Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::carbohydrates::RingPlaneFlipMover Class Reference

A Mover class for flipping the plane of a carbohydrate pyranose ring 180 degrees about its anomeric bond. More...

#include <RingPlaneFlipMover.hh>

Inheritance diagram for protocols::carbohydrates::RingPlaneFlipMover:
Inheritance graph

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...
RingPlaneFlipMoveroperator= (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 Stringsinfo ()
 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()

protocols::carbohydrates::RingPlaneFlipMover::~RingPlaneFlipMover ( )

Member Function Documentation

◆ apply()

void protocols::carbohydrates::RingPlaneFlipMover::apply ( core::pose::Pose input_pose)

◆ clone()

protocols::moves::MoverOP protocols::carbohydrates::RingPlaneFlipMover::clone ( ) const

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()

void protocols::carbohydrates::RingPlaneFlipMover::copy_data ( RingPlaneFlipMover object_to_copy_to,
RingPlaneFlipMover const &  object_to_copy_from 

◆ fresh_instance()

protocols::moves::MoverOP protocols::carbohydrates::RingPlaneFlipMover::fresh_instance ( ) const

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()

std::string protocols::carbohydrates::RingPlaneFlipMover::get_name ( ) const

Return the name of the Mover.

Implements protocols::moves::Mover.

References mover_name().

Referenced by apply().

◆ init()

void protocols::carbohydrates::RingPlaneFlipMover::init ( void  )

◆ movemap() [1/2]

void protocols::carbohydrates::RingPlaneFlipMover::movemap ( core::kinematics::MoveMapOP  new_movemap)

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()

void protocols::carbohydrates::RingPlaneFlipMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP  new_movemap_factory)

Set the MoveMapFactory.

References movemap_factory_.

Referenced by parse_my_tag().

◆ mover_name()

static std::string protocols::carbohydrates::RingPlaneFlipMover::mover_name ( )

◆ operator=()

RingPlaneFlipMover & protocols::carbohydrates::RingPlaneFlipMover::operator= ( RingPlaneFlipMover const &  object_to_copy)

References copy_data().

◆ parse_my_tag()

void protocols::carbohydrates::RingPlaneFlipMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap data 

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()

void protocols::carbohydrates::RingPlaneFlipMover::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const

Provide the citation.

Reimplemented from protocols::moves::Mover.

References mover_name().

◆ provide_xml_schema()

void protocols::carbohydrates::RingPlaneFlipMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ register_options()

void protocols::carbohydrates::RingPlaneFlipMover::register_options ( )

◆ selector() [1/2]

core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::RingPlaneFlipMover::selector ( ) const

Get the current ResidueSelector.

References selector_.

◆ selector() [2/2]

void protocols::carbohydrates::RingPlaneFlipMover::selector ( core::select::residue_selector::ResidueSelectorCOP  new_selector)

Set the ResidueSelector.

References selector_.

◆ setup_movable_torsion_pairs()

void protocols::carbohydrates::RingPlaneFlipMover::setup_movable_torsion_pairs ( core::pose::Pose const &  pose)

◆ show()

void protocols::carbohydrates::RingPlaneFlipMover::show ( std::ostream &  output = std::cout) const

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_

utility::vector1< std::pair< core::id::TorsionID, core::id::TorsionID > > protocols::carbohydrates::RingPlaneFlipMover::movable_torsion_pairs_

◆ movemap_

core::kinematics::MoveMapOP protocols::carbohydrates::RingPlaneFlipMover::movemap_

Referenced by copy_data(), and movemap().

◆ movemap_factory_

core::select::movemap::MoveMapFactoryCOP protocols::carbohydrates::RingPlaneFlipMover::movemap_factory_

Referenced by copy_data(), movemap(), and movemap_factory().

◆ selector_

core::select::residue_selector::ResidueSelectorCOP protocols::carbohydrates::RingPlaneFlipMover::selector_

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