General purpose Grafting class which: 1) superimposes the insert onto the scaffold using any overhang residues, 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the isertion will occur between. 3) Cycles of: a) SmallMover for sampling (Can be disabled)) b) CCDs both terminal ends of the scaffold using flexibility settings or movemap To close the graft. c) MinMover to help close the graft through chainbreak terms d) Closure check - will return if closed (Can be disabled) d) MonteCarlo Boltzmann criterion. More...

#include <CCDEndsGraftMover.hh>

Inheritance diagram for protocols::grafting::CCDEndsGraftMover:

[legend]

Public Member Functions
	CCDEndsGraftMover ()

	CCDEndsGraftMover (core::Size const start, core::Size const end, bool copy_pdbinfo=false)
	Start and end are the residue numbers you want your insert to go between. start->Insert<-end. More...

	CCDEndsGraftMover (core::Size const start, core::Size const end, core::pose::Pose const &piece, core::Size Nter_overhang=2, core::Size Cter_overhang=2, bool copy_pdbinfo=false)

void	apply (core::pose::Pose &pose) override
	Grafts the piece into the pose, uses CCD to close the connection. Insert does not change dihedral space, but DOES change cartesian space by default. Does not repack any sidechains. Deletes overhang and region between start and end if residues are present. More...

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...

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

bool	graft_is_closed () const

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

Public Member Functions inherited from protocols::grafting::AnchoredGraftMover
	AnchoredGraftMover ()

	AnchoredGraftMover (core::Size const start, core::Size const end, bool copy_pdbinfo=false)
	Start and end are the residue numbers you want your insert to go between. start->Insert<-end. More...

	AnchoredGraftMover (core::Size const start, core::Size const end, core::pose::Pose const &piece, core::Size Nter_overhang_length=0, core::Size Cter_overhang_length=0, bool copy_pdbinfo=false)

void	set_cycles (core::Size cycles)

void	set_defaults ()

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

void	stop_at_closure (bool stop_at_closure)
	Stop at closure of both ends? Default True. More...

bool	stop_at_closure ()
	Stop at closure of both ends? More...

void	final_repack (bool final_repack)
	Pack sidechains of flexible residues, insert and neighbors at end? Default True. More...

bool	final_repack ()
	Pack sidechains of flexible residues, insert and neighbors at end? More...

void	idealize_insert (bool idealize)

bool	idealize_insert () const

bool	graft_is_closed () const

virtual void	set_cen_scorefunction (core::scoring::ScoreFunctionCOP score)

virtual void	set_fa_scorefunction (core::scoring::ScoreFunctionCOP score)

void	set_mintype (std::string mintype)
	Sets the mintype for the MinMover. More...

void	set_skip_sampling (bool skip_sampling)
	Sets the mover to skip the small mover sampling step. More...

void	set_scaffold_flexibility (core::Size const Nter_scaffold_flexibility, core::Size const Cter_scaffold_flexibility)
	Sets scaffold flexiblity on either end of scaffold. More...

void	set_insert_flexibility (core::Size const Nter_insert_flexibility, core::Size const Cter_insert_flexibility)
	Sets insert flexibility on either end of insert. More...

virtual void	set_movemaps (core::kinematics::MoveMapCOP const scaffold_mm, core::kinematics::MoveMapCOP const insert_mm)
	Advanced way to set flexibility and residues used for CCD. More...

void	neighbor_dis (core::Real dis)
	Neighbor distance for any repacking of side-chains. More...

core::Real	neighbor_dis () const

core::Size	get_nterm_scaffold_flexibility ()

core::Size	get_cterm_scaffold_flexibility ()

core::Size	get_nterm_insert_flexibility ()

core::Size	get_cterm_insert_flexibility ()

core::Size	get_Cter_loop_end ()

protocols::loops::Loops const &	get_loops ()

Public Member Functions inherited from protocols::grafting::GraftMoverBase
	GraftMoverBase (std::string mover_name)
	Default constructor for RosettaScripts. More...

	GraftMoverBase (core::Size const start, core::Size const end, std::string mover_name)
	Start and end are the residue numbers you want your insert to go between. start->Insert<-end. More...

	GraftMoverBase (core::Size const start, core::Size const end, std::string mover_name, core::pose::Pose const &piece, core::Size Nter_overhang_length=0, core::Size Cter_overhang_length=0)

void	set_piece (core::pose::Pose const &piece, core::Size Nter_overhang_length, core::Size Cter_overhang_length)
	Sets the piece that will be inserted, and any overhang residues. More...

virtual void	set_insert_region (core::Size const start, core::Size const end)

void	copy_pdbinfo (bool copy_pdbinfo)
	Copy PDBInfo from the pose piece into pose during graft. If false(default), PDBInfo will be obsoleted. More...

bool	copy_pdbinfo () const

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

core::Size	start ()

core::Size	original_end ()

core::Size	end ()

core::Size	insertion_length ()

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::grafting::AnchoredGraftMover
static std::string	mover_name ()

static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_anchored_graft_mover (utility::tag::XMLSchemaDefinition &)

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
protocols::simple_moves::SmallMoverOP	setup_default_small_mover () const override

Private Attributes
bool	graft_is_closed_ = false

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::grafting::AnchoredGraftMover
void	setup_scorefunction ()

virtual void	set_default_fa_scorefunction ()

virtual void	set_default_cen_scorefunction ()
	Smooth version of Steven's original scorefunction used for grafting. More...

void	set_loops (protocols::loops::LoopsOP loops)

virtual void	setup_movemap_and_regions (core::pose::Pose &pose)
	sets up either the default movemap or a new combined movemap at apply time. Updates regions as needed. More...

virtual void	set_default_movemap ()
	Sets up the default movemap. More...

virtual void	set_regions_from_flexibility ()
	Sets up the regions at apply using insert variables and flexibility. More...

virtual void	set_regions_from_movemap (core::pose::Pose &pose)
	Sets up region variables from the class movemap for the combined pose. More...

void	set_test_control_mode (bool test_control_mode)
	TESTING ONLY Sets the protocol to 'randomize' the flexible residues before trying to graft. This is used to test the protocol by grafting a piece of a protein back onto itself and looking at RMSD. More...

virtual protocols::minimization_packing::MinMoverOP	setup_default_min_mover () const

void	movemap (core::kinematics::MoveMapOP movemap)

core::kinematics::MoveMapOP	movemap () const

core::scoring::ScoreFunctionOP	cen_scorefxn () const

core::scoring::ScoreFunctionOP	fa_scorefxn () const

void	use_default_movemap (bool use_default_movemap)

bool	use_default_movemap () const

bool	test_control_mode () const

core::Size	Nter_scaffold_flexibility () const

core::Size	Cter_scaffold_flexibility () const

core::Size	Nter_insert_flexibility () const

core::Size	Cter_insert_flexibility () const

core::Size	Nter_loop_start () const

core::Size	Nter_loop_end () const

core::Size	Cter_loop_start () const

core::Size	Cter_loop_end () const

std::string	mintype () const

core::Size	cycles () const

bool	skip_sampling () const

std::string const &	scaffold_start () const

std::string const &	scaffold_end () const

Protected Member Functions inherited from protocols::grafting::GraftMoverBase
core::pose::Pose	insert_piece (core::pose::Pose const &pose, core::pose::Pose &piece)
	Steven Lewis' insertion method from insert_pose_into_pose. Wrapper to his function, using variables defined in this baseclass. More...

void	original_end (core::Size original_end)
	Setters and accessors of private data. More...

void	insertion_length (core::Size insertion_length)

void	start (core::Size start)

void	end (core::Size end)

core::Size	Nter_overhang_length ()

void	Nter_overhang_length (core::Size overhang)

core::Size	Cter_overhang_length ()

void	Cter_overhang_length (core::Size overhang)

core::pose::PoseCOP	piece ()

void	piece (core::pose::PoseCOP piece)

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

General purpose Grafting class which: 1) superimposes the insert onto the scaffold using any overhang residues, 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the isertion will occur between. 3) Cycles of: a) SmallMover for sampling (Can be disabled)) b) CCDs both terminal ends of the scaffold using flexibility settings or movemap To close the graft. c) MinMover to help close the graft through chainbreak terms d) Closure check - will return if closed (Can be disabled) d) MonteCarlo Boltzmann criterion.

5) Repacks flexible residues and insert residues

Differs from AnchoredGraftMover in that the insert is held fixed in space after the superposition

example: mover = CCDEndsGraftMover(start, end, piece, cter_overhang, nter_overhang) mover.apply(pose)

Constructor & Destructor Documentation

◆ CCDEndsGraftMover() [1/3]

protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover ( )

References protocols::grafting::GraftMoverBase::Cter_overhang_length(), and protocols::grafting::GraftMoverBase::Nter_overhang_length().

◆ CCDEndsGraftMover() [2/3]

protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover	(	core::Size const	start,
		core::Size const	end,
		bool	copy_pdbinfo = `false`
	)

Start and end are the residue numbers you want your insert to go between. start->Insert<-end.

References protocols::grafting::GraftMoverBase::copy_pdbinfo(), protocols::grafting::GraftMoverBase::Cter_overhang_length(), and protocols::grafting::GraftMoverBase::Nter_overhang_length().

◆ CCDEndsGraftMover() [3/3]

protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover	(	core::Size const	start,
		core::Size const	end,
		core::pose::Pose const &	piece,
		core::Size	Nter_overhang = `2`,
		core::Size	Cter_overhang = `2`,
		bool	copy_pdbinfo = `false`
	)

References protocols::grafting::GraftMoverBase::copy_pdbinfo().

Member Function Documentation

◆ apply()

void protocols::grafting::CCDEndsGraftMover::apply ( core::pose::Pose & pose )

overridevirtual

Grafts the piece into the pose, uses CCD to close the connection. Insert does not change dihedral space, but DOES change cartesian space by default. Does not repack any sidechains. Deletes overhang and region between start and end if residues are present.

Reimplemented from protocols::grafting::AnchoredGraftMover.

Referenced by protocols::tcr::graft_cdr_to_fw().

◆ clone()

protocols::moves::MoverOP protocols::grafting::CCDEndsGraftMover::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::grafting::AnchoredGraftMover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::grafting::CCDEndsGraftMover::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::grafting::AnchoredGraftMover.