A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector. More...

#include <GlycanTreeMinMover.hh>

Inheritance diagram for protocols::carbohydrates::GlycanTreeMinMover:

[legend]

Public Member Functions
	GlycanTreeMinMover ()
	Constructors ///. More...

	GlycanTreeMinMover (core::kinematics::MoveMapOP movemap_in, ScoreFunctionCOP scorefxn_in, std::string const &min_type_in="dfpmin_armijo_nonmonotone", Real tolerance_in=.01)

	GlycanTreeMinMover (GlycanTreeMinMover const &src)
	Copy constructor (not needed unless you need deep copies) More...

virtual	~GlycanTreeMinMover ()
	Destructor (important for properly forward-declaring smart-pointer members) More...

virtual void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

void	set_movemap (core::kinematics::MoveMapCOP movemap_in) override

virtual std::string	get_name () const override
	Get the name of the Mover. More...

virtual protocols::moves::MoverOP	fresh_instance () const override
	Rosetta Scripts Support ///. More...

virtual protocols::moves::MoverOP	clone () const override
	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 &)

	~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 &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &) 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, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)

void	parse_chi_and_bb (TagCOP)

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

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

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 (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 ()

	~Mover () override

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 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

void	set_type (std::string const &setting)

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 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
	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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Static Public Member Functions
static std::string	class_name ()
	Show the contents of the Mover. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::simple_moves::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
utility::vector1< core::Size >	mm_residues_

Additional Inherited Members
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::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

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...

void	minimize (core::pose::Pose &pose, core::kinematics::MoveMap &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...

Detailed Description

A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector.

Constructor & Destructor Documentation

protocols::carbohydrates::GlycanTreeMinMover::GlycanTreeMinMover ( )

Constructors ///.

Default constructor

Referenced by clone().

protocols::carbohydrates::GlycanTreeMinMover::GlycanTreeMinMover	(	core::kinematics::MoveMapOP	movemap_in,
		ScoreFunctionCOP	scorefxn_in,
		std::string const &	min_type_in = `"dfpmin_armijo_nonmonotone"`,
		Real	tolerance_in = `.01`
	)