A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing. More...

#include <PackRotamersMover.hh>

Inheritance diagram for protocols::minimization_packing::PackRotamersMover:

[legend]

Public Types
typedef core::pack::interaction_graph::AnnealableGraphBaseOP	AnnealableGraphBaseOP

typedef core::pack::interaction_graph::AnnealableGraphBaseCOP	AnnealableGraphBaseCOP

typedef core::pack::rotamer_set::RotamerSetsOP	RotamerSetsOP

typedef core::pack::rotamer_set::RotamerSetsCOP	RotamerSetsCOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

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
	PackRotamersMover ()
	default constructor; reads the nloop_ value from the global options system. More...

	PackRotamersMover (utility::options::OptionCollection const &options)
	constructor that reads from the (possibly local) options collection object More...

	PackRotamersMover (std::string const &)
	constructor with typename; reads the nloop_ value from the global options system. More...

	PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=nullptr, core::Size nloop=1)
	Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...

	~PackRotamersMover () override

	PackRotamersMover (PackRotamersMover const &other)

void	apply (Pose &pose) override
	Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...

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

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

bool	task_is_valid (Pose const &pose) const
	when the PackerTask was not generated locally, verify compatibility with pose More...

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual void	parse_score_function (TagCOP, basic::datacache::DataMap const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagCOP, basic::datacache::DataMap const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

void	initialize_task_factory_with_operations (std::list< core::pack::task::operation::TaskOperationCOP > const &)

protocols::moves::MoverOP	fresh_instance () const override
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	clone () const override
	required in the context of the parser/scripting scheme More...

void	score_function (ScoreFunctionCOP sf)
	Sets the ScoreFunction to <sf> More...

virtual void	task_factory (TaskFactoryCOP tf)
	Sets the TaskFactory to <tf> More...

void	task (PackerTaskCOP t)
	Sets the PackerTask to <t> More...

void	nloop (core::Size nloop_in)

ScoreFunctionCOP	score_function () const
	Returns the ScoreFunction. More...

PackerTaskCOP	task () const
	Returns the PackerTask. More...

core::Size	nloop () const

TaskFactoryCOP	task_factory () const
	Returns the TaskFactory. More...

RotamerSetsCOP	rotamer_sets () const
	Returns the RotamerSets object being used for packing. More...

void	set_annealer_observer (core::pack::annealer::AnnealerObserverOP observer)

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 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 utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_pack_rotamers_mover (utility::tag::XMLSchemaDefinition &xsd)

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

static void	list_options_read (utility::options::OptionKeyList &opts)

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
virtual void	setup (Pose &pose)
	get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...

virtual core::PackerEnergy	run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const

virtual void	cleanup (core::pose::Pose &pose)
	Clean up cached pose and mover data after the fact. More...

virtual void	note_packertask_settings (Pose const &)
	note PackerTask's packable and designable residues as string info 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...

Private Member Functions
void	initialize_from_options (utility::options::OptionCollection const &options)

Private Attributes
ScoreFunctionCOP	scorefxn_

PackerTaskCOP	task_

core::Size	nloop_

TaskFactoryCOP	task_factory_

RotamerSetsOP	rotamer_sets_

AnnealableGraphBaseOP	ig_

core::pack::annealer::AnnealerObserverOP	observer_

Detailed Description

A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing.

Common Methods: PackRotamersMover.apply

Note: please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!

Member Typedef Documentation

typedef core::pack::interaction_graph::AnnealableGraphBaseCOP protocols::minimization_packing::PackRotamersMover::AnnealableGraphBaseCOP

typedef core::pack::interaction_graph::AnnealableGraphBaseOP protocols::minimization_packing::PackRotamersMover::AnnealableGraphBaseOP

typedef core::pack::task::PackerTaskCOP protocols::minimization_packing::PackRotamersMover::PackerTaskCOP

typedef core::pack::rotamer_set::RotamerSetsCOP protocols::minimization_packing::PackRotamersMover::RotamerSetsCOP

typedef core::pack::rotamer_set::RotamerSetsOP protocols::minimization_packing::PackRotamersMover::RotamerSetsOP

typedef core::scoring::ScoreFunctionCOP protocols::minimization_packing::PackRotamersMover::ScoreFunctionCOP

typedef core::pack::task::TaskFactoryCOP protocols::minimization_packing::PackRotamersMover::TaskFactoryCOP

Constructor & Destructor Documentation

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( )

default constructor; reads the nloop_ value from the global options system.

References initialize_from_options().

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( utility::options::OptionCollection const & options )

constructor that reads from the (possibly local) options collection object

References initialize_from_options().

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( std::string const & type_name )

constructor with typename; reads the nloop_ value from the global options system.

References initialize_from_options().

protocols::minimization_packing::PackRotamersMover::PackRotamersMover	(	ScoreFunctionCOP	scorefxn,
		PackerTaskCOP	task = `nullptr`,
		core::Size	nloop = `1`
	)

Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn>

ScoreFunction scorefxn /function to minimize while changine rotamers PackerTask task /object specifying what to design/pack core::Size (int) nloop /number of rounds to run packing

protocols::minimization_packing::PackRotamersMover::~PackRotamersMover ( )

overridedefault

protocols::minimization_packing::PackRotamersMover::PackRotamersMover ( PackRotamersMover const & other )

References ig_, nloop(), nloop_, rotamer_sets_, score_function(), scorefxn_, task(), task_, task_factory(), and task_factory_.

Member Function Documentation

void protocols::minimization_packing::PackRotamersMover::apply ( Pose & pose )

overridevirtual

Performs side-chain packing based on the input PackerTask using the input ScoreFunction.

example(s): packmover.apply(pose) See Also: PackerTask ScoreFunction

Implements protocols::moves::Mover.

Reimplemented in protocols::testing::BenchmarkBuildRotamersMover, protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover, protocols::minimization_packing::SetReturningPackRotamersMover, and protocols::protein_interface_design::movers::PrepackMover.

References cleanup(), nloop_, run(), and setup().

void protocols::minimization_packing::PackRotamersMover::cleanup ( core::pose::Pose & pose )

protectedvirtual

Clean up cached pose and mover data after the fact.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References ig_, core::pack::pack_rotamers_cleanup(), and rotamer_sets_.

Referenced by apply().

protocols::moves::MoverOP protocols::minimization_packing::PackRotamersMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::testing::BenchmarkBuildRotamersMover, protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover, protocols::minimization_packing::symmetry::SymPackRotamersMover, and protocols::protein_interface_design::movers::PrepackMover.

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), and protocols::moves::complex_type_name_for_mover().

Referenced by protocols::minimization_packing::symmetry::SymPackRotamersMover::provide_xml_schema(), protocols::testing::BenchmarkBuildRotamersMover::provide_xml_schema(), and provide_xml_schema().

protocols::moves::MoverOP protocols::minimization_packing::PackRotamersMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::testing::BenchmarkBuildRotamersMover, protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover, protocols::minimization_packing::symmetry::SymPackRotamersMover, and protocols::protein_interface_design::movers::PrepackMover.

std::string protocols::minimization_packing::PackRotamersMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::testing::BenchmarkBuildRotamersMover, protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover, protocols::protein_interface_design::movers::PrepackMover, protocols::minimization_packing::symmetry::SymPackRotamersMover, and protocols::minimization_packing::SetReturningPackRotamersMover.

References mover_name().

void protocols::minimization_packing::PackRotamersMover::initialize_from_options ( utility::options::OptionCollection const & options )

private

References nloop().

Referenced by PackRotamersMover().

void protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations ( std::list< core::pack::task::operation::TaskOperationCOP > const & operations )

References task_factory().

void protocols::minimization_packing::PackRotamersMover::list_options_read ( utility::options::OptionKeyList & opts )

static

std::string protocols::minimization_packing::PackRotamersMover::mover_name ( )

static

References protocols::minimization_packing::PackRotamersMoverCreator::mover_name().

Referenced by get_name(), protocols::minimization_packing::PackRotamersMoverCreator::keyname(), and provide_xml_schema().

void protocols::minimization_packing::PackRotamersMover::nloop ( core::Size nloop_in )

References nloop_.

Referenced by protocols::calc_taskop_movers::CreateSequenceMotifMover::apply(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), and PackRotamersMover().

core::Size protocols::minimization_packing::PackRotamersMover::nloop ( ) const

inline

References nloop_.

Referenced by protocols::minimization_packing::PackRotamersMoverLazy::apply_to_rotpack(), initialize_from_options(), and protocols::minimization_packing::PackRotamersMoverLazy::parse_my_tag().

void protocols::minimization_packing::PackRotamersMover::note_packertask_settings ( Pose const & pose )

protectedvirtual

note PackerTask's packable and designable residues as string info

References core::sequence::end, protocols::moves::Mover::info(), core::pose::Pose::pdb_info(), and task_.

Referenced by setup().

void protocols::minimization_packing::PackRotamersMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::minimization_packing::PackRotamersMoverLazy, protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover, and protocols::protein_interface_design::movers::PrepackMover.

References nloop_, parse_score_function(), and parse_task_operations().

void protocols::minimization_packing::PackRotamersMover::parse_score_function	(	TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

virtual

parse "scorefxn" XML option (can be employed virtually by derived Packing movers)

References core::scoring::parse_score_function(), and score_function().

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::parse_my_tag(), protocols::dna::DnaInterfaceMultiStateDesign::parse_my_tag(), protocols::minimization_packing::PackRotamersMoverLazy::parse_my_tag(), protocols::dna::DnaInterfacePacker::parse_my_tag(), and parse_my_tag().

void protocols::minimization_packing::PackRotamersMover::parse_task_operations	(	TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

virtual

parse "task_operations" XML option (can be employed virtually by derived Packing movers)

References core::pack::task::parse_task_operations(), and task_factory().

Referenced by protocols::dna::DesignProteinBackboneAroundDNA::parse_my_tag(), protocols::dna::DnaInterfaceMultiStateDesign::parse_my_tag(), protocols::minimization_packing::PackRotamersMoverLazy::parse_my_tag(), protocols::dna::DnaInterfacePacker::parse_my_tag(), and parse_my_tag().

void protocols::minimization_packing::PackRotamersMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References complex_type_generator_for_pack_rotamers_mover(), and mover_name().

Referenced by protocols::minimization_packing::PackRotamersMoverCreator::provide_xml_schema().

rotamer_set::RotamerSetsCOP protocols::minimization_packing::PackRotamersMover::rotamer_sets ( ) const

Returns the RotamerSets object being used for packing.

This is only valid after a call to setup or apply.

References rotamer_sets_.

Referenced by protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight_lazy(), protocols::dna::DnaInterfacePacker::initialized(), protocols::dna::DnaInterfacePacker::make_dna_sequence_combinations(), protocols::dna::DnaInterfacePacker::measure_specificities(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::dna::DnaInterfacePacker::reversion_scan(), and protocols::dna::DnaInterfacePacker::standard_packing().

core::PackerEnergy protocols::minimization_packing::PackRotamersMover::run	(	Pose &	pose,
		utility::vector0< int >	rot_to_pack = `utility::vector0< int >()`
	)		const

protectedvirtual

References ig_, observer_, core::pack::pack_rotamers_run(), rotamer_sets_, and task_.

Referenced by protocols::minimization_packing::SetReturningPackRotamersMover::apply(), apply(), protocols::flxbb::FlxbbDesignPack::apply(), protocols::minimization_packing::PackRotamersMoverLazy::apply_to_rotpack(), protocols::dna::DnaInterfacePacker::measure_specificities(), protocols::dna::DnaInterfacePacker::protein_scan(), protocols::dna::DnaInterfacePacker::reversion_scan(), and protocols::dna::DnaInterfacePacker::standard_packing().

void protocols::minimization_packing::PackRotamersMover::score_function ( ScoreFunctionCOP sf )

Sets the ScoreFunction to <sf>

example(s): packmover.score_function(scorefxn) See Also: PackRotamersMover PackRotamersMover.task

References scorefxn_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply(), and PackRotamersMover().

ScoreFunctionCOP protocols::minimization_packing::PackRotamersMover::score_function ( ) const

Returns the ScoreFunction.

example(s): packmover.score_function() See Also: PackRotamersMover PackRotamersMover.task

References scorefxn_.

void protocols::minimization_packing::PackRotamersMover::set_annealer_observer ( core::pack::annealer::AnnealerObserverOP observer )

inline

References observer_.

void protocols::minimization_packing::PackRotamersMover::setup ( Pose & pose )

protectedvirtual

get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask.

References core::pack::rotamer_set::RotamerSetsFactory::create_rotamer_sets(), core::scoring::get_score_function_legacy(), ig_, core::pose::symmetry::is_symmetric(), core::pack::make_symmetric_task(), nloop_, note_packertask_settings(), core::pack::pack_rotamers_setup(), core::scoring::PRE_TALARIS_2013_STANDARD_WTS, rotamer_sets_, scorefxn_, task_, task_factory_, task_is_valid(), protocols::minimization_packing::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by protocols::minimization_packing::SetReturningPackRotamersMover::apply(), protocols::testing::BenchmarkBuildRotamersMover::apply(), apply(), protocols::flxbb::FlxbbDesignPack::apply(), protocols::minimization_packing::PackRotamersMoverLazy::call_setup(), and protocols::dna::DnaInterfacePacker::init_standard().

void protocols::minimization_packing::PackRotamersMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References score_function().

Referenced by protocols::minimization_packing::operator<<().

void protocols::minimization_packing::PackRotamersMover::task ( PackerTaskCOP t )

Sets the PackerTask to <t>

example(s): packmover.task(task_pack) See Also: PackRotamersMover PackRotamersMover.task_factory

Referenced by protocols::pose_metric_calculators::RotamerBoltzCalculator::computeBoltzWeight_lazy(), and PackRotamersMover().

PackerTaskCOP protocols::minimization_packing::PackRotamersMover::task ( ) const

Returns the PackerTask.

example(s): packmover.task() See Also: PackRotamersMover PackRotamersMover.task_factory

References task_.

void protocols::minimization_packing::PackRotamersMover::task_factory ( TaskFactoryCOP tf )

virtual

Sets the TaskFactory to <tf>

example(s): packmover.task_factory(task_design) See Also: PackRotamersMover PackRotamersMover.task

References task_factory_.

Referenced by protocols::calc_taskop_movers::CreateSequenceMotifMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), PackRotamersMover(), and protocols::optimize_weights::IterativeOptEDriver::repack_and_minimize_pose().

TaskFactoryCOP protocols::minimization_packing::PackRotamersMover::task_factory ( ) const

Returns the TaskFactory.

example(s): packmover.task_factory() See Also: PackRotamersMover PackRotamersMover.task

References task_factory_.

Referenced by protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::add_states(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::minimization_packing::SetReturningPackRotamersMover::apply(), protocols::dna::DesignProteinBackboneAroundDNA::apply(), protocols::dna::DnaInterfacePacker::init_standard(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::initialize(), protocols::dna::DnaInterfaceMultiStateDesign::initialize(), initialize_task_factory_with_operations(), protocols::dna::DnaInterfacePacker::initialized(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::output_alternative_states(), protocols::protein_interface_design::movers::PrepackMover::parse_my_tag(), protocols::protein_interface_design::movers::ProteinInterfaceMultiStateDesignMover::parse_my_tag(), and parse_task_operations().

bool protocols::minimization_packing::PackRotamersMover::task_is_valid ( Pose const & pose ) const

when the PackerTask was not generated locally, verify compatibility with pose

the pose residue types must be equivalent to the ones used to generate the ResidueLevelTasks, because of the way that prevent_repacking and its associated flags work

References core::pose::Pose::residue_type_ptr(), core::pose::Pose::size(), and task_.

Referenced by protocols::minimization_packing::SetReturningPackRotamersMover::apply(), and setup().