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protocols::simple_moves::carbohydrates::RingConformationMover Class Reference

#include <RingConformationMover.hh>

Inheritance diagram for protocols::simple_moves::carbohydrates::RingConformationMover:
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Public Types

typedef std::pair< std::string,
utility::vector1< core::Angle > > 
ring_conf_def
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 RingConformationMover ()
 Default constructor. More...
 
 RingConformationMover (RingConformationMover const &object_to_copy)
 Copy constructor. More...
 
 RingConformationMover (core::kinematics::MoveMapOP input_movemap)
 Constructor with MoveMap input option. More...
 
RingConformationMoveroperator= (RingConformationMover const &object_to_copy)
 
virtual ~RingConformationMover ()
 
void show (std::ostream &output=std::cout) const
 Generate string representation of RingConformationMover for debugging purposes. More...
 
virtual std::string get_name () const
 Return the name of the Mover. More...
 
virtual protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
virtual void apply (core::pose::Pose &input_pose)
 Apply the corresponding move to <input_pose>. More...
 
core::kinematics::MoveMapCOP movemap () const
 Get the current MoveMap. More...
 
void movemap (core::kinematics::MoveMapOP new_movemap)
 Set the MoveMap. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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 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...
 
void type (const std::string &type_in)
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
std::string get_type () const
 
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...
 
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...
 
virtual bool reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Static Public Member Functions

static void register_options ()
 Register options with the option system. More...
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 

Private Member Functions

void init (core::kinematics::MoveMapOP movemap)
 
void copy_data (RingConformationMover object_to_copy_to, RingConformationMover object_to_copy_from)
 
void setup_residue_list (core::pose::Pose &pose)
 

Private Attributes

core::kinematics::MoveMapOP movemap_
 
utility::vector1< core::Sizeresidue_list_
 
utility::vector1< ring_conf_deffive_membered_ring_conformers_
 
utility::vector1< ring_conf_defsix_membered_ring_conformers_
 

Friends

std::ostream & operator<< (std::ostream &output, RingConformationMover const &object_to_output)
 

Additional Inherited Members

- 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

Based on a given MoveMap, this mover selects movable carbohydrate residues and flips their rings to an idealized energy minimum ring conformer. Six-membered rings sample chair and twist-boat conformations; five- membered rings sample envelope and half-chair. The sampling is biased towards ideally lower-energy conformers.

Remarks
This class is a work in progress....

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::carbohydrates::RingConformationMover::RingConformationMover ( )

Default constructor.

By default, all carbohydrate rings within a given pose will be moved.

References init().

Referenced by clone(), and fresh_instance().

protocols::simple_moves::carbohydrates::RingConformationMover::RingConformationMover ( RingConformationMover const &  object_to_copy)

Copy constructor.

References copy_data().

protocols::simple_moves::carbohydrates::RingConformationMover::RingConformationMover ( core::kinematics::MoveMapOP  input_movemap)

Constructor with MoveMap input option.

Parameters
<input_movemap>,:a MoveMap with desired backbone torsions set to true
Remarks
Movable carbohydrate residues will generally be a subset of residues in the MoveMap whose backbone torsions are set to true.

References init().

protocols::simple_moves::carbohydrates::RingConformationMover::~RingConformationMover ( )
virtual

Member Function Documentation

void protocols::simple_moves::carbohydrates::RingConformationMover::apply ( core::pose::Pose input_pose)
virtual

Apply the corresponding move to <input_pose>.

The mover will create a list of movable residues based on the given MoveMap and select a residue from the list at random. The torsion angles of a randomly selected ring conformer will be applied to the selected residue.

Parameters
<input_pose>,:the structure to be moved
Remarks
A work in progress... Currently, this algorithm depends on CHI angles being set in the params file to fill in for nu angles, as Rosetta has no mechanism for dealing with ring torsions. This may cause issues with other protocols using MoveMap, since MoveMap considers part of the ring as BB and part of the ring as CHI, with some overlap.

Implements protocols::moves::Mover.

References get_name(), core::pose::Pose::residue(), residue_list_, protocols::simple_moves::RG(), core::pose::Pose::set_torsion(), setup_residue_list(), show(), six_membered_ring_conformers_, and protocols::simple_moves::TR().

protocols::moves::MoverOP protocols::simple_moves::carbohydrates::RingConformationMover::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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.

References RingConformationMover().

void protocols::simple_moves::carbohydrates::RingConformationMover::copy_data ( RingConformationMover  object_to_copy_to,
RingConformationMover  object_to_copy_from 
)
private
protocols::moves::MoverOP protocols::simple_moves::carbohydrates::RingConformationMover::fresh_instance ( ) const
virtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

References RingConformationMover().

std::string protocols::simple_moves::carbohydrates::RingConformationMover::get_name ( ) const
virtual

Return the name of the Mover.

Implements protocols::moves::Mover.

References protocols::moves::Mover::type().

Referenced by apply().

void protocols::simple_moves::carbohydrates::RingConformationMover::init ( core::kinematics::MoveMapOP  movemap)
private
kinematics::MoveMapCOP protocols::simple_moves::carbohydrates::RingConformationMover::movemap ( ) const

Get the current MoveMap.

References movemap_.

Referenced by init().

void protocols::simple_moves::carbohydrates::RingConformationMover::movemap ( core::kinematics::MoveMapOP  new_movemap)

Set the MoveMap.

References movemap_.

RingConformationMover & protocols::simple_moves::carbohydrates::RingConformationMover::operator= ( RingConformationMover const &  object_to_copy)
void protocols::simple_moves::carbohydrates::RingConformationMover::register_options ( )
static

Register options with the option system.

void protocols::simple_moves::carbohydrates::RingConformationMover::setup_residue_list ( core::pose::Pose pose)
private
void protocols::simple_moves::carbohydrates::RingConformationMover::show ( std::ostream &  output = std::cout) const

Generate string representation of RingConformationMover for debugging purposes.

References movemap_, and protocols::moves::operator<<().

Referenced by apply(), and protocols::simple_moves::carbohydrates::operator<<().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  output,
RingConformationMover const &  object_to_output 
)
friend

Member Data Documentation

utility::vector1<ring_conf_def> protocols::simple_moves::carbohydrates::RingConformationMover::five_membered_ring_conformers_
private

Referenced by copy_data().

core::kinematics::MoveMapOP protocols::simple_moves::carbohydrates::RingConformationMover::movemap_
private
utility::vector1<core::Size> protocols::simple_moves::carbohydrates::RingConformationMover::residue_list_
private
utility::vector1<ring_conf_def> protocols::simple_moves::carbohydrates::RingConformationMover::six_membered_ring_conformers_
private

Referenced by apply(), copy_data(), and init().


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