current_job(), assembly_scorefxn_, core::scoring::bb_rmsd_including_O(), core::scoring::cen_env_smooth, core::scoring::cen_pair_smooth, cen_scorefxn_, protocols::jd2::current_output_name(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), fa_scorefxn_, core::chemical::FA_STANDARD, get_centroid_pose(), get_fullatom_pose(), protocols::hybridization::path, core::scoring::rg, core::scoring::rms, core::pose::Pose::size(), core::scoring::Energies::structure_has_moved(), core::scoring::Energies::total_energies(), protocols::legacy_sewing::TR(), and protocols::legacy_sewing::write_native_residue_file().

Referenced by apply(), and protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly().

◆ parse_global_requirements()

void protocols::legacy_sewing::LegacyAssemblyMover::parse_global_requirements	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

virtual

References core::sequence::end, protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory::get_global_requirement(), requirement_factory_, and requirement_set_.

Referenced by parse_requirements().

◆ parse_intra_segment_requirements()

void protocols::legacy_sewing::LegacyAssemblyMover::parse_intra_segment_requirements	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

virtual

References core::sequence::end, protocols::legacy_sewing::sampling::requirements::LegacyRequirementFactory::get_intra_segment_requirement(), requirement_factory_, and requirement_set_.

Referenced by parse_requirements().

◆ parse_my_tag()

void protocols::legacy_sewing::LegacyAssemblyMover::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::moves::Mover.

Reimplemented in protocols::legacy_sewing::LegacyRepeatAssemblyMover, protocols::legacy_sewing::LegacyMonteCarloAssemblyMover, protocols::legacy_sewing::LegacyGreedyAssemblyMover, protocols::legacy_sewing::LegacyGivenPathAssemblyMover, and protocols::legacy_sewing::LegacyEnumerateAssemblyMover.

References base_native_bonus_, edge_file_, graph_, neighbor_cutoff_, parse_requirements(), protocols::legacy_sewing::read_model_file(), requirement_set_, and protocols::legacy_sewing::TR().

Referenced by protocols::legacy_sewing::LegacyEnumerateAssemblyMover::parse_my_tag(), protocols::legacy_sewing::LegacyGivenPathAssemblyMover::parse_my_tag(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::parse_my_tag(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::parse_my_tag(), and protocols::legacy_sewing::LegacyRepeatAssemblyMover::parse_my_tag().

◆ parse_requirements()

void protocols::legacy_sewing::LegacyAssemblyMover::parse_requirements	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

virtual

References core::sequence::end, parse_global_requirements(), parse_intra_segment_requirements(), and protocols::legacy_sewing::TR().

Referenced by parse_my_tag().

◆ provide_xml_schema()

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

static

References define_assembly_mover_ct_gen(), and mover_name().

◆ refine_assembly()

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

virtual

Reimplemented in protocols::legacy_sewing::LegacyRepeatAssemblyMover, and protocols::legacy_sewing::LegacyAppendAssemblyMover.

References base_native_bonus_, protocols::relax::delete_virtual_residues(), fa_scorefxn_, get_fullatom_pose(), and neighbor_cutoff_.

Referenced by apply().

◆ reinitialize_for_new_input()

bool protocols::legacy_sewing::LegacyAssemblyMover::reinitialize_for_new_input ( ) const

overridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

Member Data Documentation

◆ assembly_scorefxn_

scoring::LegacyAssemblyScoreFunctionOP protocols::legacy_sewing::LegacyAssemblyMover::assembly_scorefxn_

protected

Referenced by apply(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::output_base_stats(), and output_stats().

◆ base_native_bonus_

core::Real protocols::legacy_sewing::LegacyAssemblyMover::base_native_bonus_

protected

Referenced by parse_my_tag(), refine_assembly(), and protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly().

◆ cen_scorefxn_

core::scoring::ScoreFunctionOP protocols::legacy_sewing::LegacyAssemblyMover::cen_scorefxn_

protected

Referenced by apply(), and output_stats().

◆ edge_file_

std::string protocols::legacy_sewing::LegacyAssemblyMover::edge_file_

protected

Referenced by protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::add_edge(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::dfs_cycle_finder(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyGivenPathAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyRepeatAssemblyMover::generate_assembly(), and parse_my_tag().

◆ fa_scorefxn_

core::scoring::ScoreFunctionOP protocols::legacy_sewing::LegacyAssemblyMover::fa_scorefxn_

protected

Referenced by apply(), output_stats(), refine_assembly(), protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly(), and protocols::legacy_sewing::LegacyRepeatAssemblyMover::refine_assembly().

◆ graph_

SewGraphOP protocols::legacy_sewing::LegacyAssemblyMover::graph_

protected

◆ neighbor_cutoff_

core::Size protocols::legacy_sewing::LegacyAssemblyMover::neighbor_cutoff_

protected

Referenced by parse_my_tag(), refine_assembly(), and protocols::legacy_sewing::LegacyAppendAssemblyMover::refine_assembly().

◆ requirement_factory_

sampling::requirements::LegacyRequirementFactory* protocols::legacy_sewing::LegacyAssemblyMover::requirement_factory_

protected

Referenced by parse_global_requirements(), and parse_intra_segment_requirements().

◆ requirement_set_

sampling::requirements::LegacyRequirementSetOP protocols::legacy_sewing::LegacyAssemblyMover::requirement_set_

protected

Referenced by protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::add_edge(), add_starting_model(), protocols::legacy_sewing::LegacyAppendAssemblyMover::apply(), apply(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::boltzman(), follow_random_edge_from_node(), protocols::legacy_sewing::LegacyEnumerateAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyGreedyAssemblyMover::generate_assembly(), protocols::legacy_sewing::LegacyMonteCarloAssemblyMover::generate_assembly(), LegacyAssemblyMover(), parse_global_requirements(), parse_intra_segment_requirements(), and parse_my_tag().

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

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

Public Member Functions

Static Public Member Functions

Protected Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ LegacyAssemblyMover()

Member Function Documentation

◆ add_starting_model()

◆ append_movie_frame()

◆ apply()

◆ define_assembly_mover_ct_gen()

◆ follow_random_edge_from_node()

◆ generate_assembly()

◆ get_centroid_pose()

◆ get_fullatom_pose()

◆ get_name()

◆ legacy_assembly_mover_ct_namer()

◆ mover_name()

◆ output_stats()

◆ parse_global_requirements()

◆ parse_intra_segment_requirements()

◆ parse_my_tag()

◆ parse_requirements()

◆ provide_xml_schema()

◆ refine_assembly()

◆ reinitialize_for_new_input()

Member Data Documentation

◆ assembly_scorefxn_

◆ base_native_bonus_

◆ cen_scorefxn_

◆ edge_file_

◆ fa_scorefxn_

◆ graph_

◆ neighbor_cutoff_

◆ requirement_factory_

◆ requirement_set_