Grafting class adapted from Steven Lewis' pose_into_pose algorithm. More...
#include <AnchoredGraftMover.hh>
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... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| Provide the citation. 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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor 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... | |
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
◆ AnchoredGraftMover() [1/3]
| protocols::grafting::AnchoredGraftMover::AnchoredGraftMover | ( | ) |
◆ AnchoredGraftMover() [2/3]
| protocols::grafting::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.
References protocols::grafting::GraftMoverBase::copy_pdbinfo(), protocols::grafting::GraftMoverBase::Cter_overhang_length(), protocols::grafting::GraftMoverBase::Nter_overhang_length(), and set_defaults().
◆ AnchoredGraftMover() [3/3]
| 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 |
||
| ) |
References protocols::grafting::GraftMoverBase::copy_pdbinfo(), and set_defaults().
Member Function Documentation
◆ apply()
|
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, core::pose::Pose::conformation(), Cter_loop_end_, protocols::loops::Loop::cut(), cycles_, protocols::grafting::GraftMoverBase::end(), fa_scorefxn_, final_repack_, core::pose::Pose::fold_tree(), protocols::grafting::graft_closed(), graft_is_closed_, protocols::grafting::idealize_combined_pose(), idealize_insert(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), 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().
◆ cen_scorefxn()
|
protected |
References cen_scorefxn_.
Referenced by apply(), protocols::grafting::CCDEndsGraftMover::apply(), and parse_my_tag().
◆ clone()
|
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.
◆ complex_type_generator_for_anchored_graft_mover()
|
static |
References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), protocols::rosetta_scripts::attributes_for_saved_reference_pose(), and protocols::moves::complex_type_name_for_mover().
Referenced by provide_xml_schema(), and protocols::grafting::CCDEndsGraftMover::provide_xml_schema().
◆ Cter_insert_flexibility()
|
protected |
References Cter_insert_flexibility_.
Referenced by set_insert_flexibility(), and setup_movemap_and_regions().
◆ Cter_loop_end()
|
protected |
References Cter_loop_end_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply().
◆ Cter_loop_start()
|
protected |
References Cter_loop_start_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply().
◆ Cter_scaffold_flexibility()
|
protected |
References Cter_scaffold_flexibility_.
Referenced by set_scaffold_flexibility().
◆ cycles()
|
protected |
References cycles_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply(), and set_cycles().
◆ fa_scorefxn()
|
protected |
References fa_scorefxn_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply(), and parse_my_tag().
◆ final_repack() [1/2]
| 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().
◆ final_repack() [2/2]
| 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().
◆ fresh_instance()
|
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.
◆ get_Cter_loop_end()
| 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_.
◆ get_cterm_insert_flexibility()
| Size protocols::grafting::AnchoredGraftMover::get_cterm_insert_flexibility | ( | ) |
References Cter_insert_flexibility_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply().
◆ get_cterm_scaffold_flexibility()
| Size protocols::grafting::AnchoredGraftMover::get_cterm_scaffold_flexibility | ( | ) |
References Cter_scaffold_flexibility_.
◆ get_loops()
|
inline |
References loops_.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Reimplemented in protocols::grafting::CCDEndsGraftMover.
References mover_name().
◆ get_nterm_insert_flexibility()
| Size protocols::grafting::AnchoredGraftMover::get_nterm_insert_flexibility | ( | ) |
References Nter_insert_flexibility_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply().
◆ get_nterm_scaffold_flexibility()
| Size protocols::grafting::AnchoredGraftMover::get_nterm_scaffold_flexibility | ( | ) |
References Nter_scaffold_flexibility_.
◆ graft_is_closed()
|
inline |
References graft_is_closed_.
◆ idealize_insert() [1/2]
|
inline |
References idealize_insert_.
Referenced by apply(), protocols::grafting::CCDEndsGraftMover::apply(), and set_defaults().
◆ idealize_insert() [2/2]
| void protocols::grafting::AnchoredGraftMover::idealize_insert | ( | bool | idealize | ) |
References idealize_insert_.
Referenced by protocols::tcr::graft_cdr_to_fw().
◆ mintype()
|
protected |
References mintype_.
Referenced by set_mintype().
◆ movemap() [1/2]
|
protected |
References movemap_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply(), movemap(), and protocols::grafting::CCDEndsGraftMover::setup_default_small_mover().
◆ movemap() [2/2]
|
protected |
◆ mover_name()
|
static |
Referenced by get_name(), protocols::grafting::AnchoredGraftMoverCreator::keyname(), and provide_xml_schema().
◆ neighbor_dis() [1/2]
| core::Real protocols::grafting::AnchoredGraftMover::neighbor_dis | ( | ) | const |
References neighbor_dis_.
Referenced by apply(), protocols::grafting::CCDEndsGraftMover::apply(), parse_my_tag(), and set_defaults().
◆ neighbor_dis() [2/2]
| void protocols::grafting::AnchoredGraftMover::neighbor_dis | ( | core::Real | dis | ) |
Neighbor distance for any repacking of side-chains.
References neighbor_dis_.
◆ Nter_insert_flexibility()
|
protected |
References Nter_insert_flexibility_.
Referenced by set_insert_flexibility(), and setup_movemap_and_regions().
◆ Nter_loop_end()
|
protected |
References Nter_loop_end_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply().
◆ Nter_loop_start()
|
protected |
References Nter_loop_start_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply().
◆ Nter_scaffold_flexibility()
|
protected |
References Nter_scaffold_flexibility_.
Referenced by set_scaffold_flexibility().
◆ parse_my_tag()
|
overridevirtual |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()
Reimplemented from protocols::moves::Mover.
References cen_scorefxn(), cen_scorefxn_, protocols::grafting::GraftMoverBase::copy_pdbinfo(), Cter_insert_flexibility_, protocols::grafting::GraftMoverBase::Cter_overhang_length(), Cter_scaffold_flexibility_, cycles_, fa_scorefxn(), fa_scorefxn_, final_repack(), final_repack_, insert_movemap_factory_, mintype_, neighbor_dis(), neighbor_dis_, Nter_insert_flexibility_, protocols::grafting::GraftMoverBase::Nter_overhang_length(), Nter_scaffold_flexibility_, protocols::rosetta_scripts::parse_named_movemap_factory_legacy(), protocols::grafting::GraftMoverBase::piece(), protocols::rosetta_scripts::saved_reference_pose(), scaffold_end_, scaffold_movemap_factory_, scaffold_start_, set_cycles(), set_mintype(), skip_sampling_, stop_at_closure(), stop_at_closure_, and protocols::TR().
◆ provide_citation_info()
|
overridevirtual |
Provide the citation.
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::grafting::CCDEndsGraftMover.
References setup_default_min_mover().
◆ provide_xml_schema()
|
static |
◆ scaffold_end()
|
protected |
References scaffold_end_.
Referenced by apply(), and protocols::grafting::CCDEndsGraftMover::apply().
◆ scaffold_start()
|
protected |
References scaffold_start_.
Referenced by apply(), and protocols::grafting::CCDEndsGraftMover::apply().
◆ set_cen_scorefunction()
|
virtual |
◆ set_cycles()
| void protocols::grafting::AnchoredGraftMover::set_cycles | ( | core::Size | cycles | ) |
References cycles(), and cycles_.
Referenced by protocols::tcr::graft_cdr_to_fw(), parse_my_tag(), and set_defaults().
◆ set_default_cen_scorefunction()
|
protectedvirtual |
Smooth version of Steven's original scorefunction used for grafting.
References core::scoring::cbeta_smooth, core::scoring::cen_env_smooth, core::scoring::cen_pair_smooth, cen_scorefxn_, core::scoring::cenpack_smooth, core::scoring::chainbreak, core::scoring::dslfc_ang, core::scoring::dslfc_bb_dih, core::scoring::dslfc_cb_dih, core::scoring::dslfc_cb_dst, core::scoring::dslfc_cen_dst, core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::linear_chainbreak, core::scoring::omega, core::scoring::rama, and core::scoring::vdw.
Referenced by setup_scorefunction().
◆ set_default_fa_scorefunction()
|
protectedvirtual |
References core::scoring::chainbreak, fa_scorefxn_, core::scoring::get_score_function(), and core::scoring::linear_chainbreak.
Referenced by setup_scorefunction().
◆ set_default_movemap()
|
protectedvirtual |
Sets up the default movemap.
References Cter_loop_end_, Cter_loop_start_, movemap_, Nter_loop_end_, Nter_loop_start_, and protocols::TR().
Referenced by setup_movemap_and_regions().
◆ set_defaults()
| void protocols::grafting::AnchoredGraftMover::set_defaults | ( | ) |
◆ set_fa_scorefunction()
|
virtual |
◆ set_insert_flexibility()
| 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().
◆ set_loops()
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protected |
References loops_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply().
◆ set_mintype()
| 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().
◆ set_movemaps()
|
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_.
◆ set_regions_from_flexibility()
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protectedvirtual |
Sets up the regions at apply using insert variables and flexibility.
References Cter_insert_flexibility_, Cter_loop_end_, Cter_loop_start_, Cter_scaffold_flexibility_, protocols::grafting::GraftMoverBase::insertion_length(), Nter_insert_flexibility_, Nter_loop_end_, Nter_loop_start_, Nter_scaffold_flexibility_, protocols::grafting::GraftMoverBase::start(), and protocols::TR().
Referenced by setup_movemap_and_regions().
◆ set_regions_from_movemap()
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protectedvirtual |
Sets up region variables from the class movemap for the combined pose.
References Cter_insert_flexibility_, Cter_loop_end_, Cter_loop_start_, protocols::grafting::GraftMoverBase::insertion_length(), movemap_, Nter_insert_flexibility_, Nter_loop_end_, Nter_loop_start_, core::pose::Pose::size(), protocols::grafting::GraftMoverBase::start(), and protocols::TR().
Referenced by setup_movemap_and_regions().
◆ set_scaffold_flexibility()
| 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().
◆ set_skip_sampling()
| 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().
◆ set_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().
◆ setup_default_min_mover()
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protectedvirtual |
References cen_scorefxn_, mintype_, and movemap_.
Referenced by apply(), protocols::grafting::CCDEndsGraftMover::apply(), provide_citation_info(), and protocols::grafting::CCDEndsGraftMover::provide_citation_info().
◆ setup_default_small_mover()
|
protectedvirtual |
Reimplemented in protocols::grafting::CCDEndsGraftMover.
References movemap_.
Referenced by apply().
◆ setup_movemap_and_regions()
|
protectedvirtual |
sets up either the default movemap or a new combined movemap at apply time. Updates regions as needed.
MOVEMAP and REGION SETUP.
References protocols::grafting::combine_movemaps_post_insertion(), Cter_insert_flexibility(), Cter_loop_end_, protocols::grafting::GraftMoverBase::end(), insert_movemap_, insert_movemap_factory_, protocols::grafting::GraftMoverBase::insertion_length(), movemap_, Nter_insert_flexibility(), Nter_loop_start_, protocols::grafting::GraftMoverBase::original_end(), scaffold_movemap_, scaffold_movemap_factory_, set_default_movemap(), set_insert_flexibility(), set_regions_from_flexibility(), set_regions_from_movemap(), and protocols::TR().
Referenced by apply(), and protocols::grafting::CCDEndsGraftMover::apply().
◆ setup_scorefunction()
|
protected |
References cen_scorefxn_, fa_scorefxn_, set_default_cen_scorefunction(), and set_default_fa_scorefunction().
Referenced by apply(), and protocols::grafting::CCDEndsGraftMover::apply().
◆ skip_sampling()
|
protected |
References skip_sampling_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply(), and set_skip_sampling().
◆ stop_at_closure() [1/2]
| bool protocols::grafting::AnchoredGraftMover::stop_at_closure | ( | ) |
Stop at closure of both ends?
References stop_at_closure_.
Referenced by apply(), protocols::grafting::CCDEndsGraftMover::apply(), parse_my_tag(), set_defaults(), and stop_at_closure().
◆ stop_at_closure() [2/2]
| 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().
◆ test_control_mode()
|
protected |
References test_control_mode_.
Referenced by protocols::grafting::CCDEndsGraftMover::apply(), and set_test_control_mode().
◆ use_default_movemap() [1/2]
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protected |
References use_default_movemap_.
Referenced by use_default_movemap().
◆ use_default_movemap() [2/2]
|
protected |
References use_default_movemap(), and use_default_movemap_.
Member Data Documentation
◆ cen_scorefxn_
|
private |
◆ Cter_insert_flexibility_
|
private |
◆ Cter_loop_end_
|
private |
◆ Cter_loop_start_
|
private |
Referenced by Cter_loop_start(), set_default_movemap(), set_regions_from_flexibility(), and set_regions_from_movemap().
◆ Cter_scaffold_flexibility_
|
private |
◆ cycles_
|
private |
Referenced by apply(), cycles(), parse_my_tag(), and set_cycles().
◆ fa_scorefxn_
|
private |
Referenced by apply(), fa_scorefxn(), parse_my_tag(), set_default_fa_scorefunction(), set_fa_scorefunction(), and setup_scorefunction().
◆ final_repack_
|
private |
Referenced by apply(), final_repack(), and parse_my_tag().
◆ graft_is_closed_
|
private |
Referenced by apply(), and graft_is_closed().
◆ idealize_insert_
|
private |
Referenced by idealize_insert().
◆ insert_movemap_
|
private |
Referenced by set_movemaps(), and setup_movemap_and_regions().
◆ insert_movemap_factory_
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private |
Referenced by parse_my_tag(), and setup_movemap_and_regions().
◆ loops_
|
private |
Referenced by apply(), get_loops(), set_defaults(), and set_loops().
◆ mintype_
|
private |
Referenced by mintype(), parse_my_tag(), set_mintype(), and setup_default_min_mover().
◆ movemap_
|
private |
◆ neighbor_dis_
|
private |
Referenced by neighbor_dis(), and parse_my_tag().
◆ Nter_insert_flexibility_
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private |
◆ Nter_loop_end_
|
private |
Referenced by Nter_loop_end(), set_default_movemap(), set_regions_from_flexibility(), and set_regions_from_movemap().
◆ Nter_loop_start_
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private |
◆ Nter_scaffold_flexibility_
|
private |
◆ scaffold_end_
|
private |
Referenced by apply(), parse_my_tag(), and scaffold_end().
◆ scaffold_movemap_
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private |
Referenced by set_movemaps(), and setup_movemap_and_regions().
◆ scaffold_movemap_factory_
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private |
Referenced by parse_my_tag(), and setup_movemap_and_regions().
◆ scaffold_start_
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private |
Referenced by apply(), parse_my_tag(), and scaffold_start().
◆ skip_sampling_
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private |
Referenced by apply(), parse_my_tag(), set_skip_sampling(), and skip_sampling().
◆ stop_at_closure_
|
private |
Referenced by parse_my_tag(), and stop_at_closure().
◆ test_control_mode_
|
private |
Referenced by apply(), set_test_control_mode(), and test_control_mode().
◆ use_default_movemap_
|
private |
Referenced by set_defaults(), and use_default_movemap().
The documentation for this class was generated from the following files:
- src/protocols/grafting/AnchoredGraftMover.hh
- src/protocols/grafting/AnchoredGraftMover.cc
