#include <RotamerTrialsMinMover.hh>

Inheritance diagram for protocols::minimization_packing::RotamerTrialsMinMover:

Public Types
typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::pack::task::PackerTask	PackerTask

typedef core::pack::task::PackerTaskOP	PackerTaskOP

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

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

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
	RotamerTrialsMinMover ()

	RotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, PackerTask &task_in)
	constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE More...

	RotamerTrialsMinMover (ScoreFunctionCOP scorefxn_in, TaskFactoryCOP factory_in)
	constructor with TaskFactory for producing the packer task More...

void	init ()

	~RotamerTrialsMinMover () override

void	apply (core::pose::Pose &pose) override
	Apply Rotamer-Trials with minimization to pose, using the score function and tasks provided by the constructor. More...

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

void	score_function (core::scoring::ScoreFunctionCOP sf)

void	task_factory (core::pack::task::TaskFactoryCOP tf)

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	Parse XML for RosettaScripts. More...

protocols::moves::MoverOP	fresh_instance () const override
	Return a new mover instance (for RosettaScripts) More...

protocols::moves::MoverOP	clone () const override
	Return a copy of this mover instance (for RosettaScripts) More...

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 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...

Protected Member Functions
ScoreFunctionCOP	scorefxn () const
	read access for derived classes More...

PackerTaskOP	task (core::pose::Pose const &pose) const
	read access for derived classes, pose needed to run TaskFactory 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 Attributes
ScoreFunctionCOP	scorefxn_
	RotamerTrailsMinMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable, but this is probably the way users expect this to behave when they use this mover). More...

PackerTaskOP	task_
	use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply() More...

TaskFactoryCOP	factory_
	TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable. More...

bool	nonideal_

bool	cartesian_

Member Typedef Documentation

typedef core::pack::task::PackerTask protocols::minimization_packing::RotamerTrialsMinMover::PackerTask

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

typedef core::pack::task::PackerTaskOP protocols::minimization_packing::RotamerTrialsMinMover::PackerTaskOP

typedef core::scoring::ScoreFunctionCOP protocols::minimization_packing::RotamerTrialsMinMover::ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP protocols::minimization_packing::RotamerTrialsMinMover::ScoreFunctionOP

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

Constructor & Destructor Documentation

protocols::minimization_packing::RotamerTrialsMinMover::RotamerTrialsMinMover ( )

References init(), and protocols::moves::Mover::type().

protocols::minimization_packing::RotamerTrialsMinMover::RotamerTrialsMinMover	(	ScoreFunctionCOP	scorefxn_in,
		PackerTask &	task_in
	)

constructor with PackerTask. use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE

Parameters

scorefxn_in	The score function used for packing and minimization (which may be modified externally)
task_in	The task that will pass to the rotamers packer

References core::pack::task::PackerTask::clone(), init(), task_, and protocols::moves::Mover::type().

protocols::minimization_packing::RotamerTrialsMinMover::RotamerTrialsMinMover	(	ScoreFunctionCOP	scorefxn_in,
		TaskFactoryCOP	factory_in
	)

constructor with TaskFactory for producing the packer task

Parameters

scorefxn_in	The score function used for packing and minimization (which may be modified externally)
factory_in	The task that will pass to the rotamers packer

References init(), and protocols::moves::Mover::type().

protocols::minimization_packing::RotamerTrialsMinMover::~RotamerTrialsMinMover ( )

overridedefault

Member Function Documentation

void protocols::minimization_packing::RotamerTrialsMinMover::apply ( core::pose::Pose & pose )

overridevirtual

Apply Rotamer-Trials with minimization to pose, using the score function and tasks provided by the constructor.

Implements protocols::moves::Mover.

Reimplemented in protocols::minimization_packing::EnergyCutRotamerTrialsMinMover.

References cartesian_, nonideal_, scorefxn_, core::pack::RTMin::set_nonideal(), and task().

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::splice::Splice::apply(), and protocols::splice::SpliceIn::rtmin().

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

overridevirtual

Return a copy of this mover instance (for RosettaScripts)

Reimplemented from protocols::moves::Mover.

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

overridevirtual

Return a new mover instance (for RosettaScripts)

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::minimization_packing::EnergyCutRotamerTrialsMinMover.

References mover_name().

void protocols::minimization_packing::RotamerTrialsMinMover::init ( void )

References cartesian_, and nonideal_.

Referenced by protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::EnergyCutRotamerTrialsMinMover(), and RotamerTrialsMinMover().

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

static

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

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

overridevirtual

Parse XML for RosettaScripts.

Reimplemented from protocols::moves::Mover.

References cartesian_, core::scoring::get_score_function(), nonideal_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), score_function(), task_factory(), and protocols::minimization_packing::TR().

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

static

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

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

void protocols::minimization_packing::RotamerTrialsMinMover::score_function ( core::scoring::ScoreFunctionCOP sf )

References scorefxn_.

Referenced by parse_my_tag().

RotamerTrialsMinMover::ScoreFunctionCOP protocols::minimization_packing::RotamerTrialsMinMover::scorefxn ( ) const

protected

read access for derived classes

References scorefxn_.

Referenced by protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::apply(), and show().

void protocols::minimization_packing::RotamerTrialsMinMover::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 scorefxn().

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

RotamerTrialsMinMover::PackerTaskOP protocols::minimization_packing::RotamerTrialsMinMover::task ( core::pose::Pose const & pose ) const

protected

read access for derived classes, pose needed to run TaskFactory

read access for derived classes

References factory_, and task_.

Referenced by apply(), and protocols::minimization_packing::EnergyCutRotamerTrialsMinMover::apply().

void protocols::minimization_packing::RotamerTrialsMinMover::task_factory ( core::pack::task::TaskFactoryCOP tf )

References factory_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::minimization_packing::RotamerTrialsMinMover::cartesian_

private

Referenced by apply(), init(), and parse_my_tag().

TaskFactoryCOP protocols::minimization_packing::RotamerTrialsMinMover::factory_

private

TaskFactory allows for nonconstant sequences to be used with RotamerTrialsMover CAUTION: the factory is externally modifiable.

Referenced by task(), and task_factory().

bool protocols::minimization_packing::RotamerTrialsMinMover::nonideal_

private

Referenced by apply(), init(), and parse_my_tag().

ScoreFunctionCOP protocols::minimization_packing::RotamerTrialsMinMover::scorefxn_

private

RotamerTrailsMinMover does not have its own score function, rather, it shares one with other classes – CAUTION: the score function is externally modifiable, but this is probably the way users expect this to behave when they use this mover).

Referenced by apply(), score_function(), and scorefxn().

PackerTaskOP protocols::minimization_packing::RotamerTrialsMinMover::task_

private

use a PackerTask ONLY for fixed-sequence work. WARNING TO ANY DESIGNER WHO PASSES IN A TASK: YOUR DESIGN STEPS WILL BE UNDONE AS THIS TASK CONCEIVES OF THE INPUT SEQUENCE THAT CORRESPONDS TO THE ORIGINAL SEQUENCE If a factory is present it overwrites this task with each call to apply()

Referenced by RotamerTrialsMinMover(), and task().

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

src/protocols/minimization_packing/RotamerTrialsMinMover.hh
src/protocols/minimization_packing/RotamerTrialsMinMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation