A protocols::moves::Mover that grafts a sequence onto the terminal helix of a helical-bundle monomer. Utilizes SimpleThreadingMover alongside. More...

#include <GraftSwitchMover.hh>

Inheritance diagram for protocols::switches::GraftSwitchMover:

[legend]

Public Types
typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

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
	GraftSwitchMover ()
	default constructor More...

	~GraftSwitchMover () override

	GraftSwitchMover (GraftSwitchMover const &other)

void	apply (Pose &pose) override
	Grafts, minimizes, and scores functional sequences grafted onto LOCKR type de novo protien switches. More...

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

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

virtual void	parse_score_function (TagCOP, basic::datacache::DataMap const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagCOP, basic::datacache::DataMap const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

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

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

void	task_factory (TaskFactoryCOP tf)
	Sets the TaskFactory to <tf> More...

void	score_function (ScoreFunctionCOP sf)
	Sets the ScoreFunction to <sf> More...

core::pose::PoseOP	get_additional_output () override
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	add_sequence (std::string seq)

void	set_start_graft (core::Size start)

void	set_end_graft (core::Size end)

void	set_important_residues (utility::vector1< core::Size > residue_list)

void	set_pack_neighbors (bool input)

void	set_pack_min (bool input)

std::list< utility::vector1 < core::Size > >	get_output_list ()

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...

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

static std::string	mover_name ()

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
core::Size	get_c_terminal_helix (core::pose::PoseOP const &pose)
	finds the residue number that starts the C-terminal helix More...

core::Size	get_n_terminal_helix (core::pose::PoseOP const &pose)
	finds the residue number that starts the C-terminal helix More...

bool	init_burial_filter (core::pose::Pose const &pose, core::Size index, core::Size thread_position)
	inital filter to determine if the key residues that need to be caged, are. More...

std::list< utility::vector1 < core::Size > >	all_threading_start_combinations ()
	returns all tuples of size n representing starting positions for each sequences More...

Private Attributes
ScoreFunctionCOP	scorefxn_

TaskFactoryCOP	task_factory_

core::Size	start_graft_

core::Size	end_graft_

bool	n_terminus_

bool	pack_neighbors_

bool	graft_loop_

bool	find_helix_

bool	seq_in_any_order_

bool	pack_min_

utility::vector1< std::string >	sequences_

utility::vector1 < utility::vector1< core::Size > >	important_residues_

std::set< core::Size >	threadable_residues_

core::Real	burial_cutoff_

std::list< utility::vector1 < core::Size > >	output_list_

core::pose::PoseOP	orig_pose_

core::select::residue_selector::ResidueSelectorOP	threadable_residues_selector_

Additional Inherited Members
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 protocols::moves::Mover that grafts a sequence onto the terminal helix of a helical-bundle monomer. Utilizes SimpleThreadingMover alongside.

Member Typedef Documentation

typedef core::pack::task::PackerTaskCOP protocols::switches::GraftSwitchMover::PackerTaskCOP

typedef core::scoring::ScoreFunctionCOP protocols::switches::GraftSwitchMover::ScoreFunctionCOP

typedef core::scoring::ScoreFunctionOP protocols::switches::GraftSwitchMover::ScoreFunctionOP

typedef core::pack::task::TaskFactoryCOP protocols::switches::GraftSwitchMover::TaskFactoryCOP

typedef core::pack::task::TaskFactoryOP protocols::switches::GraftSwitchMover::TaskFactoryOP

Constructor & Destructor Documentation

protocols::switches::GraftSwitchMover::GraftSwitchMover ( )

default constructor

protocols::switches::GraftSwitchMover::~GraftSwitchMover ( )

overridedefault

protocols::switches::GraftSwitchMover::GraftSwitchMover ( GraftSwitchMover const & other )

References burial_cutoff_, end_graft_, find_helix_, graft_loop_, important_residues_, n_terminus_, pack_min_, pack_neighbors_, scorefxn_, seq_in_any_order_, sequences_, start_graft_, task_factory_, threadable_residues_, and threadable_residues_selector_.

Member Function Documentation

void protocols::switches::GraftSwitchMover::add_sequence ( std::string seq )

inline

References sequences_.

std::list< utility::vector1< core::Size > > protocols::switches::GraftSwitchMover::all_threading_start_combinations ( )

private

returns all tuples of size n representing starting positions for each sequences

Creates a list of vectors (using a list for speed in deletion phase) where each vector is of length=number of sequences. Each number in the vector corresponds to a starting position for threading that will fit the corresponding sequence.

References protocols::mean_field::add(), seq_in_any_order_, sequences_, and threadable_residues_.

Referenced by apply().

void protocols::switches::GraftSwitchMover::apply ( Pose & pose )

overridevirtual

Grafts, minimizes, and scores functional sequences grafted onto LOCKR type de novo protien switches.

Implements protocols::moves::Mover.

References all_threading_start_combinations(), end_graft_, core::scoring::fa_intra_rep_xover4, core::scoring::fa_rep, protocols::moves::FAIL_RETRY, core::select::fill_neighbor_residues(), find_helix_, get_c_terminal_helix(), get_n_terminal_helix(), core::select::get_residue_set_from_subset(), core::scoring::get_score_function(), init_burial_filter(), protocols::mean_field::min(), protocols::moves::MS_SUCCESS, n_terminus_, orig_pose_, output_list_, pack_min_, pack_neighbors_, PACKER_ITER, scorefxn_, seq_in_any_order_, sequences_, protocols::moves::Mover::set_last_move_status(), core::pose::Pose::size(), start_graft_, task_factory_, threadable_residues_, and threadable_residues_selector_.

protocols::moves::MoverOP protocols::switches::GraftSwitchMover::clone ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::switches::GraftSwitchMover::fresh_instance ( ) const

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::pose::PoseOP protocols::switches::GraftSwitchMover::get_additional_output ( )

overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References core::select::fill_neighbor_residues(), protocols::mean_field::min(), orig_pose_, output_list_, pack_min_, pack_neighbors_, PACKER_ITER, scorefxn_, sequences_, and task_factory_.

core::Size protocols::switches::GraftSwitchMover::get_c_terminal_helix ( core::pose::PoseOP const & pose )

private

finds the residue number that starts the C-terminal helix

returns a single residue number as an integer

References core::scoring::dssp::Dssp::get_dssp_secstruct(), and graft_loop_.

Referenced by apply().

core::Size protocols::switches::GraftSwitchMover::get_n_terminal_helix ( core::pose::PoseOP const & pose )

private

finds the residue number that starts the C-terminal helix

returns a single residue number as an integer

References core::scoring::dssp::Dssp::get_dssp_secstruct(), and graft_loop_.

Referenced by apply().

std::string protocols::switches::GraftSwitchMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::list< utility::vector1<core::Size> > protocols::switches::GraftSwitchMover::get_output_list ( )

inline

References output_list_.

bool protocols::switches::GraftSwitchMover::init_burial_filter	(	core::pose::Pose const &	pose,
		core::Size	index,
		core::Size	thread_position
	)

private

inital filter to determine if the key residues that need to be caged, are.

uses NeighborsByDistanceCalculator as metric for burial

References burial_cutoff_, protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::pose::metrics::StructureDependentCalculator::get(), important_residues_, and core::pose::Pose::size().

Referenced by apply().

std::string protocols::switches::GraftSwitchMover::mover_name ( )

static

Referenced by get_name(), protocols::switches::GraftSwitchMoverCreator::keyname(), and provide_xml_schema().

void protocols::switches::GraftSwitchMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References burial_cutoff_, end_graft_, protocols::pack_daemon::error_message, find_helix_, core::select::residue_selector::get_residue_selector(), graft_loop_, important_residues_, n_terminus_, pack_min_, pack_neighbors_, parse_score_function(), parse_task_operations(), seq_in_any_order_, sequences_, start_graft_, and threadable_residues_selector_.

void protocols::switches::GraftSwitchMover::parse_score_function	(	TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

virtual

parse "scorefxn" XML option (can be employed virtually by derived Packing movers)

References core::scoring::parse_score_function(), and score_function().

Referenced by parse_my_tag().

void protocols::switches::GraftSwitchMover::parse_task_operations	(	TagCOP	tag,
		basic::datacache::DataMap const &	datamap
	)

virtual

parse "task_operations" XML option (can be employed virtually by derived Packing movers)

References core::pack::task::parse_task_operations(), and task_factory().

Referenced by parse_my_tag().

void protocols::switches::GraftSwitchMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::switches::GraftSwitchMoverCreator::provide_xml_schema().

void protocols::switches::GraftSwitchMover::score_function ( ScoreFunctionCOP sf )

Sets the ScoreFunction to <sf>

example(s): graftmover.score_function(scorefxn)

References scorefxn_.

Referenced by parse_score_function().

void protocols::switches::GraftSwitchMover::set_end_graft ( core::Size end )

inline

References core::sequence::end, and end_graft_.

void protocols::switches::GraftSwitchMover::set_important_residues ( utility::vector1< core::Size > residue_list )

inline

References important_residues_.

void protocols::switches::GraftSwitchMover::set_pack_min ( bool input )

inline

References pack_min_.

void protocols::switches::GraftSwitchMover::set_pack_neighbors ( bool input )

inline

References pack_neighbors_.

void protocols::switches::GraftSwitchMover::set_start_graft ( core::Size start )

inline

References protocols::loops::start, and start_graft_.

void protocols::switches::GraftSwitchMover::task_factory ( TaskFactoryCOP tf )

Sets the TaskFactory to <tf>

example(s): graftmover.task_factory(task_design)

References task_factory_.

Referenced by parse_task_operations().

Member Data Documentation

core::Real protocols::switches::GraftSwitchMover::burial_cutoff_

private

Referenced by GraftSwitchMover(), init_burial_filter(), and parse_my_tag().

core::Size protocols::switches::GraftSwitchMover::end_graft_

private

Referenced by apply(), GraftSwitchMover(), parse_my_tag(), and set_end_graft().

bool protocols::switches::GraftSwitchMover::find_helix_

private

Referenced by apply(), GraftSwitchMover(), and parse_my_tag().

bool protocols::switches::GraftSwitchMover::graft_loop_

private

Referenced by get_c_terminal_helix(), get_n_terminal_helix(), GraftSwitchMover(), and parse_my_tag().

utility::vector1< utility::vector1< core::Size > > protocols::switches::GraftSwitchMover::important_residues_

private

Referenced by GraftSwitchMover(), init_burial_filter(), parse_my_tag(), and set_important_residues().

bool protocols::switches::GraftSwitchMover::n_terminus_

private

Referenced by apply(), GraftSwitchMover(), and parse_my_tag().

core::pose::PoseOP protocols::switches::GraftSwitchMover::orig_pose_

private

Referenced by apply(), and get_additional_output().

std::list< utility::vector1<core::Size> > protocols::switches::GraftSwitchMover::output_list_

private

Referenced by apply(), get_additional_output(), and get_output_list().

bool protocols::switches::GraftSwitchMover::pack_min_

private

Referenced by apply(), get_additional_output(), GraftSwitchMover(), parse_my_tag(), and set_pack_min().

bool protocols::switches::GraftSwitchMover::pack_neighbors_

private

Referenced by apply(), get_additional_output(), GraftSwitchMover(), parse_my_tag(), and set_pack_neighbors().

ScoreFunctionCOP protocols::switches::GraftSwitchMover::scorefxn_

private

Referenced by apply(), get_additional_output(), GraftSwitchMover(), and score_function().

bool protocols::switches::GraftSwitchMover::seq_in_any_order_

private

Referenced by all_threading_start_combinations(), apply(), GraftSwitchMover(), and parse_my_tag().

utility::vector1< std::string > protocols::switches::GraftSwitchMover::sequences_

private

Referenced by add_sequence(), all_threading_start_combinations(), apply(), get_additional_output(), GraftSwitchMover(), and parse_my_tag().

core::Size protocols::switches::GraftSwitchMover::start_graft_

private

Referenced by apply(), GraftSwitchMover(), parse_my_tag(), and set_start_graft().

TaskFactoryCOP protocols::switches::GraftSwitchMover::task_factory_

private

Referenced by apply(), get_additional_output(), GraftSwitchMover(), and task_factory().

std::set< core::Size > protocols::switches::GraftSwitchMover::threadable_residues_

private

Referenced by all_threading_start_combinations(), apply(), and GraftSwitchMover().

core::select::residue_selector::ResidueSelectorOP protocols::switches::GraftSwitchMover::threadable_residues_selector_

private

Referenced by apply(), GraftSwitchMover(), and parse_my_tag().

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

src/protocols/switches/GraftSwitchMover.hh
src/protocols/switches/GraftSwitchMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation