Fairly abstract base class for GraftMover classes. More...

#include <GraftMoverBase.hh>

Inheritance diagram for protocols::grafting::GraftMoverBase:

[legend]

Public Member Functions
	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	apply (Pose &)=0
	Main Method. 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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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)
	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 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...

Protected Member Functions
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...

Private Attributes
core::pose::PoseCOP	piece_ = nullptr
	COP of the set pose. This is to have better support of the SavePoseMover in RosettaScripts. More...

core::Size	start_
	Residue insertion will start from. More...

core::Size	end_
	Residue insertion will end before here. Updates after insertion. More...

core::Size	original_end_
	some functions need to only work on the original numbers. (combine movemaps) More...

core::Size	insertion_length_

core::Size	Nter_overhang_length_
	Number of overhang residues on N terminus. Updates on delete_overhang_residues. More...

core::Size	Cter_overhang_length_
	Number of overhang residues on C terminus. Updates on delete_overhang_residues. More...

bool	copy_pdbinfo_

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

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...

Detailed Description

Fairly abstract base class for GraftMover classes.

Constructor & Destructor Documentation

◆ GraftMoverBase() [1/3]

protocols::grafting::GraftMoverBase::GraftMoverBase ( std::string mover_name )

Default constructor for RosettaScripts.

◆ GraftMoverBase() [2/3]

protocols::grafting::GraftMoverBase::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.

◆ GraftMoverBase() [3/3]

protocols::grafting::GraftMoverBase::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`
	)

References Cter_overhang_length(), Nter_overhang_length(), piece(), and set_piece().

Member Function Documentation

◆ copy_pdbinfo() [1/2]

bool protocols::grafting::GraftMoverBase::copy_pdbinfo ( ) const

inline

References copy_pdbinfo_.

Referenced by protocols::grafting::AnchoredGraftMover::AnchoredGraftMover(), protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover(), copy_pdbinfo(), and protocols::grafting::AnchoredGraftMover::parse_my_tag().

◆ copy_pdbinfo() [2/2]

void protocols::grafting::GraftMoverBase::copy_pdbinfo ( bool copy_pdbinfo )

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

References copy_pdbinfo(), and copy_pdbinfo_.

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

◆ Cter_overhang_length() [1/2]

Size protocols::grafting::GraftMoverBase::Cter_overhang_length ( )

protected

References Cter_overhang_length_.

Referenced by protocols::grafting::AnchoredGraftMover::AnchoredGraftMover(), protocols::grafting::CCDEndsGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover(), GraftMoverBase(), protocols::grafting::AnchoredGraftMover::parse_my_tag(), and set_piece().

◆ Cter_overhang_length() [2/2]

void protocols::grafting::GraftMoverBase::Cter_overhang_length ( core::Size overhang )

protected

References Cter_overhang_length_.

◆ end() [1/2]

Size protocols::grafting::GraftMoverBase::end ( )

References end_.

Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), end(), set_insert_region(), and protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions().

◆ end() [2/2]

void protocols::grafting::GraftMoverBase::end ( core::Size end )

protected

References end(), end_, and original_end_.

◆ get_name()

std::string protocols::grafting::GraftMoverBase::get_name ( ) const

overridevirtual

Return the name of the Mover.

Implements protocols::moves::Mover.

◆ insert_piece()

Pose protocols::grafting::GraftMoverBase::insert_piece	(	core::pose::Pose const &	pose,
		core::pose::Pose &	piece
	)

protected

Steven Lewis' insertion method from insert_pose_into_pose. Wrapper to his function, using variables defined in this baseclass.

Need to set piece to use. Deletes any overhang in piece. Deletes any region from start to end in pose. Updates end_. Recommended use is within apply method.

References copy_pdbinfo_, Cter_overhang_length_, protocols::grafting::delete_overhang_residues(), protocols::grafting::delete_region(), end_, protocols::grafting::insert_pose_into_pose(), insertion_length_, core::chemical::LOWER_TERMINUS_VARIANT, Nter_overhang_length_, piece(), core::pose::remove_variant_type_from_pose_residue(), start_, protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by protocols::grafting::AnchoredGraftMover::apply(), and protocols::grafting::CCDEndsGraftMover::apply().

◆ insertion_length() [1/2]

Size protocols::grafting::GraftMoverBase::insertion_length ( )

References insertion_length_.

Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), insertion_length(), protocols::grafting::AnchoredGraftMover::set_regions_from_flexibility(), protocols::grafting::AnchoredGraftMover::set_regions_from_movemap(), and protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions().

◆ insertion_length() [2/2]

void protocols::grafting::GraftMoverBase::insertion_length ( core::Size insertion_length )

protected

References insertion_length(), and insertion_length_.

◆ Nter_overhang_length() [1/2]

Size protocols::grafting::GraftMoverBase::Nter_overhang_length ( )

protected

References Nter_overhang_length_.

Referenced by protocols::grafting::AnchoredGraftMover::AnchoredGraftMover(), protocols::grafting::CCDEndsGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::CCDEndsGraftMover(), GraftMoverBase(), protocols::grafting::AnchoredGraftMover::parse_my_tag(), and set_piece().

◆ Nter_overhang_length() [2/2]

void protocols::grafting::GraftMoverBase::Nter_overhang_length ( core::Size overhang )

protected

References Nter_overhang_length_.

◆ original_end() [1/2]

Size protocols::grafting::GraftMoverBase::original_end ( )

References original_end_.

Referenced by protocols::grafting::CCDEndsGraftMover::apply(), original_end(), and protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions().

◆ original_end() [2/2]

void protocols::grafting::GraftMoverBase::original_end ( core::Size original_end )

protected

Setters and accessors of private data.

References original_end(), and original_end_.

◆ piece() [1/2]

PoseCOP protocols::grafting::GraftMoverBase::piece ( )

protected

References piece_.

Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), GraftMoverBase(), insert_piece(), protocols::grafting::AnchoredGraftMover::parse_my_tag(), piece(), and set_piece().

◆ piece() [2/2]

void protocols::grafting::GraftMoverBase::piece ( core::pose::PoseCOP piece )

protected

References piece(), and piece_.

◆ set_insert_region()

void protocols::grafting::GraftMoverBase::set_insert_region	(	core::Size const	start,
		core::Size const	end
	)

virtual

References end(), end_, original_end_, start(), and start_.

Referenced by protocols::grafting::AnchoredGraftMover::apply(), and protocols::grafting::CCDEndsGraftMover::apply().

◆ set_piece()

void protocols::grafting::GraftMoverBase::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.

Overhang residues are residues not being inserted into the scaffold. These residues are deleted before insertion and are used by classes usually for superposition or Initial orientation of the insert relative to the scaffold.

References Cter_overhang_length(), Cter_overhang_length_, insertion_length_, Nter_overhang_length(), Nter_overhang_length_, piece(), and piece_.

Referenced by GraftMoverBase().

◆ start() [1/2]

Size protocols::grafting::GraftMoverBase::start ( )

References start_.

Referenced by protocols::grafting::AnchoredGraftMover::apply(), protocols::grafting::CCDEndsGraftMover::apply(), set_insert_region(), protocols::grafting::AnchoredGraftMover::set_regions_from_flexibility(), protocols::grafting::AnchoredGraftMover::set_regions_from_movemap(), and start().

◆ start() [2/2]

void protocols::grafting::GraftMoverBase::start ( core::Size start )

protected

References start(), and start_.

Member Data Documentation

◆ copy_pdbinfo_

bool protocols::grafting::GraftMoverBase::copy_pdbinfo_

private

Referenced by copy_pdbinfo(), and insert_piece().

◆ Cter_overhang_length_

core::Size protocols::grafting::GraftMoverBase::Cter_overhang_length_

private

Number of overhang residues on C terminus. Updates on delete_overhang_residues.

Referenced by Cter_overhang_length(), insert_piece(), and set_piece().

◆ end_

core::Size protocols::grafting::GraftMoverBase::end_

private

Residue insertion will end before here. Updates after insertion.

Referenced by end(), insert_piece(), and set_insert_region().

◆ insertion_length_

core::Size protocols::grafting::GraftMoverBase::insertion_length_

private

Referenced by insert_piece(), insertion_length(), and set_piece().

◆ Nter_overhang_length_

core::Size protocols::grafting::GraftMoverBase::Nter_overhang_length_

private

Number of overhang residues on N terminus. Updates on delete_overhang_residues.

Referenced by insert_piece(), Nter_overhang_length(), and set_piece().

◆ original_end_

core::Size protocols::grafting::GraftMoverBase::original_end_

private

some functions need to only work on the original numbers. (combine movemaps)

Referenced by end(), original_end(), and set_insert_region().

◆ piece_

core::pose::PoseCOP protocols::grafting::GraftMoverBase::piece_ = nullptr

private

COP of the set pose. This is to have better support of the SavePoseMover in RosettaScripts.

Referenced by piece(), and set_piece().

◆ start_

core::Size protocols::grafting::GraftMoverBase::start_

private

Residue insertion will start from.

Referenced by insert_piece(), set_insert_region(), and start().

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

src/protocols/grafting/GraftMoverBase.hh
src/protocols/grafting/GraftMoverBase.cc

Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ GraftMoverBase() [1/3]

◆ GraftMoverBase() [2/3]

◆ GraftMoverBase() [3/3]

Member Function Documentation

◆ copy_pdbinfo() [1/2]

◆ copy_pdbinfo() [2/2]

◆ Cter_overhang_length() [1/2]

◆ Cter_overhang_length() [2/2]

◆ end() [1/2]

◆ end() [2/2]

◆ get_name()

◆ insert_piece()

◆ insertion_length() [1/2]

◆ insertion_length() [2/2]

◆ Nter_overhang_length() [1/2]

◆ Nter_overhang_length() [2/2]

◆ original_end() [1/2]

◆ original_end() [2/2]

◆ piece() [1/2]

◆ piece() [2/2]

◆ set_insert_region()

◆ set_piece()

◆ start() [1/2]

◆ start() [2/2]

Member Data Documentation

◆ copy_pdbinfo_

◆ Cter_overhang_length_

◆ end_

◆ insertion_length_

◆ Nter_overhang_length_

◆ original_end_

◆ piece_

◆ start_