#include <RemodelDesignMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelDesignMover:

Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef core::kinematics::MoveMap	MoveMap

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::pack::task::PackerTaskOP	PackerTaskOP

typedef core::pack::task::PackerTask	PackerTask

typedef protocols::moves::MoverOP	MoverOP

typedef protocols::forge::remodel::RemodelData	RemodelData

typedef protocols::forge::remodel::RemodelWorkingSet	RemodelWorkingSet

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

Public Member Functions
	RemodelDesignMover ()

	RemodelDesignMover (RemodelData const &remodel_data, RemodelWorkingSet const &working_model, ScoreFunctionOP const &sfxn)
	value constructor More...

	~RemodelDesignMover () override
	default destructor More...

MoverOP	clone () const override
	clone this object More...

MoverOP	fresh_instance () const override
	create this type of object More...

core::pack::task::PackerTaskOP &	task ()
	packer task accessor More...

void	scorefunction (ScoreFunctionOP const &sfxn)
	score function setter More...

void	mode1_packertask (Pose &pose)
	these are split up for convenience reasons, so one can bypass blueprint setting if needed be More...

void	mode1_1_packertask (Pose &pose)
	these are split up for convenience reasons, so one can bypass blueprint setting if needed be More...

void	mode2_packertask (Pose &pose)

void	mode3_packertask (Pose &pose)

void	mode4_packertask (Pose &pose)

void	mode5_packertask (Pose &pose)

void	mode6_packertask (Pose &pose)

void	reduce_task (Pose &pose, PackerTaskOP &task, bool core, bool boundary, bool surface)

bool	check_state ()

void	set_state (std::string state_tag)

bool	find_disulfides_in_the_neighborhood (Pose &pose, utility::vector1< std::pair< Size, Size > > &disulf_partners, const core::Energy &match_rt_limit, const Size &rosetta_scripts_min_loop, const bool &rosetta_scripts_include_current_ds, const bool &rosetta_scripts_keep_current_ds, const bool &relax_bb_for_disulf, const bool &use_match_rt, const bool &use_disulf_fa_score, const core::Real disulf_fa_max)

void	make_disulfide (Pose &pose, utility::vector1< std::pair< Size, Size > > &disulf_partners, core::kinematics::MoveMapOP mm)

void	make_disulfide_fast (Pose &pose, utility::vector1< std::pair< Size, Size > > &disulf_partners)

void	apply (Pose &pose) override
	Apply method for Mover. Checks value of option -remodel::design::no_design -remodel::design::find_neighbors -remodel::design::design_neigbors -remodel::design::skip_partial. More...

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

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

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

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...

Private Types
typedef protocols::moves::Mover	Super

Private Member Functions
void	run_calculator (core::pose::Pose const &pose, std::string const &calculator, std::string const &calculation, utility::vector1_bool &residues)

Private Attributes
RemodelData	remodel_data_

RemodelWorkingSet	working_model_

PackerTaskOP	archived_starting_task_

utility::vector1< bool >	non_default_positions_

std::string	state_

ScoreFunctionOP	score_fxn_

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. 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...

Member Typedef Documentation

typedef core::kinematics::MoveMap protocols::forge::remodel::RemodelDesignMover::MoveMap

typedef protocols::moves::MoverOP protocols::forge::remodel::RemodelDesignMover::MoverOP

typedef core::pack::task::PackerTask protocols::forge::remodel::RemodelDesignMover::PackerTask

typedef core::pack::task::PackerTaskOP protocols::forge::remodel::RemodelDesignMover::PackerTaskOP

typedef core::pose::Pose protocols::forge::remodel::RemodelDesignMover::Pose

typedef core::Real protocols::forge::remodel::RemodelDesignMover::Real

typedef protocols::forge::remodel::RemodelData protocols::forge::remodel::RemodelDesignMover::RemodelData

typedef protocols::forge::remodel::RemodelWorkingSet protocols::forge::remodel::RemodelDesignMover::RemodelWorkingSet

typedef core::scoring::ScoreFunction protocols::forge::remodel::RemodelDesignMover::ScoreFunction

typedef core::scoring::ScoreFunctionOP protocols::forge::remodel::RemodelDesignMover::ScoreFunctionOP

typedef core::Size protocols::forge::remodel::RemodelDesignMover::Size

typedef protocols::moves::Mover protocols::forge::remodel::RemodelDesignMover::Super

private

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover ( )

protocols::forge::remodel::RemodelDesignMover::RemodelDesignMover	(	RemodelData const &	remodel_data,
		RemodelWorkingSet const &	working_model,
		ScoreFunctionOP const &	sfxn
	)

value constructor

References protocols::forge::remodel::RemodelData::blueprint, protocols::forge::remodel::RemodelWorkingSet::manager, protocols::forge::remodel::RemodelWorkingSet::task, protocols::forge::remodel::TR(), and protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions().

protocols::forge::remodel::RemodelDesignMover::~RemodelDesignMover ( )

overridedefault

default destructor

Member Function Documentation

void protocols::forge::remodel::RemodelDesignMover::apply ( Pose & pose )

overridevirtual

Apply method for Mover. Checks value of option -remodel::design::no_design -remodel::design::find_neighbors -remodel::design::design_neigbors -remodel::design::skip_partial.

Implements protocols::moves::Mover.

References core::conformation::find_neighbors(), core::pack::pack_rotamers(), and protocols::forge::remodel::TR().

Referenced by protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), and protocols::forge::remodel::RemodelMover::design_refine_seq_relax().

bool protocols::forge::remodel::RemodelDesignMover::check_state ( )

References protocols::forge::remodel::TR().

RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::clone ( ) const

overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

bool protocols::forge::remodel::RemodelDesignMover::find_disulfides_in_the_neighborhood	(	Pose &	pose,
		utility::vector1< std::pair< Size, Size > > &	disulf_partners,
		const core::Energy &	match_rt_limit,
		const Size &	rosetta_scripts_min_loop,
		const bool &	rosetta_scripts_include_current_ds,
		const bool &	rosetta_scripts_keep_current_ds,
		const bool &	relax_bb_for_disulf,
		const bool &	use_match_rt,
		const bool &	use_disulf_fa_score,
		const core::Real	disulf_fa_max
	)

References core::conformation::Residue::aa(), core::chemical::aa_gly, protocols::simple_moves::MutateResidue::apply(), protocols::forge::remodel::build_and_score_disulfide(), core::chemical::DISULFIDE, core::scoring::dslf_fa13, core::sequence::end, core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_bonded(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::forge::remodel::TR(), and core::conformation::Residue::xyz().

Referenced by protocols::forge::remodel::RemodelMover::apply().

RemodelDesignMover::MoverOP protocols::forge::remodel::RemodelDesignMover::fresh_instance ( ) const

overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::forge::remodel::RemodelDesignMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::forge::remodel::RemodelDesignMover::make_disulfide	(	Pose &	pose,
		utility::vector1< std::pair< Size, Size > > &	disulf_partners,
		core::kinematics::MoveMapOP	mm
	)

References core::pose::Pose::conformation(), core::conformation::form_disulfide(), core::util::rebuild_disulfide(), and protocols::forge::remodel::TR().

Referenced by protocols::forge::remodel::RemodelMover::apply().

void protocols::forge::remodel::RemodelDesignMover::make_disulfide_fast	(	Pose &	pose,
		utility::vector1< std::pair< Size, Size > > &	disulf_partners
	)

References core::pose::Pose::conformation(), core::conformation::form_disulfide(), and protocols::forge::remodel::TR().

Referenced by protocols::forge::remodel::RemodelMover::apply().

void protocols::forge::remodel::RemodelDesignMover::mode1_1_packertask ( Pose & pose )

these are split up for convenience reasons, so one can bypass blueprint setting if needed be

References protocols::forge::methods::remodel_generic_taskfactory(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode1_packertask ( Pose & pose )

these are split up for convenience reasons, so one can bypass blueprint setting if needed be

References protocols::forge::methods::remodel_generic_taskfactory(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode2_packertask ( Pose & pose )

References protocols::forge::methods::remodel_generic_taskfactory(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode3_packertask ( Pose & pose )

References protocols::forge::methods::remodel_generic_taskfactory(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode4_packertask ( Pose & pose )

References protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode5_packertask ( Pose & pose )

References core::pose::symmetry::extract_asymmetric_unit(), core::pose::symmetry::is_symmetric(), protocols::forge::methods::parse_resfile_string_with_no_lockdown(), protocols::forge::methods::remodel_generic_taskfactory(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::mode6_packertask ( Pose & pose )

References protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::reduce_task	(	Pose &	pose,
		PackerTaskOP &	task,
		bool	core,
		bool	boundary,
		bool	surface
	)

References protocols::forge::methods::calc_rsd_sasa(), core::pose::Pose::metric(), core::conformation::Residue::name(), protocols::sic_dock::neighbor_count(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::forge::remodel::TR().

void protocols::forge::remodel::RemodelDesignMover::run_calculator	(	core::pose::Pose const &	pose,
		std::string const &	calculator,
		std::string const &	calculation,
		utility::vector1_bool &	residues
	)

private

References core::pose::Pose::metric(), and core::pose::Pose::size().

void protocols::forge::remodel::RemodelDesignMover::scorefunction ( ScoreFunctionOP const & sfxn )

score function setter

Referenced by protocols::forge::remodel::RemodelMover::apply().

void protocols::forge::remodel::RemodelDesignMover::set_state ( std::string state_tag )

Referenced by protocols::forge::remodel::RemodelEnzdesCstModule::apply(), protocols::forge::remodel::RemodelMover::apply(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::forge::remodel::RemodelMover::design_refine_cart_relax(), and protocols::forge::remodel::RemodelMover::design_refine_seq_relax().

core::pack::task::PackerTaskOP & protocols::forge::remodel::RemodelDesignMover::task ( )

packer task accessor

Member Data Documentation

PackerTaskOP protocols::forge::remodel::RemodelDesignMover::archived_starting_task_

private

utility::vector1<bool> protocols::forge::remodel::RemodelDesignMover::non_default_positions_

private

RemodelData protocols::forge::remodel::RemodelDesignMover::remodel_data_

private

ScoreFunctionOP protocols::forge::remodel::RemodelDesignMover::score_fxn_

private

std::string protocols::forge::remodel::RemodelDesignMover::state_

private

RemodelWorkingSet protocols::forge::remodel::RemodelDesignMover::working_model_

private

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

src/protocols/forge/remodel/RemodelDesignMover.hh
src/protocols/forge/remodel/RemodelDesignMover.cc

Public Types

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation