#include <DnaInterfaceMinMover.hh>

Inheritance diagram for protocols::dna::DnaInterfaceMinMover:

Public Types
typedef utility::tag::TagCOP	TagCOP

Public Types inherited from protocols::minimization_packing::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::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Public Member Functions
	DnaInterfaceMinMover ()

	DnaInterfaceMinMover (DnaInterfaceMinMover const &)

DnaInterfaceMinMover &	operator= (DnaInterfaceMinMover const &)

	~DnaInterfaceMinMover () override

	DnaInterfaceMinMover (DnaInterfaceFinderOP)

void	apply (core::pose::Pose &) override
	Main Method. More...

void	use_interface (DnaInterfaceFinderOP)

void	chi (bool value)

void	bb (bool value)

void	reset_from_interface ()

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

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

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

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

Public Member Functions inherited from protocols::minimization_packing::MinMover
	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 void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::minimization_packing::MinMover
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...

Private Attributes
DnaInterfaceFinderOP	interface_

bool	chi_

bool	bb_

Additional Inherited Members
Protected Member Functions inherited from protocols::minimization_packing::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...

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...