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protocols::grafting::CCDEndsGraftMover Class Reference

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>

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

 CCDEndsGraftMover ()
 
 CCDEndsGraftMover (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...
 
 CCDEndsGraftMover (core::Size const start, core::Size const end, core::pose::Pose const &piece, core::Size Nter_overhang=2, core::Size Cter_overhang=2, bool copy_pdbinfo=false)
 
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...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool graft_is_closed () const
 
void provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
 Provide the citation. More...
 
- Public Member Functions inherited from protocols::grafting::AnchoredGraftMover
 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 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 ()
 
- 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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- Static Public Member Functions inherited from protocols::grafting::AnchoredGraftMover
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...
 

Private Member Functions

protocols::simple_moves::SmallMoverOP setup_default_small_mover () const override
 

Private Attributes

bool graft_is_closed_ = false
 

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
 
- 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...
 
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
 
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...
 

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)

see also: grafting/util.hh.

Uses two CCD arms on either side of the scaffold to close graft. Insert is held fixed in cartesian space after superposition of any overhang residues by default.

****Nter_loop_start--—> | Piece | <-—Nter_loop_end**** (Note that Nter_loop_start and Nter_loop_end points to redidue BEFORE loop and AFTER loop) Default flexibility on Nter and Cter is only two residues (–> part of diagram). Will delete any residues between start and end of the scaffold, and any overhang residues from the insert.

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). Repacks sidechains of insert and overhang residues after insertion is complete By default, will stop apply once graft is closed. Closure is measured as all bond lengths and angles of loop being acceptable.

Constructor & Destructor Documentation

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

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

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

Member Function Documentation

void protocols::grafting::CCDEndsGraftMover::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.

Reimplemented from protocols::grafting::AnchoredGraftMover.

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(), protocols::grafting::AnchoredGraftMover::cen_scorefxn(), core::chemical::CENTROID, protocols::grafting::AnchoredGraftMover::Cter_loop_end(), protocols::grafting::AnchoredGraftMover::Cter_loop_start(), protocols::grafting::GraftMoverBase::Cter_overhang_length(), protocols::grafting::AnchoredGraftMover::cycles(), protocols::grafting::GraftMoverBase::end(), protocols::grafting::AnchoredGraftMover::fa_scorefxn(), protocols::grafting::AnchoredGraftMover::final_repack(), protocols::grafting::AnchoredGraftMover::get_cterm_insert_flexibility(), protocols::grafting::AnchoredGraftMover::get_nterm_insert_flexibility(), protocols::grafting::graft_closed(), graft_is_closed_, protocols::grafting::idealize_combined_pose(), protocols::grafting::AnchoredGraftMover::idealize_insert(), protocols::grafting::GraftMoverBase::insert_piece(), protocols::grafting::GraftMoverBase::insertion_length(), protocols::grafting::AnchoredGraftMover::movemap(), protocols::grafting::AnchoredGraftMover::neighbor_dis(), protocols::grafting::AnchoredGraftMover::Nter_loop_end(), protocols::grafting::AnchoredGraftMover::Nter_loop_start(), protocols::grafting::GraftMoverBase::Nter_overhang_length(), protocols::grafting::GraftMoverBase::original_end(), 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(), protocols::grafting::AnchoredGraftMover::scaffold_end(), protocols::grafting::AnchoredGraftMover::scaffold_start(), protocols::grafting::GraftMoverBase::set_insert_region(), protocols::grafting::AnchoredGraftMover::set_loops(), protocols::grafting::AnchoredGraftMover::setup_default_min_mover(), setup_default_small_mover(), protocols::grafting::AnchoredGraftMover::setup_movemap_and_regions(), protocols::grafting::AnchoredGraftMover::setup_scorefunction(), protocols::grafting::AnchoredGraftMover::skip_sampling(), protocols::grafting::GraftMoverBase::start(), protocols::grafting::AnchoredGraftMover::stop_at_closure(), protocols::grafting::superimpose_overhangs_heavy(), protocols::grafting::AnchoredGraftMover::test_control_mode(), and protocols::TR().

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

protocols::moves::MoverOP protocols::grafting::CCDEndsGraftMover::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::grafting::AnchoredGraftMover.

protocols::moves::MoverOP protocols::grafting::CCDEndsGraftMover::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::grafting::AnchoredGraftMover.

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

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

Reimplemented from protocols::grafting::AnchoredGraftMover.

References mover_name().

bool protocols::grafting::CCDEndsGraftMover::graft_is_closed ( ) const
inline
std::string protocols::grafting::CCDEndsGraftMover::mover_name ( )
static
void protocols::grafting::CCDEndsGraftMover::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const
overridevirtual
void protocols::grafting::CCDEndsGraftMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
SmallMoverOP protocols::grafting::CCDEndsGraftMover::setup_default_small_mover ( ) const
overrideprivatevirtual

Member Data Documentation

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

Referenced by apply(), and graft_is_closed().


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