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protocols::grafting::GraftMoverBase Class Reference

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

#include <GraftMoverBase.hh>

Inheritance diagram for protocols::grafting::GraftMoverBase:
Inheritance graph
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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 Stringsinfo ()
 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

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

Default constructor for RosettaScripts.

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.

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 set_piece().

Member Function Documentation

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().

bool protocols::grafting::GraftMoverBase::copy_pdbinfo ( ) const
inline
Size protocols::grafting::GraftMoverBase::Cter_overhang_length ( )
protected
void protocols::grafting::GraftMoverBase::Cter_overhang_length ( core::Size  overhang)
protected

References Cter_overhang_length_.

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

References end(), end_, and original_end_.

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

Return the name of the Mover.

Implements protocols::moves::Mover.

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_, core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::size(), start_, protocols::TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

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

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

References Nter_overhang_length_.

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

Setters and accessors of private data.

References original_end(), and original_end_.

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

References piece(), and piece_.

void protocols::grafting::GraftMoverBase::set_insert_region ( core::Size const  start,
core::Size const  end 
)
virtual
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(), piece_, and core::pose::Pose::size().

Referenced by GraftMoverBase().

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

References start(), and start_.

Member Data Documentation

bool protocols::grafting::GraftMoverBase::copy_pdbinfo_
private

Referenced by copy_pdbinfo(), and insert_piece().

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().

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().

core::Size protocols::grafting::GraftMoverBase::insertion_length_
private
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().

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().

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().

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: