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protocols::grafting::AnchoredGraftMover Class Reference

Grafting class adapted from Steven Lewis' pose_into_pose algorithm. More...

#include <AnchoredGraftMover.hh>

Inheritance diagram for protocols::grafting::AnchoredGraftMover:
Inheritance graph
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Public Member Functions

 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 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...
 
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 ()
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Although this mover is published, it can also provide information for unpublished modules that it invokes. More...
 
- 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 

Static Public Member Functions

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...
 

Protected Member Functions

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
 
virtual
protocols::simple_moves::SmallMoverOP 
setup_default_small_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...
 

Private Attributes

core::Size cycles_
 
std::string mintype_
 
bool skip_sampling_
 
bool test_control_mode_
 
utility::pointer::DeepCopyOP
< core::kinematics::MoveMap
movemap_ = nullptr
 
utility::pointer::DeepCopyOP
< core::kinematics::MoveMap
const > 
scaffold_movemap_ = nullptr
 
utility::pointer::DeepCopyOP
< core::kinematics::MoveMap
const > 
insert_movemap_ = nullptr
 
core::select::movemap::MoveMapFactoryCOP scaffold_movemap_factory_ = nullptr
 
core::select::movemap::MoveMapFactoryCOP insert_movemap_factory_ = nullptr
 
utility::pointer::DeepCopyOP
< core::scoring::ScoreFunction
cen_scorefxn_ = nullptr
 
utility::pointer::DeepCopyOP
< core::scoring::ScoreFunction
fa_scorefxn_ = nullptr
 
bool use_default_movemap_
 
core::Size Nter_scaffold_flexibility_
 
core::Size Nter_insert_flexibility_
 
core::Size Nter_loop_start_
 
core::Size Nter_loop_end_
 
core::Size Cter_scaffold_flexibility_
 
core::Size Cter_insert_flexibility_
 
core::Size Cter_loop_start_
 
core::Size Cter_loop_end_
 
bool stop_at_closure_
 
bool final_repack_
 
core::Real neighbor_dis_
 
std::string scaffold_start_
 
std::string scaffold_end_
 
bool idealize_insert_
 
bool graft_is_closed_ = false
 
utility::pointer::DeepCopyOP
< protocols::loops::Loops
loops_ = nullptr
 

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
 

Detailed Description

Grafting class adapted from Steven Lewis' pose_into_pose algorithm.

1) Inserts the pose piece into the scaffold pose, deleting any overhang residues or residues in the region the insertion will occur between. 2) Connects the left side of the piece to the scaffold by inserting ideal geometry (aka superposition of terminal overhangs is not needed) 3) Cycles of: a) SmallMover for sampling b) CCD to close right (Nter) side of the graft. The insert is included as dihedral-inflexible residues in the CCD arm. Residues on either side of the scaffold are used by default to close the loop. A Moevemap can be given to include more residues for CCD to use, such as loops connecting secondary structural elements c) MinMover to help close the graft through chainbreak terms d) Closure check - will stop if closed (This can be overridden) d) MonteCarlo Boltzmann criterion

5) Repack flexible residues, insert residues, connecting residues between scaffold and insert, and neighbors

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

see also: grafting/util.hh.

Uses a single arm to close the loop by default. ****Nter_loop_start-—>Piece-—> | Cter_loop_end**** Default movemap keeps insert Frozen in dihedral angle space, But think of the insert as part of a CCD giant arm. Default flexibility on Nter and Cter is only two residues (–> part of diagram). Will delete any residues between start and end, and any overhang residues from the insert.

Algorithm originally from pose_into_pose: The insert will be left unchanged in internal-coordinate space except for the phi on the first residue, and the psi/omega on the last residue, and atoms whose bonding partners change as a result of the insertion. Internally, apply performs the insertion, idealizes the loop residues (omegas to 180, peptide bonds idealized) and the newly made polymer connections at the insert point, and then attempts to close the loop(s). It is intended, but not guaranteed, to produce a graft with good rama, omega, and chainbreak/peptide_bond scores. All-atom minimization of graft or pose after insertion is recommended.

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::grafting::AnchoredGraftMover::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.

Implements protocols::moves::Mover.

Reimplemented in protocols::grafting::CCDEndsGraftMover.

References protocols::grafting::add_cutpoint_variants_for_ccd(), core::pose::add_variant_type_to_pose_residue(), protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::id::BB, protocols::moves::MonteCarlo::boltzmann(), cen_scorefxn(), cen_scorefxn_, core::chemical::CENTROID, Cter_loop_end_, cycles_, protocols::grafting::GraftMoverBase::end(), fa_scorefxn_, final_repack_, protocols::grafting::graft_closed(), graft_is_closed_, protocols::grafting::idealize_combined_pose(), idealize_insert(), protocols::grafting::GraftMoverBase::insert_piece(), protocols::grafting::GraftMoverBase::insertion_length(), loops_, movemap_, neighbor_dis(), Nter_loop_start_, core::pose::parse_resnum(), protocols::grafting::perturb_backbone_for_test(), core::id::phi_torsion(), protocols::grafting::GraftMoverBase::piece(), core::id::psi_torsion(), protocols::moves::MonteCarlo::recover_low(), protocols::grafting::remove_cutpoint_variants_for_ccd(), protocols::grafting::repack_connection_and_residues_in_movemap_and_piece_and_neighbors(), scaffold_end(), scaffold_end_, scaffold_start(), scaffold_start_, protocols::grafting::GraftMoverBase::set_insert_region(), setup_default_min_mover(), setup_default_small_mover(), setup_movemap_and_regions(), setup_scorefunction(), protocols::grafting::setup_single_loop_single_arm_remodeling_foldtree(), skip_sampling_, protocols::grafting::GraftMoverBase::start(), stop_at_closure(), test_control_mode_, and protocols::TR().

ScoreFunctionOP protocols::grafting::AnchoredGraftMover::cen_scorefxn ( ) const
protected
protocols::moves::MoverOP protocols::grafting::AnchoredGraftMover::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::moves::Mover.

Reimplemented in protocols::grafting::CCDEndsGraftMover.

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::grafting::AnchoredGraftMover::complex_type_generator_for_anchored_graft_mover ( utility::tag::XMLSchemaDefinition &  xsd)
static
Size protocols::grafting::AnchoredGraftMover::Cter_insert_flexibility ( ) const
protected
Size protocols::grafting::AnchoredGraftMover::Cter_loop_end ( ) const
protected
Size protocols::grafting::AnchoredGraftMover::Cter_loop_start ( ) const
protected
Size protocols::grafting::AnchoredGraftMover::Cter_scaffold_flexibility ( ) const
protected
Size protocols::grafting::AnchoredGraftMover::cycles ( ) const
protected
ScoreFunctionOP protocols::grafting::AnchoredGraftMover::fa_scorefxn ( ) const
protected
void protocols::grafting::AnchoredGraftMover::final_repack ( bool  final_repack)

Pack sidechains of flexible residues, insert and neighbors at end? Default True.

References final_repack(), and final_repack_.

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

bool protocols::grafting::AnchoredGraftMover::final_repack ( )

Pack sidechains of flexible residues, insert and neighbors at end?

References final_repack_.

Referenced by protocols::grafting::CCDEndsGraftMover::apply(), final_repack(), parse_my_tag(), and set_defaults().

protocols::moves::MoverOP protocols::grafting::AnchoredGraftMover::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::moves::Mover.

Reimplemented in protocols::grafting::CCDEndsGraftMover.

core::Size protocols::grafting::AnchoredGraftMover::get_Cter_loop_end ( )
Returns
the Cterminal loop end (Last flexible residue). Useful to use after insertion.

References Cter_loop_end_.

Size protocols::grafting::AnchoredGraftMover::get_cterm_insert_flexibility ( )
Size protocols::grafting::AnchoredGraftMover::get_cterm_scaffold_flexibility ( )
protocols::loops::Loops const& protocols::grafting::AnchoredGraftMover::get_loops ( void  )
inline

References loops_.

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

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Reimplemented in protocols::grafting::CCDEndsGraftMover.

References mover_name().

Size protocols::grafting::AnchoredGraftMover::get_nterm_insert_flexibility ( )
Size protocols::grafting::AnchoredGraftMover::get_nterm_scaffold_flexibility ( )
bool protocols::grafting::AnchoredGraftMover::graft_is_closed ( ) const
inline

References graft_is_closed_.

void protocols::grafting::AnchoredGraftMover::idealize_insert ( bool  idealize)
bool protocols::grafting::AnchoredGraftMover::idealize_insert ( ) const
inline
std::string protocols::grafting::AnchoredGraftMover::mintype ( ) const
protected

References mintype_.

Referenced by set_mintype().

void protocols::grafting::AnchoredGraftMover::movemap ( core::kinematics::MoveMapOP  movemap)
protected

References movemap(), and movemap_.

MoveMapOP protocols::grafting::AnchoredGraftMover::movemap ( ) const
protected
std::string protocols::grafting::AnchoredGraftMover::mover_name ( )
static
bool protocols::grafting::AnchoredGraftMover::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::grafting::CCDEndsGraftMover.

void protocols::grafting::AnchoredGraftMover::neighbor_dis ( core::Real  dis)

Neighbor distance for any repacking of side-chains.

References neighbor_dis_.

core::Real protocols::grafting::AnchoredGraftMover::neighbor_dis ( ) const
Size protocols::grafting::AnchoredGraftMover::Nter_insert_flexibility ( ) const
protected
Size protocols::grafting::AnchoredGraftMover::Nter_loop_end ( ) const
protected
Size protocols::grafting::AnchoredGraftMover::Nter_loop_start ( ) const
protected
Size protocols::grafting::AnchoredGraftMover::Nter_scaffold_flexibility ( ) const
protected
void protocols::grafting::AnchoredGraftMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::grafting::AnchoredGraftMover::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Although this mover is published, it can also provide information for unpublished modules that it invokes.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::grafting::CCDEndsGraftMover.

References protocols::moves::Mover::provide_authorship_info_for_unpublished(), and setup_default_min_mover().

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::grafting::AnchoredGraftMover::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::grafting::CCDEndsGraftMover.

References protocols::moves::Mover::provide_citation_info(), and setup_default_min_mover().

void protocols::grafting::AnchoredGraftMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
std::string const & protocols::grafting::AnchoredGraftMover::scaffold_end ( ) const
protected
std::string const & protocols::grafting::AnchoredGraftMover::scaffold_start ( ) const
protected
void protocols::grafting::AnchoredGraftMover::set_cen_scorefunction ( core::scoring::ScoreFunctionCOP  score)
virtual
void protocols::grafting::AnchoredGraftMover::set_cycles ( core::Size  cycles)
void protocols::grafting::AnchoredGraftMover::set_default_cen_scorefunction ( )
protectedvirtual
void protocols::grafting::AnchoredGraftMover::set_default_fa_scorefunction ( )
protectedvirtual
void protocols::grafting::AnchoredGraftMover::set_default_movemap ( )
protectedvirtual
void protocols::grafting::AnchoredGraftMover::set_defaults ( )
void protocols::grafting::AnchoredGraftMover::set_fa_scorefunction ( core::scoring::ScoreFunctionCOP  score)
virtual
void protocols::grafting::AnchoredGraftMover::set_insert_flexibility ( core::Size const  Nter_insert_flexibility,
core::Size const  Cter_insert_flexibility 
)

Sets insert flexibility on either end of insert.

References Cter_insert_flexibility(), Cter_insert_flexibility_, Nter_insert_flexibility(), and Nter_insert_flexibility_.

Referenced by set_defaults(), and setup_movemap_and_regions().

void protocols::grafting::AnchoredGraftMover::set_loops ( protocols::loops::LoopsOP  loops)
protected
void protocols::grafting::AnchoredGraftMover::set_mintype ( std::string  mintype)

Sets the mintype for the MinMover.

References mintype(), and mintype_.

Referenced by parse_my_tag(), and set_defaults().

void protocols::grafting::AnchoredGraftMover::set_movemaps ( core::kinematics::MoveMapCOP const  scaffold_mm,
core::kinematics::MoveMapCOP const  insert_mm 
)
virtual

Advanced way to set flexibility and residues used for CCD.

Will combine the movemaps for apply, and renumber everything. Flexible residues in multiple chains not recommended. From the first bb flexible residue to the last will act as one giant CCD arm, using those residues for minimization and CCD that have bb true in movemap. This can be amazing as you can use loop regions in various parts of your protein to help the graft complete. 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.

References insert_movemap_, and scaffold_movemap_.

void protocols::grafting::AnchoredGraftMover::set_regions_from_flexibility ( )
protectedvirtual
void protocols::grafting::AnchoredGraftMover::set_regions_from_movemap ( core::pose::Pose pose)
protectedvirtual
void protocols::grafting::AnchoredGraftMover::set_scaffold_flexibility ( core::Size const  Nter_scaffold_flexibility,
core::Size const  Cter_scaffold_flexibility 
)

Sets scaffold flexiblity on either end of scaffold.

References Cter_scaffold_flexibility(), Cter_scaffold_flexibility_, Nter_scaffold_flexibility(), and Nter_scaffold_flexibility_.

Referenced by set_defaults().

void protocols::grafting::AnchoredGraftMover::set_skip_sampling ( bool  skip_sampling)

Sets the mover to skip the small mover sampling step.

References skip_sampling(), and skip_sampling_.

Referenced by set_defaults().

void protocols::grafting::AnchoredGraftMover::set_test_control_mode ( bool  test_control_mode)
protected

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.

References test_control_mode(), and test_control_mode_.

Referenced by set_defaults().

MinMoverOP protocols::grafting::AnchoredGraftMover::setup_default_min_mover ( ) const
protectedvirtual
SmallMoverOP protocols::grafting::AnchoredGraftMover::setup_default_small_mover ( ) const
protectedvirtual

Reimplemented in protocols::grafting::CCDEndsGraftMover.

References movemap_.

Referenced by apply().

void protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions ( core::pose::Pose pose)
protectedvirtual
void protocols::grafting::AnchoredGraftMover::setup_scorefunction ( )
protected
bool protocols::grafting::AnchoredGraftMover::skip_sampling ( ) const
protected
void protocols::grafting::AnchoredGraftMover::stop_at_closure ( bool  stop_at_closure)

Stop at closure of both ends? Default True.

References stop_at_closure(), and stop_at_closure_.

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

bool protocols::grafting::AnchoredGraftMover::stop_at_closure ( )
bool protocols::grafting::AnchoredGraftMover::test_control_mode ( ) const
protected
void protocols::grafting::AnchoredGraftMover::use_default_movemap ( bool  use_default_movemap)
protected
bool protocols::grafting::AnchoredGraftMover::use_default_movemap ( ) const
protected

References use_default_movemap_.

Referenced by use_default_movemap().

Member Data Documentation

utility::pointer::DeepCopyOP< core::scoring::ScoreFunction > protocols::grafting::AnchoredGraftMover::cen_scorefxn_ = nullptr
private
core::Size protocols::grafting::AnchoredGraftMover::Cter_insert_flexibility_
private
core::Size protocols::grafting::AnchoredGraftMover::Cter_loop_end_
private
core::Size protocols::grafting::AnchoredGraftMover::Cter_loop_start_
private
core::Size protocols::grafting::AnchoredGraftMover::Cter_scaffold_flexibility_
private
core::Size protocols::grafting::AnchoredGraftMover::cycles_
private
utility::pointer::DeepCopyOP< core::scoring::ScoreFunction > protocols::grafting::AnchoredGraftMover::fa_scorefxn_ = nullptr
private
bool protocols::grafting::AnchoredGraftMover::final_repack_
private

Referenced by apply(), final_repack(), and parse_my_tag().

bool protocols::grafting::AnchoredGraftMover::graft_is_closed_ = false
private

Referenced by apply(), and graft_is_closed().

bool protocols::grafting::AnchoredGraftMover::idealize_insert_
private

Referenced by idealize_insert().

utility::pointer::DeepCopyOP< core::kinematics::MoveMap const > protocols::grafting::AnchoredGraftMover::insert_movemap_ = nullptr
private
core::select::movemap::MoveMapFactoryCOP protocols::grafting::AnchoredGraftMover::insert_movemap_factory_ = nullptr
private
utility::pointer::DeepCopyOP< protocols::loops::Loops > protocols::grafting::AnchoredGraftMover::loops_ = nullptr
private
std::string protocols::grafting::AnchoredGraftMover::mintype_
private
utility::pointer::DeepCopyOP< core::kinematics::MoveMap > protocols::grafting::AnchoredGraftMover::movemap_ = nullptr
private
core::Real protocols::grafting::AnchoredGraftMover::neighbor_dis_
private

Referenced by neighbor_dis(), and parse_my_tag().

core::Size protocols::grafting::AnchoredGraftMover::Nter_insert_flexibility_
private
core::Size protocols::grafting::AnchoredGraftMover::Nter_loop_end_
private
core::Size protocols::grafting::AnchoredGraftMover::Nter_loop_start_
private
core::Size protocols::grafting::AnchoredGraftMover::Nter_scaffold_flexibility_
private
std::string protocols::grafting::AnchoredGraftMover::scaffold_end_
private

Referenced by apply(), parse_my_tag(), and scaffold_end().

utility::pointer::DeepCopyOP< core::kinematics::MoveMap const > protocols::grafting::AnchoredGraftMover::scaffold_movemap_ = nullptr
private
core::select::movemap::MoveMapFactoryCOP protocols::grafting::AnchoredGraftMover::scaffold_movemap_factory_ = nullptr
private
std::string protocols::grafting::AnchoredGraftMover::scaffold_start_
private

Referenced by apply(), parse_my_tag(), and scaffold_start().

bool protocols::grafting::AnchoredGraftMover::skip_sampling_
private
bool protocols::grafting::AnchoredGraftMover::stop_at_closure_
private

Referenced by parse_my_tag(), and stop_at_closure().

bool protocols::grafting::AnchoredGraftMover::test_control_mode_
private
bool protocols::grafting::AnchoredGraftMover::use_default_movemap_
private

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