#include <LoopRemodel.hh>

Inheritance diagram for protocols::protein_interface_design::movers::LoopRemodel:

Public Member Functions
	LoopRemodel ()

	LoopRemodel (std::string const &protocol, std::string const &loop_start, std::string const &loop_end, core::Size const cycles, bool const perturb, bool const refine, bool const hurry, core::scoring::ScoreFunctionOP hires_score, core::scoring::ScoreFunctionOP lores_score, protocols::loops::LoopsCOP loops, core::fragment::FragSetOP frag1, core::fragment::FragSetOP frag3, core::fragment::FragSetOP frag9)

bool	perturb ()

void	perturb (bool const setting)

bool	refine ()

void	refine (bool const setting)

bool	hurry ()

void	hurry (bool const setting)

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	apply (core::pose::Pose &pose) override
	a dummy apply so that instantiation of this baseclass would be possible. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

	~LoopRemodel () override

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

Public Member Functions inherited from protocols::calc_taskop_movers::DesignRepackMover
	DesignRepackMover ()

	DesignRepackMover (std::string const &name)

void	setup_packer_and_movemap (core::pose::Pose const &pose)

void	min_rb (utility::vector1< bool > const &min_rb)

void	min_rb (bool const min_rb)
	in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...

utility::vector1< bool > const &	min_rb () const

bool	min_rb_set () const

void	min_sc (core::select::residue_selector::ResidueSelectorOP min_sc)

utility::vector1< bool >	min_sc (core::pose::Pose const &pose) const

bool	min_sc_set () const

void	min_bb (core::select::residue_selector::ResidueSelectorOP min_bb)

utility::vector1< bool >	min_bb (core::pose::Pose const &pose) const

bool	min_bb_set () const

bool	optimize_foldtree () const

void	optimize_foldtree (bool const opt)

void	prevent_repacking (utility::vector1< core::Size > const &p)

utility::vector1< core::Size > const &	prevent_repacking () const

void	restrict_to_repacking (utility::vector1< core::Size > const &p)

utility::vector1< core::Size > const &	restrict_to_repacking () const

void	design (bool const des)

bool	design () const

void	set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)

void	set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)

core::scoring::ScoreFunctionOP	scorefxn_repack () const

core::scoring::ScoreFunctionOP	scorefxn_minimize () const

core::pack::task::PackerTaskCOP	task () const

core::pack::task::PackerTaskOP &	task ()

void	clear_task ()
	after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...

void	clear_task_factory ()

void	use_preset_task (bool const bt)

bool	use_preset_task () const

void	task_factory (core::pack::task::TaskFactoryOP p)

core::pack::task::TaskFactoryOP &	task_factory ()

core::pack::task::TaskFactoryOP	task_factory () const

	~DesignRepackMover () override

void	target_residues (core::select::residue_selector::ResidueSelectorCOP setting)
	Replace the current target_residue setting with the passed residue selector. More...

core::select::residue_selector::ResidueSelectorCOP	target_residues () const

utility::vector1< core::Size >	target_residues (core::pose::Pose const &pose) const

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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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 bool	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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::calc_taskop_movers::DesignRepackMover
static utility::tag::XMLSchemaComplexTypeGeneratorOP	get_xsd_complex_type ()

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 Member Functions
bool	pick_loop_frags (protocols::loops::LoopsCOP loops, std::string const &full_seqeuence, std::string const &full_ss)

Private Attributes
std::string	protocol_

core::scoring::ScoreFunctionOP	hires_score_

core::scoring::ScoreFunctionOP	lores_score_

std::string	loop_start_

std::string	loop_end_

core::Size	cycles_

bool	perturb_

bool	refine_

bool	hurry_

protocols::loops::LoopsOP	loops_

core::fragment::FragSetOP	frag1_

core::fragment::FragSetOP	frag3_

core::fragment::FragSetOP	frag9_

Additional Inherited Members
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::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...

Protected Attributes inherited from protocols::calc_taskop_movers::DesignRepackMover
core::scoring::ScoreFunctionOP	scorefxn_repack_

core::scoring::ScoreFunctionOP	scorefxn_minimize_

bool	repack_partner1_

bool	repack_partner2_

bool	design_partner1_

bool	design_partner2_

utility::vector1< bool >	min_rb_

utility::vector1< bool >	curr_min_sc_

utility::vector1< bool >	curr_min_bb_

utility::vector1< bool >	curr_min_rb_

bool	min_rb_set_

core::Real	interface_distance_cutoff_

bool	repack_non_ala_

bool	optimize_foldtree_

bool	automatic_repacking_definition_

core::pack::task::PackerTaskOP	task_

bool	use_preset_task_

utility::vector1< bool >	allowed_aas_

utility::vector1< core::Size >	prevent_repacking_

utility::vector1< core::Size >	restrict_to_repacking_

core::pack::task::TaskFactoryOP	task_factory_

bool	symmetry_

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel ( )

protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel	(	std::string const &	protocol,
		std::string const &	loop_start,
		std::string const &	loop_end,
		core::Size const	cycles,
		bool const	perturb,
		bool const	refine,
		bool const	hurry,
		core::scoring::ScoreFunctionOP	hires_score,
		core::scoring::ScoreFunctionOP	lores_score,
		protocols::loops::LoopsCOP	loops,
		core::fragment::FragSetOP	frag1,
		core::fragment::FragSetOP	frag3,
		core::fragment::FragSetOP	frag9
	)

References frag1_, frag3_, frag9_, hires_score_, loops_, and lores_score_.

protocols::protein_interface_design::movers::LoopRemodel::~LoopRemodel ( )

overridedefault

Member Function Documentation

void protocols::protein_interface_design::movers::LoopRemodel::apply ( core::pose::Pose & )

overridevirtual

a dummy apply so that instantiation of this baseclass would be possible.

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::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.

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::fresh_instance ( ) const

inlineoverridevirtual

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.

std::string protocols::protein_interface_design::movers::LoopRemodel::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References mover_name().

bool protocols::protein_interface_design::movers::LoopRemodel::hurry ( )

inline

References hurry_.

void protocols::protein_interface_design::movers::LoopRemodel::hurry ( bool const setting )

inline

References hurry_.

std::string protocols::protein_interface_design::movers::LoopRemodel::mover_name ( )

static

Referenced by get_name(), protocols::protein_interface_design::movers::LoopRemodelCreator::keyname(), and provide_xml_schema().

void protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

overridevirtual

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

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::calc_taskop_movers::DesignRepackMover.

References cycles_, protocols::calc_taskop_movers::DesignRepackMover::design(), core::pose::get_resnum_string(), core::scoring::get_score_function_name(), hires_score_, hurry_, loop_end_, loop_start_, loops_, lores_score_, core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), perturb_, protocol_, refine_, protocols::calc_taskop_movers::DesignRepackMover::task_factory(), and protocols::protein_interface_design::movers::TR().

bool protocols::protein_interface_design::movers::LoopRemodel::perturb ( )

inline

References perturb_.

Referenced by apply().

void protocols::protein_interface_design::movers::LoopRemodel::perturb ( bool const setting )

inline

References perturb_.

bool protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags	(	protocols::loops::LoopsCOP	loops,
		std::string const &	full_seqeuence,
		std::string const &	full_ss
	)