a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either 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 <MinPackMover.hh>

Inheritance diagram for protocols::minimization_packing::MinPackMover:

[legend]

Public Types
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
	MinPackMover ()
	default constructor More...

	MinPackMover (std::string const &)
	constructor with typename More...

	MinPackMover (ScoreFunctionCOP scorefxn)

	MinPackMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task)

	~MinPackMover () override

	MinPackMover (MinPackMover const &other)

void	init ()

void	apply (Pose &pose) override
	Main Method. 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...

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)

void	task_factory (TaskFactoryCOP tf)

void	task (PackerTaskCOP t)

ScoreFunctionCOP	score_function () const

PackerTaskCOP	task () const

TaskFactoryCOP	task_factory () const

void	off_rotamer_pack (bool)

bool	off_rotamer_pack () const

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 Attributes
ScoreFunctionCOP	scorefxn_

PackerTaskCOP	task_

TaskFactoryCOP	task_factory_

bool	off_rotamer_pack_

bool	nonideal_

bool	cartesian_

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...

Detailed Description

a mover that packs and minimizes the side-chains. It uses a ScoreFunction for packing and either a PackerTask, or a TaskFactory that generates a PackerTask for instructions on what rotamer sets are allowed at each residue position during packing.

Member Typedef Documentation

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

typedef core::scoring::ScoreFunctionCOP protocols::minimization_packing::MinPackMover::ScoreFunctionCOP

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

Constructor & Destructor Documentation

protocols::minimization_packing::MinPackMover::MinPackMover ( )

default constructor

References init().

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

constructor with typename

References init().

protocols::minimization_packing::MinPackMover::MinPackMover ( ScoreFunctionCOP scorefxn )

References init().

protocols::minimization_packing::MinPackMover::MinPackMover	(	ScoreFunctionCOP	scorefxn,
		PackerTaskCOP	task
	)

References init().

protocols::minimization_packing::MinPackMover::~MinPackMover ( )

overridedefault

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

References cartesian_, nonideal_, score_function(), scorefxn_, task(), task_, task_factory(), and task_factory_.

Member Function Documentation

void protocols::minimization_packing::MinPackMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References cartesian_, core::scoring::get_score_function_legacy(), core::pack::min_pack(), nonideal_, core::pack::off_rotamer_pack(), off_rotamer_pack_, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, scorefxn_, task(), task_, task_factory_, task_is_valid(), and protocols::minimization_packing::TR().

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::minimization_packing::MinPackMover::init ( void )

References cartesian_, and nonideal_.

Referenced by MinPackMover().

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

static

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

void protocols::minimization_packing::MinPackMover::off_rotamer_pack ( bool setting )

References off_rotamer_pack_.

bool protocols::minimization_packing::MinPackMover::off_rotamer_pack ( ) const

References off_rotamer_pack_.

void protocols::minimization_packing::MinPackMover::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.

References cartesian_, nonideal_, off_rotamer_pack_, parse_score_function(), and parse_task_operations().

void protocols::minimization_packing::MinPackMover::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 parse_my_tag().

void protocols::minimization_packing::MinPackMover::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 parse_my_tag().

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

static

References core::scoring::attributes_for_parse_score_function_w_description(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

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

References scorefxn_.

Referenced by MinPackMover().

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

References scorefxn_.

Referenced by parse_score_function().

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

Referenced by MinPackMover().

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

References task_.

Referenced by apply().

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

References task_factory_.

Referenced by MinPackMover().

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

References task_factory_.

Referenced by parse_task_operations().

bool protocols::minimization_packing::MinPackMover::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 apply().