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>

Public Member Functions
	CCDEndsGraftMover ()

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

	CCDEndsGraftMover (CCDEndsGraftMover const &src)

virtual	~CCDEndsGraftMover ()

virtual void	apply (core::pose::Pose &pose)
	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...

virtual void	set_movemaps (MoveMapCOP const scaffold_mm, MoveMapCOP const insert_mm)
	Advanced way to set flexibility. More...

std::string	get_name ()

protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

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

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

	AnchoredGraftMover (AnchoredGraftMover const &src)

virtual	~AnchoredGraftMover ()

void	set_cycles (Size cycles)

virtual void	set_defaults ()

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, moves::Movers_map const &movers, Pose const &pose)
	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

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...

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

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

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

core::Real	neighbor_dis () const

Size	get_nterm_scaffold_flexibility ()

Size	get_cterm_scaffold_flexibility ()

Size	get_Cter_loop_end ()

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

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

	GraftMoverBase (GraftMoverBase const &src)
	copy ctor More...

virtual	~GraftMoverBase ()

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

virtual void	set_insert_region (Size const start, 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

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

Size	start ()

Size	original_end ()

Size	end ()

Size	insertion_length ()

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

std::string	get_type () const

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...

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	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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
virtual SmallMoverOP	setup_default_small_mover ()

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

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::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...

virtual void	setup_movemap_and_regions (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 (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 MinMoverOP	setup_default_min_mover ()

void	movemap (MoveMapOP movemap)

MoveMapOP	movemap () const

void	scaffold_movemap (MoveMapCOP scaffold_movemap)

MoveMapCOP	scaffold_movemap () const

void	insert_movemap (MoveMapCOP insert_movemap)

MoveMapCOP	insert_movemap () const

ScoreFunctionOP	cen_scorefxn () const

ScoreFunctionOP	fa_scorefxn () const

void	use_default_movemap (bool use_default_movemap)

bool	use_default_movemap () const

bool	test_control_mode () const

Size	Nter_scaffold_flexibility () const

Size	Cter_scaffold_flexibility () const

Size	Nter_insert_flexibility () const

Size	Cter_insert_flexibility () const

Size	Nter_loop_start () const

Size	Nter_loop_end () const

Size	Cter_loop_start () const

Size	Cter_loop_end () const

std::string	mintype () const

Size	cycles () const

bool	skip_sampling () const

TagCOP	tag () const

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

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

void	insertion_length (Size insertion_length)

void	start (core::Size start)

void	end (core::Size end)

Size	Nter_overhang_length ()

void	Nter_overhang_length (core::Size overhang)

Size	Cter_overhang_length ()

void	Cter_overhang_length (core::Size overhang)

PoseOP	piece ()

void	piece (PoseOP 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

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

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

Referenced by clone(), and fresh_instance().

protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover	(	Size const	start,
		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().

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

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

protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover ( CCDEndsGraftMover const & src )

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

virtual

Member Function Documentation

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

virtual

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::antibody::design::AntibodyGraftDesignMover::graft_cdr().

protocols::moves::MoverOP protocols::grafting::CCDEndsGraftMover::clone ( ) const

virtual

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.

References CCDEndsGraftMover().

protocols::moves::MoverOP protocols::grafting::CCDEndsGraftMover::fresh_instance ( ) const

virtual

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.

References CCDEndsGraftMover().

std::string protocols::grafting::CCDEndsGraftMover::get_name ( )

void protocols::grafting::CCDEndsGraftMover::set_movemaps	(	MoveMapCOP const	scaffold_mm,
		MoveMapCOP const	insert_mm
	)

virtual

Advanced way to set flexibility.

Will combine the movemaps for apply, and renumber everything. Flexible residues in multiple chains not recommended. One arm Will go from first flexible N terminal residue to after start_+any contiguous residues on in the movemap from there. Opposite for Cter side. This way any loop regions within a chain on either side can be used as flexible residues to close full graft.

Note: Will disregard flexibility settings, as the movemaps will be used as primary way to define flexibility. May want to consider turning off the sampling step when passing crazy movemaps.

Reimplemented from protocols::grafting::AnchoredGraftMover.

References protocols::grafting::AnchoredGraftMover::insert_movemap(), and protocols::grafting::AnchoredGraftMover::scaffold_movemap().

SmallMoverOP protocols::grafting::CCDEndsGraftMover::setup_default_small_mover ( )

privatevirtual

Reimplemented from protocols::grafting::AnchoredGraftMover.

References core::id::BB, and protocols::grafting::AnchoredGraftMover::movemap().

Referenced by apply().

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

src/protocols/grafting/CCDEndsGraftMover.hh
src/protocols/grafting/CCDEndsGraftMover.cc

Public Member Functions

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation