#include <ReturnSidechainMover.hh>
Public Member Functions | |
| ReturnSidechainMover () | |
| default constructor More... | |
| ReturnSidechainMover (core::pose::Pose const &pose_in, core::Size start_res=0, core::Size end_res=0) | |
| constructor with pose More... | |
| ReturnSidechainMover (core::pose::Pose const &pose_in, utility::vector1< bool > const &allow_chi_in, core::Size start_res=0, core::Size end_res=0) | |
| constructor with pose and copiable residue array More... | |
| ReturnSidechainMover (ReturnSidechainMover const &object_to_copy) | |
| copy constructor More... | |
| ~ReturnSidechainMover () override | |
| void | apply (core::pose::Pose &pose) override |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
| void | show (std::ostream &output=std::cout) const override |
| Outputs details about the Mover, including current settings. 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... | |
| core::Size | get_start_res () const |
| core::Size | get_end_res () const |
 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 |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual 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... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Public Attributes | |
| bool | copy_all_chi_ |
| utility::vector1< bool > | allow_chi_copy_ |
Private Attributes | |
| core::pose::Pose const | remembered_pose_ |
| remembered old pose More... | |
| core::Size | start_res_ |
| residue numbers for which residues to loop over for recovery More... | |
| core::Size | end_res_ |
Additional Inherited Members | |
| Public Types inherited from protocols::moves::Mover | |
| typedef utility::tag::TagCOP | TagCOP |
| typedef core::pose::Pose | Pose |
| typedef core::pose::PoseCOP | PoseCOP |
| typedef std::list< std::string > | Strings |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
| 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
This class takes two poses, one at instantiation and one at apply. It copies the residue type set and chi information from its kept pose to the apply pose. The intended purpose is for "returning" known sidechains to a pose that was temporarily in centroid mode, although it may work with other residue type sets.
Constructor & Destructor Documentation
◆ ReturnSidechainMover() [1/4]
| protocols::simple_moves::ReturnSidechainMover::ReturnSidechainMover | ( | ) |
default constructor
References copy_all_chi_, and protocols::moves::Mover::type().
◆ ReturnSidechainMover() [2/4]
| protocols::simple_moves::ReturnSidechainMover::ReturnSidechainMover | ( | core::pose::Pose const & | pose_in, |
| core::Size | start_res = 0, |
||
| core::Size | end_res = 0 |
||
| ) |
constructor with pose
References copy_all_chi_, end_res_, core::pose::Pose::size(), start_res_, and protocols::moves::Mover::type().
◆ ReturnSidechainMover() [3/4]
| protocols::simple_moves::ReturnSidechainMover::ReturnSidechainMover | ( | core::pose::Pose const & | pose_in, |
| utility::vector1< bool > const & | allow_chi_in, | ||
| core::Size | start_res = 0, |
||
| core::Size | end_res = 0 |
||
| ) |
constructor with pose and copiable residue array
References copy_all_chi_, end_res_, core::pose::Pose::size(), start_res_, and protocols::moves::Mover::type().
◆ ReturnSidechainMover() [4/4]
|
default |
copy constructor
◆ ~ReturnSidechainMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
this code was copied from protocols/loops/loops_main.cc:187-204, revision 21282
Implements protocols::moves::Mover.
References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::add_variant_type_to_pose_residue(), allow_chi_copy_, core::scoring::Energies::clear(), core::pose::Pose::conformation(), copy_all_chi_, end_res_, core::pose::Pose::energies(), core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::ResidueTypeBase::has_variant_type(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueTypeBase::name(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueTypeBase::properties(), remembered_pose_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), start_res_, protocols::simple_moves::TR(), core::conformation::Residue::type(), and core::chemical::variants_match().
Referenced by protocols::abinitio::DomainAssembly::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), protocols::antibody::AntibodyModelerProtocol::apply(), protocols::protein_interface_design::movers::DockAndRetrieveSidechains::apply(), protocols::antibody_legacy::CDRH3Modeler::apply(), protocols::antibody_legacy::GraftMover::apply(), protocols::antibody_legacy::CloseOneMover::apply(), protocols::ub_e2c::ubi_e2c_modeler::apply(), protocols::antibody::design::GeneralAntibodyModeler::dock_low_res(), protocols::ub_e2c::ubi_e2c_modeler::evaluate_native(), protocols::tcr::ind_remodel_tcr_cdr_loops(), protocols::floppy_tail::FloppyTailMover::low_res(), protocols::ub_e2c::ubi_e2c_modeler::monoub_apply(), protocols::flexpep_docking::FlexPepDockingAbInitio::to_allatom(), and protocols::flexpep_docking::FlexPepDockingLowRes::to_allatom().
◆ 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.
◆ 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.
◆ get_end_res()
| core::Size protocols::simple_moves::ReturnSidechainMover::get_end_res | ( | ) | const |
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ get_start_res()
| core::Size protocols::simple_moves::ReturnSidechainMover::get_start_res | ( | ) | const |
References start_res_.
Referenced by show().
◆ show()
|
overridevirtual |
Outputs details about the Mover, including current settings.
Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.
Reimplemented from protocols::moves::Mover.
References get_end_res(), get_start_res(), and protocols::moves::Mover::show().
Referenced by protocols::simple_moves::operator<<().
Member Data Documentation
◆ allow_chi_copy_
| utility::vector1<bool> protocols::simple_moves::ReturnSidechainMover::allow_chi_copy_ |
Referenced by apply().
◆ copy_all_chi_
| bool protocols::simple_moves::ReturnSidechainMover::copy_all_chi_ |
Referenced by apply(), and ReturnSidechainMover().
◆ end_res_
|
private |
Referenced by apply(), get_end_res(), and ReturnSidechainMover().
◆ remembered_pose_
|
private |
remembered old pose
Referenced by apply().
◆ start_res_
|
private |
residue numbers for which residues to loop over for recovery
Referenced by apply(), get_start_res(), and ReturnSidechainMover().
The documentation for this class was generated from the following files:
- src/protocols/simple_moves/ReturnSidechainMover.hh
- src/protocols/simple_moves/ReturnSidechainMover.cc
