protocols::minimization_packing::MinMover Class Reference

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::minimization_packing::MinMover:

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::TagCOP	TagCOP
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef std::list< std::string >	Strings

Public Member Functions
	MinMover ()
	Constructs a MinMover minmover = protocols::minimization_packing::MinMover() More...
	MinMover (std::string const &)
	~MinMover () override
	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)
	constructor with arguments More...
void	apply (core::pose::Pose &pose) override
	Minimizes the DOFs of <pose_> specified in the MoveMap using the 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...
void	cartesian (bool newval)
bool	cartesian () const
void	abs_score_convergence_threshold (Real newval)
Real	abs_score_convergence_threshold () const
protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...
protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...
void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	Called by protocols::moves::MoverFactory when constructing new protocols::moves::Movers. Takes care of the specific mover's parsing. More...
void	parse_opts (TagCOP, basic::datacache::DataMap &data_map)
void	parse_movemap_factory (TagCOP, basic::datacache::DataMap &)
void	parse_dof_tasks (TagCOP tag, basic::datacache::DataMap &data)
void	parse_dof_task_type (std::string const &tag_name, core::id::DOF_Type dof_type, core::id::TorsionType torsion_type, TagCOP tag, basic::datacache::DataMap &data)
	helper function for parse_of_tasks More...
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	min_options (MinimizerOptionsOP min_options)
	directly set 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...
void	set_movemap (core::kinematics::MoveMapCOP movemap_in) override
virtual void	movemap_factory (core::select::movemap::MoveMapFactoryCOP mmf)
	Sets the MoveMapFactory The MoveMapFactory will be used to construct a MoveMap if an explicit one isn't set. More...
core::kinematics::MoveMapCOP	movemap (core::pose::Pose const &pose) const override
	Get the movemap for the pose. More...
core::kinematics::MoveMapCOP	explicitly_set_movemap () const
	Get the explicitly set movemap object, if present, nullptr if not Will not create a default or look at the MoveMapFactory. More...
virtual void	score_function (ScoreFunctionCOP scorefxn_in)
	Sets the ScoreFunction to <scorefxn_in> determines which function to minimize. More...
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)
	Indicate whether or not a handful of optimizations regarding the neighbor list should be enabled. More...
virtual void	deriv_check (bool deriv_check_in)
virtual void	max_iter (core::Size max_iter_in)
Real	tolerance () const
std::string	min_type () const
bool	nb_list () const
	Indicate whether or not a handful of optimizations regarding the neighbor list have been enabled. More...
bool	deriv_check () const
bool	omega () const
void	omega (bool const b)
Real	score_diff_after_minimization () const
Real	abs_score_diff_after_minimization () const
Public Member Functions inherited from protocols::moves::MoveMapMover
	MoveMapMover ()
	MoveMapMover (std::string const &name)
	MoveMapMover (MoveMapMover const &)=default
	~MoveMapMover () override=default
virtual void	initialize (core::pose::Pose &)
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_min_mover (utility::tag::XMLSchemaDefinition &xsd)
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
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...
void	minimize (core::pose::Pose &pose, core::kinematics::MoveMap const &active_movemap)
	run the minimizer (cartesian or torsion) based on set options, with the final movemap setup. Will call inner_run_minimizer multiple times if abs_score_convergence_threshold is set 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 protocols::moves::MoveMapMover	Parent
typedef std::map< std::pair < core::id::DOF_Type, core::id::TorsionType > , core::pack::task::TaskFactoryOP >	DOF_TaskMap

Private Member Functions
void	inner_run_minimizer (core::pose::Pose &pose, core::kinematics::MoveMap const &active_movemap)
	actual call to the minimizer, in helper function so it can be run multiple times by minimize() More...

Private Attributes
core::select::movemap::MoveMapFactoryCOP	movemap_factory_
core::kinematics::MoveMapOP	movemap_
bool	omega_
ScoreFunctionCOP	scorefxn_
MinimizerOptionsOP	min_options_
Real	abs_score_convergence_threshold_
Real	score_before_minimization_
Real	score_after_minimization_
bool	cartesian_
DOF_TaskMap	dof_tasks_

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::minimization_packing::MinMover::DOF_TaskMap

private

typedef core::optimization::MinimizerOptionsCOP protocols::minimization_packing::MinMover::MinimizerOptionsCOP

typedef core::optimization::MinimizerOptionsOP protocols::minimization_packing::MinMover::MinimizerOptionsOP

typedef protocols::moves::MoveMapMover protocols::minimization_packing::MinMover::Parent

private

typedef core::Real protocols::minimization_packing::MinMover::Real

typedef core::scoring::ScoreFunctionCOP protocols::minimization_packing::MinMover::ScoreFunctionCOP

Constructor & Destructor Documentation

protocols::minimization_packing::MinMover::MinMover

(

)

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

References min_options_, and omega_.

protocols::minimization_packing::MinMover::MinMover

(

std::string const &

name

)

References min_options_, and omega_.

protocols::minimization_packing::MinMover::~MinMover ( )

overridedefault

protocols::minimization_packing::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
	)

constructor with arguments

min_type_in indicates the type of minimizer to use. This is different for cartesion. Current recommendation (Jan 2016) is "dfpmin_armijo_nonmonotone"

tolerance_in indicates the tolerance on the minimizer. Smaller tolerance will result in lower energies, but increased runtime. Generally one would use .01

use_nb_list_in The neighbor list is based on the move map. It includes any atoms that can be moved by the minimizer plus their neighbors. This list is not updated during minimization. All scores for atoms and atom pairs outside the neighbor list are held fixed. All scores for atoms and atom pairs within the list are not cached (usually they would be), since it assumed that they will be changing rapidly. These optimizations are effective when a large number of small moves are being made. You may prefer to enable this option when minimizing in fullatom mode, and to disable it in centroid mode.

See also

core::scoring::AtomNeighbor

Member Function Documentation

void protocols::minimization_packing::MinMover::abs_score_convergence_threshold ( Real  newval )

inline

References abs_score_convergence_threshold_.

Real protocols::minimization_packing::MinMover::abs_score_convergence_threshold ( ) const

inline

References abs_score_convergence_threshold_.

Referenced by minimize(), and parse_opts().

Real protocols::minimization_packing::MinMover::abs_score_diff_after_minimization

(

)

const

References score_diff_after_minimization().

Referenced by minimize().

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

overridevirtual

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.

References apply_dof_tasks_to_movemap(), clone(), core::scoring::get_score_function(), core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), minimize(), movemap(), and scorefxn_.

Referenced by protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::backrub::BackrubProtocol::apply(), protocols::minimization_packing::symmetry::TaskAwareSymMinMover::apply(), protocols::simple_moves::DisulfideInsertionMover::apply(), protocols::minimization_packing::DisulfideOptimizationMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::peptide_deriver::PeptideDeriverFilter::generate_N2C_cyclic_peptide_protein_complex(), protocols::flexpep_docking::FlexPepDockingProtocol::hires_fpdock_protocol(), protocols::splice::SpliceOut::min_mover(), protocols::splice::min_seg(), protocols::peptide_deriver::PeptideDeriverFilter::minimize(), protocols::simple_moves::PeptideStapleMover::minimize_(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), protocols::antibody::design::GeneralAntibodyModeler::minimize_interface(), protocols::flexpep_docking::FlexPepDockingProtocol::minimize_only(), protocols::make_rot_lib::MakeRotLibMover::minimize_rotamer(), protocols::pose_creation::MergePDBMover::pack_and_minimize(), protocols::enzdes::MinimizeStoredRBConfs::rb_minimize_all_confs(), protocols::flexpep_docking::FlexPepDockingProtocol::rigidbody_monte_carlo_minimize(), protocols::carbohydrates::run_shear_min_pack(), protocols::farnesyl::SampleFarnesylMover::sample_farnesyl(), protocols::farnesyl::InstallFarnesylMover::sample_first(), protocols::farnesyl::InstallFarnesylMover::sample_second(), protocols::farnesyl::InstallFarnesylMover::sample_third(), and protocols::flexpep_docking::FlexPepDockingProtocol::torsions_monte_carlo_minimize().

void protocols::minimization_packing::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 core::id::BB, dof_tasks_, core::conformation::Residue::is_protein(), core::conformation::Residue::natoms(), omega_, core::id::omega_torsion(), core::id::PHI, core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::minimization_packing::TR().

Referenced by apply().

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

inline

References cartesian_.

Referenced by protocols::ncbb::SecStructFinder::apply(), and protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs().

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

inline

References cartesian_.

Referenced by inner_run_minimizer(), and parse_opts().

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

overridevirtual

Return a clone of the Mover object.

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::minimization_packing::symmetry::SymMinMover.

Referenced by apply().

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::minimization_packing::MinMover::complex_type_generator_for_min_mover ( utility::tag::XMLSchemaDefinition &  xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), core::select::movemap::attributes_for_parse_movemap_factory_default_attr_name(), core::scoring::attributes_for_parse_score_function(), and protocols::moves::complex_type_name_for_mover().

Referenced by protocols::minimization_packing::symmetry::SymMinMover::provide_xml_schema(), and provide_xml_schema().

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

virtual

References min_options_.

bool protocols::minimization_packing::MinMover::deriv_check

(

)

const

References min_options_.

Referenced by show().

core::kinematics::MoveMapCOP protocols::minimization_packing::MinMover::explicitly_set_movemap

(

)

const

Get the explicitly set movemap object, if present, nullptr if not Will not create a default or look at the MoveMapFactory.

References movemap_.

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

overridevirtual

Generates a new Mover object freshly created with the default ctor.

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::minimization_packing::symmetry::SymMinMover.

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

inlineoverridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::minimization_packing::symmetry::SymMinMover.

References mover_name().

void protocols::minimization_packing::MinMover::inner_run_minimizer ( core::pose::Pose &  pose, core::kinematics::MoveMap const &  active_movemap  )

private

actual call to the minimizer, in helper function so it can be run multiple times by minimize()

References cartesian(), core::pose::symmetry::is_symmetric(), min_options_, score_after_minimization_, score_before_minimization_, and scorefxn_.

Referenced by minimize().

void protocols::minimization_packing::MinMover::max_iter ( core::Size  max_iter_in )

virtual

References min_options_.

Referenced by parse_opts().

MinimizerOptionsOP protocols::minimization_packing::MinMover::min_options ( )

virtual

allow non-const access to the internal minimizer options object

References min_options_.

Referenced by protocols::dna::DnaInterfaceMinMover::apply(), protocols::carbohydrates::GlycanTreeModeler::apply(), protocols::simple_moves::PeptideStapleMover::minimize_(), and protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs().

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

virtual

allow const access to the internal minimizer options object

References min_options_.

void protocols::minimization_packing::MinMover::min_options ( MinimizerOptionsOP  min_options )

virtual

directly set the internal minimizer options object

References min_options(), and min_options_.

Referenced by min_options().

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

virtual

References min_options_.

Referenced by protocols::backrub::BackrubProtocol::apply(), protocols::antibody::design::GeneralAntibodyModeler::minimize_cdrs(), and protocols::optimize_weights::IterativeOptEDriver::repack_and_minimize_pose().

std::string protocols::minimization_packing::MinMover::min_type

(

)

const

References min_options_.

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

void protocols::minimization_packing::MinMover::minimize ( core::pose::Pose &  pose, core::kinematics::MoveMap const &  active_movemap  )

protected

run the minimizer (cartesian or torsion) based on set options, with the final movemap setup. Will call inner_run_minimizer multiple times if abs_score_convergence_threshold is set

References abs_score_convergence_threshold(), abs_score_diff_after_minimization(), inner_run_minimizer(), scorefxn_, and protocols::minimization_packing::TR().

Referenced by apply().

virtual void protocols::minimization_packing::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::dna::DnaInterfaceMinMover::apply(), protocols::backrub::BackrubProtocol::apply(), apply(), protocols::enzdes::RemoveLigandFilter::RemoveLigandFilter(), protocols::dna::DnaInterfaceMinMover::reset_from_interface(), and set_movemap().

MoveMapCOP protocols::minimization_packing::MinMover::movemap ( core::pose::Pose const &  pose ) const

overridevirtual

Get the movemap for the pose.

This is the preferred version to call.

Implements protocols::moves::MoveMapMover.

References movemap_, and movemap_factory_.

void protocols::minimization_packing::MinMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP  mmf )

virtual

Sets the MoveMapFactory The MoveMapFactory will be used to construct a MoveMap if an explicit one isn't set.

References movemap_factory_.

Referenced by parse_movemap_factory().

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

static

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

Referenced by get_name(), and provide_xml_schema().

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

virtual

Indicate whether or not a handful of optimizations regarding the neighbor list should be enabled.

The neighbor list is based on the move map. It includes any atoms that can be moved by the minimizer plus their neighbors. This list is not updated during minimization. All scores for atoms and atom pairs outside the neighbor list are held fixed. All scores for atoms and atom pairs within the list are not cached (usually they would be), since it assumed that they will be changing rapidly. These optimizations are effective when a large number of small moves are being made. You may prefer to enable this option when minimizing in fullatom mode, and to disable it in centroid mode.

Note

I wrote this docstring after I reading through a bunch of code to figure out what this option meant, but I don't have any expertise with the minimizer. So the above represents my understanding of this option, but there could very well be errors or misstatements.

See also

core::scoring::AtomNeighbor

References min_options_.

bool protocols::minimization_packing::MinMover::nb_list

(

)

const

Indicate whether or not a handful of optimizations regarding the neighbor list have been enabled.

References min_options_.

Referenced by show().

bool protocols::minimization_packing::MinMover::omega ( ) const

inline

References omega_.

void protocols::minimization_packing::MinMover::omega ( bool const  b )

inline

References protocols::match::upstream::b, and omega_.

void protocols::minimization_packing::MinMover::parse_dof_task_type	(	std::string const &	tag_name,
		core::id::DOF_Type	dof_type,
		core::id::TorsionType	torsion_type,
		TagCOP	tag,
		basic::datacache::DataMap &	data
	)

helper function for parse_of_tasks

References dof_tasks_, and protocols::minimization_packing::TR().

Referenced by parse_dof_tasks().

void protocols::minimization_packing::MinMover::parse_dof_tasks	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

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

Referenced by parse_my_tag().

void protocols::minimization_packing::MinMover::parse_movemap_factory	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

References core::select::movemap::mm_enable, movemap_factory(), omega_, core::select::movemap::parse_movemap_factory(), protocols::rosetta_scripts::parse_movemap_factory_legacy(), and protocols::minimization_packing::TR().

Referenced by parse_my_tag().

void protocols::minimization_packing::MinMover::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References parse_dof_tasks(), parse_movemap_factory(), and parse_opts().

void protocols::minimization_packing::MinMover::parse_opts	(	TagCOP	tag,
		basic::datacache::DataMap &	data_map
	)

References abs_score_convergence_threshold(), cartesian(), max_iter(), min_type(), core::scoring::parse_score_function(), score_function(), and tolerance().

Referenced by parse_my_tag().

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

static

References complex_type_generator_for_min_mover(), and mover_name().

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

Real protocols::minimization_packing::MinMover::score_diff_after_minimization

(

)

const

References score_after_minimization_, and score_before_minimization_.

Referenced by abs_score_diff_after_minimization().

void protocols::minimization_packing::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::backrub::BackrubProtocol::apply().

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

virtual

References scorefxn_.

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

void protocols::minimization_packing::MinMover::set_movemap ( core::kinematics::MoveMapCOP  movemap_in )

overridevirtual

Implements protocols::moves::MoveMapMover.

References movemap().

Referenced by protocols::splice::SpliceOut::min_mover().

void protocols::minimization_packing::MinMover::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 deriv_check(), min_type(), movemap_, nb_list(), score_function(), and tolerance().

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

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

virtual

References min_options_.

Real protocols::minimization_packing::MinMover::tolerance

(

)

const

References min_options_.

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

Member Data Documentation

Real protocols::minimization_packing::MinMover::abs_score_convergence_threshold_

private

Referenced by abs_score_convergence_threshold().

bool protocols::minimization_packing::MinMover::cartesian_

private

Referenced by cartesian().

DOF_TaskMap protocols::minimization_packing::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::minimization_packing::MinMover::min_options_

private

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

core::kinematics::MoveMapOP protocols::minimization_packing::MinMover::movemap_

private

Referenced by explicitly_set_movemap(), movemap(), and show().

core::select::movemap::MoveMapFactoryCOP protocols::minimization_packing::MinMover::movemap_factory_

private

Referenced by movemap(), and movemap_factory().

bool protocols::minimization_packing::MinMover::omega_

private

Referenced by apply_dof_tasks_to_movemap(), MinMover(), omega(), and parse_movemap_factory().

Real protocols::minimization_packing::MinMover::score_after_minimization_

private

Referenced by inner_run_minimizer(), and score_diff_after_minimization().

Real protocols::minimization_packing::MinMover::score_before_minimization_

private

Referenced by inner_run_minimizer(), and score_diff_after_minimization().

ScoreFunctionCOP protocols::minimization_packing::MinMover::scorefxn_

private

Referenced by apply(), inner_run_minimizer(), minimize(), and score_function().

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

• src/protocols/minimization_packing/MinMover.hh
• src/protocols/minimization_packing/MinMover.cc