#include <DnaInterfaceMinMover.hh>

Inheritance diagram for protocols::dna::DnaInterfaceMinMover:

Collaboration diagram for protocols::dna::DnaInterfaceMinMover:

Public Types
typedef utility::tag::TagPtr	TagPtr

Public Types inherited from protocols::simple_moves::MinMover
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
	DnaInterfaceMinMover ()

	DnaInterfaceMinMover (DnaInterfaceMinMover const &)

DnaInterfaceMinMover &	operator= (DnaInterfaceMinMover const &)

virtual	~DnaInterfaceMinMover ()

	DnaInterfaceMinMover (DnaInterfaceFinderOP)

virtual void	apply (core::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	use_interface (DnaInterfaceFinderOP)

void	chi (bool value)

void	bb (bool value)

void	reset_from_interface ()

virtual void	parse_my_tag (TagPtr const, moves::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, core::pose::Pose const &)
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme More...

virtual moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme More...

Public Member Functions inherited from protocols::simple_moves::MinMover
	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)

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

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

Private Attributes
DnaInterfaceFinderOP	interface_

bool	chi_

bool	bb_

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...

Protected Member Functions inherited from protocols::simple_moves::MinMover
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...

Detailed Description

Definition at line 31 of file DnaInterfaceMinMover.hh.

Member Typedef Documentation

typedef utility::tag::TagPtr protocols::dna::DnaInterfaceMinMover::TagPtr

Definition at line 33 of file DnaInterfaceMinMover.hh.

Constructor & Destructor Documentation

protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( )

Definition at line 75 of file DnaInterfaceMinMover.cc.

References protocols::simple_moves::MinMover::min_type(), and protocols::simple_moves::MinMover::tolerance().

Referenced by clone(), and fresh_instance().

protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( DnaInterfaceMinMover const & src)

Definition at line 85 of file DnaInterfaceMinMover.cc.

protocols::dna::DnaInterfaceMinMover::~DnaInterfaceMinMover ( )

virtual

Definition at line 102 of file DnaInterfaceMinMover.cc.

protocols::dna::DnaInterfaceMinMover::DnaInterfaceMinMover ( DnaInterfaceFinderOP interface)

Definition at line 104 of file DnaInterfaceMinMover.cc.

References protocols::simple_moves::MinMover::min_type(), reset_from_interface(), and protocols::simple_moves::MinMover::tolerance().

Member Function Documentation

void protocols::dna::DnaInterfaceMinMover::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

Reimplemented from protocols::simple_moves::MinMover.

Definition at line 143 of file DnaInterfaceMinMover.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), interface_, protocols::simple_moves::MinMover::min_options(), protocols::simple_moves::MinMover::movemap(), reset_from_interface(), and protocols::simple_moves::MinMover::score_function().

void protocols::dna::DnaInterfaceMinMover::bb ( bool value)

inline

Definition at line 46 of file DnaInterfaceMinMover.hh.

References bb_.

void protocols::dna::DnaInterfaceMinMover::chi ( bool value)

inline

Definition at line 45 of file DnaInterfaceMinMover.hh.

References chi_.

MoverOP protocols::dna::DnaInterfaceMinMover::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::MinMover.

Definition at line 210 of file DnaInterfaceMinMover.cc.

References DnaInterfaceMinMover().

MoverOP protocols::dna::DnaInterfaceMinMover::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::MinMover.

Definition at line 203 of file DnaInterfaceMinMover.cc.

References DnaInterfaceMinMover().

std::string protocols::dna::DnaInterfaceMinMover::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::MinMover.

Definition at line 162 of file DnaInterfaceMinMover.cc.

References protocols::dna::DnaInterfaceMinMoverCreator::mover_name().

DnaInterfaceMinMover & protocols::dna::DnaInterfaceMinMover::operator= ( DnaInterfaceMinMover const & src)

Definition at line 93 of file DnaInterfaceMinMover.cc.

References bb_, chi_, and interface_.

void protocols::dna::DnaInterfaceMinMover::parse_my_tag	(	TagPtr const	tag,
		moves::DataMap &	datamap,
		protocols::filters::Filters_map const &	,
		moves::Movers_map const &	,
		core::pose::Pose const &
	)