Delete a region of a pose. Mover Wrapper to grafting utility function. More...

#include <DeleteRegionMover.hh>

Inheritance diagram for protocols::grafting::simple_movers::DeleteRegionMover:

[legend]

Public Member Functions
	DeleteRegionMover ()

	DeleteRegionMover (core::Size const res_start, core::Size const res_end)

	DeleteRegionMover (DeleteRegionMover const &src)

	~DeleteRegionMover () override

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

void	region (std::string const &res_start, std::string const &res_end)
	Set the region of the pose where deletion will occur. More...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Sets the residue selector. More...

void	set_rechain (bool rechain)

void	set_add_terminal_types_on_rechain (bool add)

void	set_add_jump_on_rechain (bool add)

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 tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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

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...

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::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
void	add_terminus_variants (core::pose::Pose &pose, core::Size const resid) const
	Adds terminal variants to residues resid and resid-1. More...

void	add_cutpoint_variants (core::pose::Pose &pose, core::Size const resid) const
	Adds cutpoint variants to residues resid and resid-1. More...

Private Attributes
core::select::residue_selector::ResidueSelectorCOP	selector_

core::Size	nter_overhang_

core::Size	cter_overhang_

bool	rechain_

bool	add_terminal_types_on_rechain_

bool	add_jump_on_rechain_

bool	detect_disulfides_ = true

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 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...

Detailed Description

Delete a region of a pose. Mover Wrapper to grafting utility function.

Constructor & Destructor Documentation

◆ DeleteRegionMover() [1/3]

protocols::grafting::simple_movers::DeleteRegionMover::DeleteRegionMover ( )

◆ DeleteRegionMover() [2/3]

protocols::grafting::simple_movers::DeleteRegionMover::DeleteRegionMover	(	core::Size const	res_start,
		core::Size const	res_end
	)

References core::sequence::end, region(), and protocols::loops::start.

◆ DeleteRegionMover() [3/3]

protocols::grafting::simple_movers::DeleteRegionMover::DeleteRegionMover ( DeleteRegionMover const & src )

References selector_.

◆ ~DeleteRegionMover()

protocols::grafting::simple_movers::DeleteRegionMover::~DeleteRegionMover ( )

overridedefault

Member Function Documentation

◆ add_cutpoint_variants()

void protocols::grafting::simple_movers::DeleteRegionMover::add_cutpoint_variants	(	core::pose::Pose &	pose,
		core::Size const	resid
	)		const

private

Adds cutpoint variants to residues resid and resid-1.

Adds terminal variants to residues resid and resid-1.

Parameters

[in,out]	pose	Pose to be modified
[in]	resid	Residue number for the residue that would have the lower cutpoint variant

Residue resid-1 will have upper_cutpoint variant, and residue resid will have lower_cutpoit variant

Parameters

[in,out]	pose	Pose to be modified
[in]	resid	Residue number for the residue that would have the lower terminus variant

Residue resid-1 will have upper_terminus variant, and residue resid will have lower_terminus variant

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, and core::pose::Pose::size().

Referenced by apply().

◆ add_terminus_variants()

void protocols::grafting::simple_movers::DeleteRegionMover::add_terminus_variants	(	core::pose::Pose &	pose,
		core::Size const	resid
	)		const

private

Adds terminal variants to residues resid and resid-1.

Parameters

[in,out]	pose	Pose to be modified
[in]	resid	Residue number for the residue that would have the lower terminus variant

Residue resid-1 will have upper_terminus variant, and residue resid will have lower_terminus variant

References core::pose::add_lower_terminus_type_to_pose_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), and core::pose::Pose::size().

Referenced by apply().

◆ apply()

void protocols::grafting::simple_movers::DeleteRegionMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References add_cutpoint_variants(), add_jump_on_rechain_, add_terminal_types_on_rechain_, add_terminus_variants(), core::conformation::Conformation::chain_endings(), core::conformation::Conformation::chains_from_termini(), core::pose::Pose::conformation(), cter_overhang_, protocols::grafting::delete_region(), detect_disulfides_, core::pose::Pose::fold_tree(), core::conformation::Conformation::insert_chain_ending(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::new_jump(), nter_overhang_, protocols::sic_dock::range(), rechain_, selector_, and core::pose::Pose::size().

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::compute(), protocols::denovo_design::components::Segment::delete_residue(), protocols::denovo_design::movers::AlignResiduesMover::delete_residues(), and protocols::fold_from_loops::movers::SplitAndMixPoseMover::split_pose().

◆ clone()

protocols::moves::MoverOP protocols::grafting::simple_movers::DeleteRegionMover::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.

◆ fresh_instance()

protocols::moves::MoverOP protocols::grafting::simple_movers::DeleteRegionMover::fresh_instance ( ) const

overridevirtual

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.

◆ get_name()

std::string protocols::grafting::simple_movers::DeleteRegionMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ mover_name()

std::string protocols::grafting::simple_movers::DeleteRegionMover::mover_name ( )

static

Referenced by get_name(), protocols::grafting::simple_movers::DeleteRegionMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::grafting::simple_movers::DeleteRegionMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_jump_on_rechain_, add_terminal_types_on_rechain_, cter_overhang_, detect_disulfides_, core::sequence::end, nter_overhang_, core::select::residue_selector::parse_residue_selector(), rechain_, region(), selector_, and protocols::loops::start.

◆ provide_citation_info()

void protocols::grafting::simple_movers::DeleteRegionMover::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References selector_.

◆ provide_xml_schema()

void protocols::grafting::simple_movers::DeleteRegionMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::select::residue_selector::attributes_for_parse_residue_selector(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::grafting::simple_movers::DeleteRegionMoverCreator::provide_xml_schema().

◆ region()

void protocols::grafting::simple_movers::DeleteRegionMover::region	(	std::string const &	res_start,
		std::string const &	res_end
	)

Set the region of the pose where deletion will occur.

References selector_.

Referenced by DeleteRegionMover(), and parse_my_tag().

◆ set_add_jump_on_rechain()

void protocols::grafting::simple_movers::DeleteRegionMover::set_add_jump_on_rechain ( bool add )

inline

References protocols::mean_field::add(), and add_jump_on_rechain_.

◆ set_add_terminal_types_on_rechain()

void protocols::grafting::simple_movers::DeleteRegionMover::set_add_terminal_types_on_rechain ( bool add )

inline

References protocols::mean_field::add(), and add_terminal_types_on_rechain_.

◆ set_rechain()

void protocols::grafting::simple_movers::DeleteRegionMover::set_rechain ( bool rechain )

inline

References rechain_.

◆ set_residue_selector()

void protocols::grafting::simple_movers::DeleteRegionMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Sets the residue selector.

References selector_.

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), protocols::fold_from_loops::filters::RmsdFromResidueSelectorFilter::compute(), protocols::fold_from_loops::filters::ScorePoseSegmentFromResidueSelectorFilter::compute(), protocols::denovo_design::movers::AlignResiduesMover::delete_residues(), and protocols::fold_from_loops::movers::SplitAndMixPoseMover::split_pose().

Member Data Documentation

◆ add_jump_on_rechain_

bool protocols::grafting::simple_movers::DeleteRegionMover::add_jump_on_rechain_

private

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

◆ add_terminal_types_on_rechain_

bool protocols::grafting::simple_movers::DeleteRegionMover::add_terminal_types_on_rechain_

private

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

◆ cter_overhang_

core::Size protocols::grafting::simple_movers::DeleteRegionMover::cter_overhang_

private

Referenced by apply(), and parse_my_tag().

◆ detect_disulfides_

bool protocols::grafting::simple_movers::DeleteRegionMover::detect_disulfides_ = true

private

Referenced by apply(), and parse_my_tag().

◆ nter_overhang_

core::Size protocols::grafting::simple_movers::DeleteRegionMover::nter_overhang_

private

Referenced by apply(), and parse_my_tag().

◆ rechain_

bool protocols::grafting::simple_movers::DeleteRegionMover::rechain_

private

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

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::grafting::simple_movers::DeleteRegionMover::selector_

private

Referenced by apply(), DeleteRegionMover(), parse_my_tag(), provide_citation_info(), region(), and set_residue_selector().

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

src/protocols/grafting/simple_movers/DeleteRegionMover.hh
src/protocols/grafting/simple_movers/DeleteRegionMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DeleteRegionMover() [1/3]

◆ DeleteRegionMover() [2/3]

◆ DeleteRegionMover() [3/3]

◆ ~DeleteRegionMover()

Member Function Documentation

◆ add_cutpoint_variants()

◆ add_terminus_variants()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ region()

◆ set_add_jump_on_rechain()

◆ set_add_terminal_types_on_rechain()

◆ set_rechain()

◆ set_residue_selector()

Member Data Documentation

◆ add_jump_on_rechain_

◆ add_terminal_types_on_rechain_

◆ cter_overhang_

◆ detect_disulfides_

◆ nter_overhang_

◆ rechain_

◆ selector_