#include <RotamerTrialsMinMover.hh>

Inheritance diagram for protocols::simple_moves::RotamerTrialsMinMover:

Collaboration diagram for protocols::simple_moves::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::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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 ()

virtual	~RotamerTrialsMinMover ()

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

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

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

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

virtual void	parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	Parse XML for RosettaScripts. More...

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

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

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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

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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

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_

Friends
std::ostream &	operator<< (std::ostream &os, RotamerTrialsMinMover const &mover)

Additional Inherited Members
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Detailed Description

Definition at line 41 of file RotamerTrialsMinMover.hh.

Member Typedef Documentation

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

Definition at line 46 of file RotamerTrialsMinMover.hh.

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

Definition at line 48 of file RotamerTrialsMinMover.hh.

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

Definition at line 47 of file RotamerTrialsMinMover.hh.

typedef core::scoring::ScoreFunctionCOP protocols::simple_moves::RotamerTrialsMinMover::ScoreFunctionCOP

Definition at line 45 of file RotamerTrialsMinMover.hh.

typedef core::scoring::ScoreFunctionOP protocols::simple_moves::RotamerTrialsMinMover::ScoreFunctionOP

Definition at line 44 of file RotamerTrialsMinMover.hh.

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

Definition at line 49 of file RotamerTrialsMinMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::RotamerTrialsMinMover::RotamerTrialsMinMover ( )

Definition at line 53 of file RotamerTrialsMinMover.cc.

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

Referenced by fresh_instance().

protocols::simple_moves::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

Definition at line 60 of file RotamerTrialsMinMover.cc.

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

protocols::simple_moves::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

Definition at line 71 of file RotamerTrialsMinMover.cc.

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

protocols::simple_moves::RotamerTrialsMinMover::~RotamerTrialsMinMover ( )

virtual

Definition at line 88 of file RotamerTrialsMinMover.cc.

Member Function Documentation

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::EnergyCutRotamerTrialsMinMover.

Definition at line 95 of file RotamerTrialsMinMover.cc.

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

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply().

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

virtual

Return a copy of this mover instance (for RosettaScripts)

Reimplemented from protocols::moves::Mover.

Definition at line 173 of file RotamerTrialsMinMover.cc.

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

virtual

Return a new mover instance (for RosettaScripts)

Reimplemented from protocols::moves::Mover.

Definition at line 166 of file RotamerTrialsMinMover.cc.

References RotamerTrialsMinMover().

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::EnergyCutRotamerTrialsMinMover.

Definition at line 107 of file RotamerTrialsMinMover.cc.

void protocols::simple_moves::RotamerTrialsMinMover::init ( void )

Definition at line 81 of file RotamerTrialsMinMover.cc.

References cartesian_, and nonideal_.

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

void protocols::simple_moves::RotamerTrialsMinMover::parse_my_tag	(	TagPtr const	tag,
		protocols::moves::DataMap &	datamap,
		Filters_map const &	,
		protocols::moves::Movers_map const &	,
		Pose const &
	)

virtual

Parse XML for RosettaScripts.

Reimplemented from protocols::moves::Mover.

Definition at line 132 of file RotamerTrialsMinMover.cc.

References cartesian_, core::scoring::getScoreFunction(), nonideal_, protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), score_function(), task_factory(), and protocols::simple_moves::TR().

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

Definition at line 91 of file RotamerTrialsMinMover.cc.

References scorefxn_.

Referenced by parse_my_tag().

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

protected

read access for derived classes

Definition at line 113 of file RotamerTrialsMinMover.cc.

References scorefxn_.

Referenced by protocols::simple_moves::EnergyCutRotamerTrialsMinMover::apply(), and protocols::simple_moves::operator<<().

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

protected

read access for derived classes, pose needed to run TaskFactory

read access for derived classes

Definition at line 120 of file RotamerTrialsMinMover.cc.

References factory_, and task_.

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

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

Definition at line 92 of file RotamerTrialsMinMover.cc.

References factory_.

Referenced by parse_my_tag().

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		RotamerTrialsMinMover const &	mover
	)

friend

Definition at line 178 of file RotamerTrialsMinMover.cc.

Member Data Documentation

bool protocols::simple_moves::RotamerTrialsMinMover::cartesian_

private

Definition at line 135 of file RotamerTrialsMinMover.hh.

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

TaskFactoryCOP protocols::simple_moves::RotamerTrialsMinMover::factory_

private

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

Definition at line 133 of file RotamerTrialsMinMover.hh.

Referenced by task(), and task_factory().

bool protocols::simple_moves::RotamerTrialsMinMover::nonideal_

private

Definition at line 134 of file RotamerTrialsMinMover.hh.

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

ScoreFunctionCOP protocols::simple_moves::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).

Definition at line 123 of file RotamerTrialsMinMover.hh.

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

PackerTaskOP protocols::simple_moves::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()

Definition at line 129 of file RotamerTrialsMinMover.hh.

Referenced by RotamerTrialsMinMover(), and task().

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

src/protocols/simple_moves/RotamerTrialsMinMover.hh
src/protocols/simple_moves/RotamerTrialsMinMover.cc

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation