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protocols::grafting::GraftMoverBase Class Reference

Base class for GraftMovers. Created for simplicity and control for C++ programmer, as well as PyRosetta user. More...

#include <GraftMoverBase.hh>

Inheritance diagram for protocols::grafting::GraftMoverBase:
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Collaboration diagram for protocols::grafting::GraftMoverBase:
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Public Member Functions

 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...
 
virtual ~GraftMoverBase ()
 copy ctor More...
 
virtual void set_piece (Pose &piece, Size Nter_overhang, Size Cter_overhang)
 Sets the piece that will be inserted, and any overhang residues. More...
 
virtual void set_insert_region (Size const start, Size const end)
 Set the region if changed since construction. More...
 
virtual void set_cen_scorefunction (core::scoring::ScoreFunctionOP score)
 
virtual void set_fa_scorefunction (core::scoring::ScoreFunctionOP score)
 
virtual void set_default_fa_scorefunction ()
 Grabs the scorefunction from command line options. More...
 
virtual void set_default_cen_scorefunction ()
 Grabs the cen scorefunction set in command line loops option group. More...
 
void superimpose_overhangs_heavy (Pose const &pose, bool ca_only, bool silence_rms)
 uses rms_util to superimpose piece onto pose. Not run during apply for added control to user. More...
 
virtual std::string get_name () const
 Return the name of the Mover. More...
 
- 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)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
virtual void apply (Pose &)=0
 
std::string const & type () const
 
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)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Member Functions

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...
 
virtual core::Real perturb_backbone_for_test (Pose &pose, MoveMapOP mm)
 Uses a small mover at high KT to perturb residues in the movemap for testing. More...
 
MoveMapOP combine_movemaps (MoveMap const &scaffold_mm, MoveMap const &insert_mm)
 combines the two main movemaps to use after the insertion. More...
 
void delete_overhang_residues ()
 deletes overhang residues of the pose piece set. Recommended use is within apply method More...
 
void set_overhang (Size Nter_overhang, Size Cter_overhang)
 Set overhang residues. 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...
 
virtual void setup_single_loop_single_arm_remodeling_foldtree (Pose &pose, Size const Nter_loop_start, Size const Cter_loop_end, bool loop_modeling=false)
 ****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is Cter_loop_end-1 More...
 
virtual void setup_single_loop_double_arm_remodeling_foldtree (Pose &pose, Size const Nter_loop_start, Size const Cter_loop_end, bool loop_modeling=false)
 ****Nter_loop_start-—>Piece | <-—Nter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is end_-1 More...
 
- 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...
 

Protected Attributes

Pose piece_
 
Size start_
 Residue insertion will start from. More...
 
Size end_
 Residue insertion will end before here. Updates after insertion. More...
 
Size original_end_
 some functions need to only work on the original numbers. (combine movemaps) More...
 
Size insertion_length_
 
core::scoring::ScoreFunctionOP cen_scorefxn_
 
core::scoring::ScoreFunctionOP fa_scorefxn_
 
Size Nter_overhang_
 Number of overhang residues on N terminus. Updates on delete_overhang_residues. More...
 
Size Cter_overhang_
 Number of overhang residues on C terminus. Updates on delete_overhang_residues. More...
 
MoveMapOP movemap_
 
MoveMapOP scaffold_movemap_
 
MoveMapOP insert_movemap_
 
bool use_default_movemap_
 
Size Nter_scaffold_flexibility_
 
Size Nter_insert_flexibility_
 
Size Nter_loop_start_
 
Size Nter_loop_end_
 
Size Cter_scaffold_flexibility_
 
Size Cter_insert_flexibility_
 
Size Cter_loop_start_
 
Size Cter_loop_end_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 

Detailed Description

Base class for GraftMovers. Created for simplicity and control for C++ programmer, as well as PyRosetta user.

Feel free to add.

Constructor & Destructor Documentation

protocols::grafting::GraftMoverBase::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.

protocols::grafting::GraftMoverBase::~GraftMoverBase ( )
virtual

copy ctor

Member Function Documentation

MoveMapOP protocols::grafting::GraftMoverBase::combine_movemaps ( MoveMap const &  scaffold_mm,
MoveMap const &  insert_mm 
)
protected

combines the two main movemaps to use after the insertion.

Pose piece must be set.

References insertion_length_, core::kinematics::MoveMap::movemap_torsion_id_begin(), core::kinematics::MoveMap::movemap_torsion_id_end(), original_end_, start_, and protocols::TR().

Referenced by setup_movemap_and_regions().

void protocols::grafting::GraftMoverBase::delete_overhang_residues ( )
protected

deletes overhang residues of the pose piece set. Recommended use is within apply method

References core::pose::Pose::conformation(), Cter_overhang_, core::conformation::Conformation::delete_residue_slow(), Nter_overhang_, piece_, set_overhang(), and core::pose::Pose::total_residue().

Referenced by insert_piece().

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

Return the name of the Mover.

Implements protocols::moves::Mover.

Pose protocols::grafting::GraftMoverBase::insert_piece ( Pose const &  pose)
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 delete_overhang_residues(), protocols::grafting::delete_region(), end_, protocols::grafting::insert_pose_into_pose(), insertion_length_, core::chemical::LOWER_TERMINUS, piece_, core::pose::remove_variant_type_from_pose_residue(), start_, protocols::TR(), and core::chemical::UPPER_TERMINUS.

Referenced by protocols::grafting::AnchoredGraftMover::apply().

core::Real protocols::grafting::GraftMoverBase::perturb_backbone_for_test ( Pose pose,
MoveMapOP  mm 
)
protectedvirtual
void protocols::grafting::GraftMoverBase::set_cen_scorefunction ( core::scoring::ScoreFunctionOP  score)
virtual
void protocols::grafting::GraftMoverBase::set_default_cen_scorefunction ( )
virtual

Grabs the cen scorefunction set in command line loops option group.

Reimplemented in protocols::grafting::AnchoredGraftMover.

References cen_scorefxn_, and protocols::loops::get_cen_scorefxn().

void protocols::grafting::GraftMoverBase::set_default_fa_scorefunction ( )
virtual

Grabs the scorefunction from command line options.

References fa_scorefxn_, and core::scoring::getScoreFunction().

void protocols::grafting::GraftMoverBase::set_default_movemap ( )
protectedvirtual
void protocols::grafting::GraftMoverBase::set_fa_scorefunction ( core::scoring::ScoreFunctionOP  score)
virtual

References fa_scorefxn_.

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

Set the region if changed since construction.

References core::sequence::end, end_, original_end_, protocols::loops::start, and start_.

void protocols::grafting::GraftMoverBase::set_overhang ( Size  Nter_overhang,
Size  Cter_overhang 
)
protected

Set overhang residues.

References Cter_overhang_, and Nter_overhang_.

Referenced by delete_overhang_residues().

void protocols::grafting::GraftMoverBase::set_piece ( Pose piece,
Size  Nter_overhang,
Size  Cter_overhang 
)
virtual

Sets the piece that will be inserted, and any overhang residues.

Overhang will be deleted upon insertion. They are used for the base class function superimpose_overhangs. Useful if using Double loop methods which keep the insertion frozen in cartesian space.

References Cter_overhang_, insertion_length_, Nter_overhang_, piece_, and core::pose::Pose::total_residue().

void protocols::grafting::GraftMoverBase::set_regions_from_flexibility ( )
protectedvirtual
void protocols::grafting::GraftMoverBase::set_regions_from_movemap ( Pose pose)
protectedvirtual
void protocols::grafting::GraftMoverBase::setup_movemap_and_regions ( Pose pose)
protectedvirtual

sets up either the default movemap or a new combined movemap at apply time. Updates regions as needed.

MOVEMAP and REGION SETUP Note: Only these functions interact with class variables defined here. To be used optionally in apply.

References combine_movemaps(), Cter_loop_end_, insert_movemap_, movemap_, Nter_loop_start_, scaffold_movemap_, set_default_movemap(), set_regions_from_flexibility(), set_regions_from_movemap(), and use_default_movemap_.

Referenced by protocols::grafting::AnchoredGraftMover::apply().

void protocols::grafting::GraftMoverBase::setup_single_loop_double_arm_remodeling_foldtree ( Pose pose,
Size const  Nter_loop_start,
Size const  Cter_loop_end,
bool  loop_modeling = false 
)
protectedvirtual

****Nter_loop_start-—>Piece | <-—Nter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is end_-1

References core::kinematics::FoldTree::clear(), end_, core::pose::Pose::fold_tree(), insertion_length_, piece_, core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::apply().

void protocols::grafting::GraftMoverBase::setup_single_loop_single_arm_remodeling_foldtree ( Pose pose,
Size const  Nter_loop_start,
Size const  Cter_loop_end,
bool  loop_modeling = false 
)
protectedvirtual

****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Insert will move in cartesian space lower_cutpoint for CCD and loops is Cter_loop_end-1

FOLDTREE SETUP. options depending on how you want your graft algorithm to work! —Indicates Flexible regions, | indicates cutpoint. Arrows are direction of ARMs used to close the loop in conjunction with algorithm. (CCD, KIC)

References core::kinematics::FoldTree::clear(), core::pose::Pose::fold_tree(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by protocols::grafting::AnchoredGraftMover::apply().

void protocols::grafting::GraftMoverBase::superimpose_overhangs_heavy ( Pose const &  pose,
bool  ca_only,
bool  silence_rms 
)

Member Data Documentation

core::scoring::ScoreFunctionOP protocols::grafting::GraftMoverBase::cen_scorefxn_
protected
Size protocols::grafting::GraftMoverBase::Cter_insert_flexibility_
protected
Size protocols::grafting::GraftMoverBase::Cter_loop_end_
protected
Size protocols::grafting::GraftMoverBase::Cter_loop_start_
protected
Size protocols::grafting::GraftMoverBase::Cter_overhang_
protected

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

Referenced by delete_overhang_residues(), set_overhang(), set_piece(), and superimpose_overhangs_heavy().

Size protocols::grafting::GraftMoverBase::Cter_scaffold_flexibility_
protected
Size protocols::grafting::GraftMoverBase::end_
protected
core::scoring::ScoreFunctionOP protocols::grafting::GraftMoverBase::fa_scorefxn_
protected
MoveMapOP protocols::grafting::GraftMoverBase::insert_movemap_
protected
Size protocols::grafting::GraftMoverBase::insertion_length_
protected
MoveMapOP protocols::grafting::GraftMoverBase::movemap_
protected
Size protocols::grafting::GraftMoverBase::Nter_insert_flexibility_
protected
Size protocols::grafting::GraftMoverBase::Nter_loop_end_
protected
Size protocols::grafting::GraftMoverBase::Nter_loop_start_
protected
Size protocols::grafting::GraftMoverBase::Nter_overhang_
protected

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

Referenced by delete_overhang_residues(), set_overhang(), set_piece(), and superimpose_overhangs_heavy().

Size protocols::grafting::GraftMoverBase::Nter_scaffold_flexibility_
protected
Size protocols::grafting::GraftMoverBase::original_end_
protected

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

Referenced by combine_movemaps(), and set_insert_region().

Pose protocols::grafting::GraftMoverBase::piece_
protected
MoveMapOP protocols::grafting::GraftMoverBase::scaffold_movemap_
protected
Size protocols::grafting::GraftMoverBase::start_
protected
bool protocols::grafting::GraftMoverBase::use_default_movemap_
protected

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