#include <RingConformationMover.hh>

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

Collaboration diagram for protocols::simple_moves::carbohydrates::RingConformationMover:

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...

RingConformationMover &	operator= (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)

Mover &	operator= (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 Strings &	info ()
	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::Size >	residue_list_

utility::vector1< ring_conf_def >	five_membered_ring_conformers_

utility::vector1< ring_conf_def >	six_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....

Definition at line 41 of file RingConformationMover.hh.

Member Typedef Documentation

typedef std::pair<std::string, utility::vector1<core::Angle> > protocols::simple_moves::carbohydrates::RingConformationMover::ring_conf_def

Definition at line 48 of file RingConformationMover.hh.

Constructor & Destructor Documentation

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

Default constructor.

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

Definition at line 59 of file RingConformationMover.cc.

References init().

Referenced by clone(), and fresh_instance().

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

Copy constructor.

Definition at line 71 of file RingConformationMover.cc.

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.

Definition at line 80 of file RingConformationMover.cc.

References init().

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

virtual

Definition at line 100 of file RingConformationMover.cc.

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.

Definition at line 151 of file RingConformationMover.cc.

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.

Definition at line 130 of file RingConformationMover.cc.

References RingConformationMover().

void protocols::simple_moves::carbohydrates::RingConformationMover::copy_data	(	RingConformationMover	object_to_copy_to,
		RingConformationMover	object_to_copy_from
	)

private

Definition at line 296 of file RingConformationMover.cc.

References five_membered_ring_conformers_, movemap_, residue_list_, and six_membered_ring_conformers_.

Referenced by operator=(), and RingConformationMover().

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.

Definition at line 136 of file RingConformationMover.cc.

References RingConformationMover().

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

virtual

Return the name of the Mover.

Implements protocols::moves::Mover.

Definition at line 124 of file RingConformationMover.cc.

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

Referenced by apply().

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

private

Definition at line 230 of file RingConformationMover.cc.

References core::scoring::packstat::old::angles, movemap(), movemap_, six_membered_ring_conformers_, and protocols::moves::Mover::type().

Referenced by RingConformationMover().

kinematics::MoveMapCOP protocols::simple_moves::carbohydrates::RingConformationMover::movemap ( ) const

Get the current MoveMap.

Definition at line 215 of file RingConformationMover.cc.

References movemap_.

Referenced by init().

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

Set the MoveMap.

Definition at line 221 of file RingConformationMover.cc.

References movemap_.

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

Definition at line 87 of file RingConformationMover.cc.

References copy_data(), and protocols::moves::Mover::operator=().

void protocols::simple_moves::carbohydrates::RingConformationMover::register_options ( )

static

Register options with the option system.

Definition at line 106 of file RingConformationMover.cc.

void protocols::simple_moves::carbohydrates::RingConformationMover::setup_residue_list ( core::pose::Pose & pose)

private

Definition at line 311 of file RingConformationMover.cc.

References core::conformation::Residue::carbohydrate_info(), core::conformation::Residue::is_carbohydrate(), movemap_, core::pose::Pose::residue(), residue_list_, and core::pose::Pose::total_residue().

Referenced by apply().

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

Generate string representation of RingConformationMover for debugging purposes.

Definition at line 112 of file RingConformationMover.cc.

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

Definition at line 331 of file RingConformationMover.cc.

Member Data Documentation

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

private

Definition at line 115 of file RingConformationMover.hh.

Referenced by copy_data().

core::kinematics::MoveMapOP protocols::simple_moves::carbohydrates::RingConformationMover::movemap_

private

Definition at line 111 of file RingConformationMover.hh.

Referenced by copy_data(), init(), movemap(), setup_residue_list(), and show().

utility::vector1<core::Size> protocols::simple_moves::carbohydrates::RingConformationMover::residue_list_

private

Definition at line 112 of file RingConformationMover.hh.

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

utility::vector1<ring_conf_def> protocols::simple_moves::carbohydrates::RingConformationMover::six_membered_ring_conformers_

private

Definition at line 116 of file RingConformationMover.hh.

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

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

src/protocols/simple_moves/carbohydrates/RingConformationMover.hh
src/protocols/simple_moves/carbohydrates/RingConformationMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation