A Mover class for flipping the plane of a carbohydrate pyranose ring 180 degrees about its anomeric bond. More...
#include <RingPlaneFlipMover.hh>
Public Member Functions | |
| RingPlaneFlipMover () | |
| Default constructor. More... | |
| RingPlaneFlipMover (RingPlaneFlipMover const &object_to_copy) | |
| Copy constructor. More... | |
| RingPlaneFlipMover (core::kinematics::MoveMapOP input_movemap) | |
| Constructor with MoveMap input option. More... | |
| RingPlaneFlipMover (core::select::residue_selector::ResidueSelectorCOP selector) | |
| Constructor with ResidueSelector input option. More... | |
| RingPlaneFlipMover & | operator= (RingPlaneFlipMover const &object_to_copy) |
| ~RingPlaneFlipMover () override=default | |
| void | show (std::ostream &output=std::cout) const override |
| Generate string representation of RingPlaneFlipMover for debugging purposes. More... | |
| std::string | get_name () const override |
| Return the name of the Mover. 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 (TagCOP tag, basic::datacache::DataMap &data) override |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | apply (core::pose::Pose &input_pose) override |
| Apply the corresponding move to <input_pose>. More... | |
| void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const override |
| Provide the citation. More... | |
| core::kinematics::MoveMapCOP | movemap (core::pose::Pose const &pose) const |
| Get the current MoveMap, creating it if needed. More... | |
| core::select::residue_selector::ResidueSelectorCOP | selector () const |
| Get the current ResidueSelector. More... | |
| void | movemap (core::kinematics::MoveMapOP new_movemap) |
| Set the MoveMap. More... | |
| void | movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory) |
| Set the MoveMapFactory. More... | |
| void | selector (core::select::residue_selector::ResidueSelectorCOP new_selector) |
| Set the ResidueSelector. More... | |
 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 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 void | register_options () |
| Register options with the option system. More... | |
| static std::string | mover_name () |
| 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 | |
| void | init () |
| void | copy_data (RingPlaneFlipMover &object_to_copy_to, RingPlaneFlipMover const &object_to_copy_from) |
| void | setup_movable_torsion_pairs (core::pose::Pose const &pose) |
Private Attributes | |
| core::kinematics::MoveMapOP | movemap_ |
| core::select::movemap::MoveMapFactoryCOP | movemap_factory_ |
| core::select::residue_selector::ResidueSelectorCOP | selector_ |
| utility::vector1< std::pair< core::id::TorsionID, core::id::TorsionID > > | movable_torsion_pairs_ |
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::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
A Mover class for flipping the plane of a carbohydrate pyranose ring 180 degrees about its anomeric bond.
Based on a given ResidueSelector and limited by a MoveMap, this mover selects applicable cyclic residues and performs a 180-degree shearing move in which the anomeric bond and the main-chain bond on the opposite side of the ring are moved in opposite directions. An "applicable" residue is limited to 1,4-linked aldopyranoses or 2,5- linked ketopyranoses for which both the anomeric bond and the glycosidic linkage bond are equatorial.
Constructor & Destructor Documentation
◆ RingPlaneFlipMover() [1/4]
| protocols::carbohydrates::RingPlaneFlipMover::RingPlaneFlipMover | ( | ) |
Default constructor.
References init().
◆ RingPlaneFlipMover() [2/4]
| protocols::carbohydrates::RingPlaneFlipMover::RingPlaneFlipMover | ( | RingPlaneFlipMover const & | object_to_copy | ) |
Copy constructor.
References copy_data().
◆ RingPlaneFlipMover() [3/4]
| protocols::carbohydrates::RingPlaneFlipMover::RingPlaneFlipMover | ( | core::kinematics::MoveMapOP | input_movemap | ) |
Constructor with MoveMap input option.
References init().
◆ RingPlaneFlipMover() [4/4]
| protocols::carbohydrates::RingPlaneFlipMover::RingPlaneFlipMover | ( | core::select::residue_selector::ResidueSelectorCOP | selector | ) |
Constructor with ResidueSelector input option.
References init().
◆ ~RingPlaneFlipMover()
|
overridedefault |
Member Function Documentation
◆ apply()
|
overridevirtual |
Apply the corresponding move to <input_pose>.
- Parameters
-
<input_pose> the structure to be moved
Implements protocols::moves::Mover.
References protocols::moves::FAIL_DO_NOT_RETRY, get_name(), movable_torsion_pairs_, core::scoring::rg, protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_torsion(), setup_movable_torsion_pairs(), show(), core::pose::Pose::torsion(), protocols::TR(), and protocols::moves::Mover::type().
◆ 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.
◆ copy_data()
|
private |
References movable_torsion_pairs_, movemap_, movemap_factory_, and selector_.
Referenced by operator=(), and RingPlaneFlipMover().
◆ 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_name()
|
overridevirtual |
Return the name of the Mover.
Implements protocols::moves::Mover.
References mover_name().
Referenced by apply().
◆ init()
|
private |
References mover_name(), and protocols::moves::Mover::type().
Referenced by RingPlaneFlipMover().
◆ movemap() [1/2]
|
inline |
Set the MoveMap.
References movemap_.
◆ movemap() [2/2]
| core::kinematics::MoveMapCOP protocols::carbohydrates::RingPlaneFlipMover::movemap | ( | core::pose::Pose const & | pose | ) | const |
Get the current MoveMap, creating it if needed.
References movemap_, and movemap_factory_.
Referenced by setup_movable_torsion_pairs().
◆ movemap_factory()
|
inline |
◆ mover_name()
|
inlinestatic |
◆ operator=()
| RingPlaneFlipMover & protocols::carbohydrates::RingPlaneFlipMover::operator= | ( | RingPlaneFlipMover const & | object_to_copy | ) |
References copy_data().
◆ 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 movemap_factory(), core::select::movemap::parse_movemap_factory(), protocols::rosetta_scripts::parse_movemap_factory_legacy(), core::select::residue_selector::parse_residue_selector(), selector_, and protocols::TR().
◆ provide_citation_info()
|
overridevirtual |
◆ provide_xml_schema()
|
static |
References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), core::select::movemap::attributes_for_parse_movemap_factory_default_attr_name(), protocols::rosetta_scripts::attributes_for_parse_residue_selector(), mover_name(), protocols::moves::Mover::name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().
Referenced by protocols::carbohydrates::RingPlaneFlipMoverCreator::provide_xml_schema().
◆ register_options()
|
static |
Register options with the option system.
References protocols::moves::Mover::register_options().
Referenced by protocols::glycan_docking::GlycanDockProtocol::register_options().
◆ selector() [1/2]
|
inline |
Get the current ResidueSelector.
References selector_.
◆ selector() [2/2]
|
inline |
Set the ResidueSelector.
References selector_.
◆ setup_movable_torsion_pairs()
|
private |
References core::id::TorsionID::BOGUS_TORSION_ID(), core::conformation::Residue::carbohydrate_info(), core::pose::Pose::conformation(), core::conformation::Conformation::contains_carbohydrate_residues(), core::chemical::rings::EQUATORIAL, core::conformation::carbohydrates::find_seqpos_of_saccharides_child_residue_at(), core::conformation::carbohydrates::get_non_NU_TorsionID_from_AtomIDs(), core::conformation::carbohydrates::get_reference_atoms_for_phi(), core::conformation::carbohydrates::get_reference_atoms_for_psi(), protocols::moves::Mover::info(), core::chemical::rings::is_atom_axial_or_equatorial_to_ring(), core::conformation::Residue::is_branch_point(), core::conformation::Residue::is_carbohydrate(), core::conformation::Residue::is_upper_terminus(), movable_torsion_pairs_, movemap(), core::conformation::Residue::name(), core::pose::Pose::residue(), selector_, core::pose::Pose::size(), protocols::TR(), core::conformation::Residue::type(), protocols::moves::Mover::type(), and core::conformation::Residue::xyz().
Referenced by apply().
◆ show()
|
overridevirtual |
Generate string representation of RingPlaneFlipMover for debugging purposes.
Reimplemented from protocols::moves::Mover.
References protocols::moves::Mover::show().
Referenced by apply(), and protocols::carbohydrates::operator<<().
Member Data Documentation
◆ movable_torsion_pairs_
|
private |
Referenced by apply(), copy_data(), and setup_movable_torsion_pairs().
◆ movemap_
|
mutableprivate |
Referenced by copy_data(), and movemap().
◆ movemap_factory_
|
private |
Referenced by copy_data(), movemap(), and movemap_factory().
◆ selector_
|
private |
Referenced by copy_data(), parse_my_tag(), selector(), and setup_movable_torsion_pairs().
The documentation for this class was generated from the following files:
- src/protocols/carbohydrates/RingPlaneFlipMover.hh
- src/protocols/carbohydrates/RingPlaneFlipMover.cc
