A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set. More...

#include <MinMover.hh>

Inheritance diagram for protocols::simple_moves::MinMover:

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Collaboration diagram for protocols::simple_moves::MinMover:

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Public Types
typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::optimization::MinimizerOptionsOP	MinimizerOptionsOP

typedef core::optimization::MinimizerOptionsCOP	MinimizerOptionsCOP

typedef core::Real	Real

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
	MinMover ()
	Constructs a MinMover minmover = protocols::simple_moves::MinMover() More...

	MinMover (std::string const &)

virtual	~MinMover ()

	MinMover (core::kinematics::MoveMapOP movemap_in, ScoreFunctionCOP scorefxn_in, std::string const &min_type_in, Real tolerance_in, bool use_nb_list_in, bool deriv_check_in=false, bool deriv_check_verbose_in=false)

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

virtual void	parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover's parsing. More...

void	parse_opts (TagPtr const, protocols::moves::DataMap &data_map, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)

void	parse_chi_and_bb (TagPtr const )

void	parse_dof_tasks (TagPtr const tag, protocols::moves::DataMap &data)

void	parse_dof_task_type (std::string const &tag_name, core::id::DOF_Type dof_type, core::id::TorsionType torsion_type, TagPtr const tag, protocols::moves::DataMap &data)
	helper function for parse_of_tasks More...

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

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

virtual MinimizerOptionsOP	min_options ()
	allow non-const access to the internal minimizer options object More...

virtual MinimizerOptionsCOP	min_options () const
	allow const access to the internal minimizer options object More...

virtual void	movemap (core::kinematics::MoveMapCOP movemap_in)
	Sets the MoveMap to <movemap_in> determines which DOF to minimize. More...

virtual core::kinematics::MoveMapCOP	movemap () const

virtual void	score_function (ScoreFunctionCOP scorefxn_in)
	Sets the ScoreFunction to <scorefxn_in> determines which function to minimize. More...

virtual void	score_function (core::scoring::ScoreFunction const &scorefxn_in)

virtual ScoreFunctionCOP	score_function () const

virtual void	min_type (std::string min_type_in)

virtual void	tolerance (Real tolerance_in)

virtual void	nb_list (bool nb_list_in)

virtual void	deriv_check (bool deriv_check_in)

Real	tolerance () const

std::string	min_type () const

bool	nb_list () const

bool	deriv_check () const

virtual void	apply (core::pose::Pose &pose_)
	Minimizes the DOFs of <pose_> specified in the MoveMap using the ScoreFunction. More...

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

void	cartesian (bool newval)

bool	cartesian () const

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	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
void	apply_dof_tasks_to_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap) const
	for use with RosettaScripts current method of using TaskOperations to specify residue sets. 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 Types
typedef std::map< std::pair < core::id::DOF_Type, core::id::TorsionType > , core::pack::task::TaskFactoryOP >	DOF_TaskMap

Private Attributes
core::kinematics::MoveMapOP	movemap_

ScoreFunctionCOP	scorefxn_

MinimizerOptionsOP	min_options_

Real	threshold_

bool	cartesian_

DOF_TaskMap	dof_tasks_

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

A protocols::moves::Mover that minimizes a Pose to a local energy minimum by performing energy minimization of a ScoreFunction over the allowable degrees of freedom, defined by a MoveMap. The minimization type, minimization tolerance, and various other options can be also be set.

Common Methods: MinMover.apply MinMover.movemap MinMover.score_function

Member Typedef Documentation

typedef std::map< std::pair< core::id::DOF_Type, core::id::TorsionType >, core::pack::task::TaskFactoryOP > protocols::simple_moves::MinMover::DOF_TaskMap

private

typedef core::optimization::MinimizerOptionsCOP protocols::simple_moves::MinMover::MinimizerOptionsCOP

typedef core::optimization::MinimizerOptionsOP protocols::simple_moves::MinMover::MinimizerOptionsOP

typedef core::Real protocols::simple_moves::MinMover::Real

typedef core::scoring::ScoreFunctionCOP protocols::simple_moves::MinMover::ScoreFunctionCOP

Constructor & Destructor Documentation

protocols::simple_moves::MinMover::MinMover ( )

Constructs a MinMover minmover = protocols::simple_moves::MinMover()

References min_options_.

Referenced by fresh_instance().

protocols::simple_moves::MinMover::MinMover ( std::string const & name)

References min_options_.

protocols::simple_moves::MinMover::~MinMover ( )

virtual

protocols::simple_moves::MinMover::MinMover	(	core::kinematics::MoveMapOP	movemap_in,
		ScoreFunctionCOP	scorefxn_in,
		std::string const &	min_type_in,
		Real	tolerance_in,
		bool	use_nb_list_in,
		bool	deriv_check_in = `false`,
		bool	deriv_check_verbose_in = `false`
	)

Member Function Documentation

void protocols::simple_moves::MinMover::apply ( core::pose::Pose & pose_)

virtual

Minimizes the DOFs of <pose_> specified in the MoveMap using the ScoreFunction.

example(s): minmover.apply(pose) See also: MinMover MinMover.movemap MinMover.score_function

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

References apply_dof_tasks_to_movemap(), cartesian(), core::scoring::getScoreFunction(), min_options_, movemap(), and scorefxn_.

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::MakeRotLib::calc_std_dev(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::MakeRotLib::min_rotamers(), protocols::simple_moves::PeptideStapleMover::minimize_(), protocols::flexpep_docking::FlexPepDockingProtocol::minimize_only(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), protocols::flexpep_docking::FlexPepDockingProtocol::rigidbody_monte_carlo_minimize(), and protocols::flexpep_docking::FlexPepDockingProtocol::torsions_monte_carlo_minimize().

void protocols::simple_moves::MinMover::apply_dof_tasks_to_movemap	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMap &	movemap
	)		const

protected

for use with RosettaScripts current method of using TaskOperations to specify residue sets.

restrict the move map by the packer task: If a residue is not designable, the backbone is fixes If a residue is not packable, the sidechain is fixed

WARNING: This is extending the abuse of using task operations for general ResidueSubsets

When TaskOperations replaced with ResidueSetOperations please change this too!

References dof_tasks_, core::id::PHI, and core::scoring::hbonds::t().

Referenced by protocols::simple_moves::symmetry::SymMinMover::apply(), and apply().

void protocols::simple_moves::MinMover::cartesian ( bool newval)

inline

References cartesian_.

bool protocols::simple_moves::MinMover::cartesian ( ) const

inline

References cartesian_.

Referenced by protocols::simple_moves::symmetry::SymMinMover::apply(), apply(), parse_def_opts(), and parse_opts().

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

virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

Referenced by parse_def_opts().

void protocols::simple_moves::MinMover::deriv_check ( bool deriv_check_in)

virtual

References min_options_.

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

bool protocols::simple_moves::MinMover::deriv_check ( ) const

References min_options_.

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

virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

References MinMover().

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

References protocols::simple_moves::MinMoverCreator::mover_name().

MinimizerOptionsOP protocols::simple_moves::MinMover::min_options ( )

virtual

allow non-const access to the internal minimizer options object

References min_options_.

Referenced by protocols::dna::DnaInterfaceMinMover::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), and protocols::simple_moves::PeptideStapleMover::minimize_().

MinimizerOptionsCOP protocols::simple_moves::MinMover::min_options ( ) const

virtual

allow const access to the internal minimizer options object

References min_options_.

void protocols::simple_moves::MinMover::min_type ( std::string min_type_in)

virtual

References min_options_.

Referenced by protocols::simple_moves::operator<<(), and protocols::optimize_weights::IterativeOptEDriver::repack_and_minimize_pose().

std::string protocols::simple_moves::MinMover::min_type ( ) const

References min_options_.

Referenced by protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover(), parse_def_opts(), protocols::dna::DnaInterfaceMinMover::parse_my_tag(), and parse_opts().

virtual void protocols::simple_moves::MinMover::movemap ( core::kinematics::MoveMapCOP movemap_in)

virtual

Sets the MoveMap to <movemap_in> determines which DOF to minimize.

example(s): minmover.movemap(movemap1) See also: MinMover MinMover.apply MinMover.score_function MoveMap

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

MoveMapCOP protocols::simple_moves::MinMover::movemap ( ) const

virtual

References movemap_.

Referenced by protocols::dna::DnaInterfaceMinMover::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), apply(), and protocols::dna::DnaInterfaceMinMover::reset_from_interface().

void protocols::simple_moves::MinMover::nb_list ( bool nb_list_in)

virtual

References min_options_.

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

bool protocols::simple_moves::MinMover::nb_list ( ) const

References min_options_.

void protocols::simple_moves::MinMover::parse_chi_and_bb ( TagPtr const tag)

References core::id::D, movemap_, and core::id::THETA.

Referenced by parse_my_tag().

void protocols::simple_moves::MinMover::parse_def	(	utility::lua::LuaObject const &	def,
		utility::lua::LuaObject const &	score_fxns,
		utility::lua::LuaObject const &	tasks,
		protocols::moves::MoverCacheSP	cache
	)

virtual

Reimplemented from protocols::moves::Mover.

References movemap_, parse_def_opts(), and protocols::elscripts::parse_movemapdef().

void protocols::simple_moves::MinMover::parse_def_opts	(	utility::lua::LuaObject const &	def,
		utility::lua::LuaObject const &	score_fxns,
		utility::lua::LuaObject const &	tasks,
		protocols::moves::MoverCacheSP	cache
	)

virtual

References cartesian(), clone(), core::sequence::end, min_type(), movemap_, protocols::elscripts::parse_scoredef(), score_function(), and tolerance().

Referenced by parse_def().

void protocols::simple_moves::MinMover::parse_dof_task_type	(	std::string const &	tag_name,
		core::id::DOF_Type	dof_type,
		core::id::TorsionType	torsion_type,
		TagPtr const	tag,
		protocols::moves::DataMap &	data
	)

helper function for parse_of_tasks

References dof_tasks_, protocols::moves::DataMap::get(), and protocols::moves::DataMap::has().

Referenced by parse_dof_tasks().

void protocols::simple_moves::MinMover::parse_dof_tasks	(	TagPtr const	tag,
		protocols::moves::DataMap &	data
	)

References core::id::BB, core::id::CHI, core::id::D, parse_dof_task_type(), core::id::PHI, and core::id::THETA.

Referenced by parse_my_tag().

void protocols::simple_moves::MinMover::parse_my_tag	(	TagPtr const	tag,
		protocols::moves::DataMap &	data,
		Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		Pose const &	pose
	)

virtual

Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover's parsing.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::symmetry::SymMinMover, and protocols::dna::DnaInterfaceMinMover.

References movemap_, parse_chi_and_bb(), parse_dof_tasks(), protocols::rosetta_scripts::parse_movemap(), and parse_opts().

Referenced by protocols::simple_moves::symmetry::SymMinMover::parse_my_tag().

void protocols::simple_moves::MinMover::parse_opts	(	TagPtr const	tag,
		protocols::moves::DataMap &	data_map,
		Filters_map const &	,
		protocols::moves::Movers_map const &	,
		Pose const &
	)

References cartesian(), protocols::moves::DataMap::get(), min_type(), movemap_, score_function(), and tolerance().

Referenced by parse_my_tag().

void protocols::simple_moves::MinMover::score_function ( ScoreFunctionCOP scorefxn_in)

virtual

Sets the ScoreFunction to <scorefxn_in> determines which function to minimize.

example(s): minmover.score_function(scorefxn) See also: MinMover MinMover.apply MinMover.movemap ScoreFunction

References scorefxn_.

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

void protocols::simple_moves::MinMover::score_function ( core::scoring::ScoreFunction const & scorefxn_in)

virtual

References core::scoring::ScoreFunction::clone(), and scorefxn_.

ScoreFunctionCOP protocols::simple_moves::MinMover::score_function ( ) const

virtual

References scorefxn_.

Referenced by protocols::dna::DnaInterfaceMinMover::apply(), protocols::simple_moves::symmetry::SymMinMover::apply(), parse_def_opts(), protocols::dna::DnaInterfaceMinMover::parse_my_tag(), and parse_opts().

void protocols::simple_moves::MinMover::tolerance ( Real tolerance_in)

virtual

References min_options_.

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

Real protocols::simple_moves::MinMover::tolerance ( ) const

References min_options_.

Referenced by protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover(), parse_def_opts(), protocols::dna::DnaInterfaceMinMover::parse_my_tag(), and parse_opts().

Member Data Documentation

bool protocols::simple_moves::MinMover::cartesian_

private

Referenced by cartesian().

DOF_TaskMap protocols::simple_moves::MinMover::dof_tasks_

private

Until ResidueSubsetOperations are implemented, RosettaScripts uses TaskOperations as a generic way to specify sets of residues, so it is necessary to have a method of controling a movemap from a set of task operations. This is not suppose to be a general interface for MinMover, so only expose it through the parse_my_tag. Another small complication is that TaskOperations must be defined in the context of a pose, so hang on to it here until the apply. In case MinMover is applied multiple times, to avoid accumulating state, reset the move map to before the task operations were applied at the end of apply.

Referenced by apply_dof_tasks_to_movemap(), and parse_dof_task_type().

MinimizerOptionsOP protocols::simple_moves::MinMover::min_options_

private

Referenced by apply(), deriv_check(), min_options(), min_type(), MinMover(), nb_list(), and tolerance().