#include <RotamerSizedComb.hh>

Public Member Functions
	RotamerSizedComb ()

	RotamerSizedComb (RotamerSizedOP outer_loop_rotamer, RotamerSizedOP inner_loop_rotamer)

virtual	~RotamerSizedComb ()

virtual void	init ()
	Initialization. More...

virtual void	reset ()
	Reset to the first (or random if random()) rotamer. More...

virtual void	operator++ ()
	Move to next rotamer. More...

virtual void	apply (core::pose::Pose &pose)
	Apply the current rotamer to pose. More...

virtual void	apply (core::pose::Pose &pose, Size const id)
	Apply the i-th rotamer to pose. More...

virtual core::Size	size () const
	Get the total number of rotamers in sampler. More...

virtual void	add_rotamer (RotamerSizedOP const &rotamer)
	Add one more rotamer sampler to this sampler. More...

virtual void	clear_rotamer ()
	Clear all rotamer samplers stored in this sampler. More...

void	fast_forward (Size const sampler_number)
	Move sampler to end. More...

virtual std::string	get_name () const
	Name of the class. More...

virtual RotamerType	type () const
	Type of class (see enum in RotamerTypes.hh) More...

virtual void	set_random (bool const setting)
	Set the random sampling state. More...

Public Member Functions inherited from protocols::rotamer_sampler::RotamerSized
	RotamerSized ()

virtual	~RotamerSized ()

virtual bool	not_end () const
	Check if reach the end of rotamer list. More...

Size const &	id () const

virtual void	fast_forward ()

virtual void	set_id (Size const setting)

Public Member Functions inherited from protocols::rotamer_sampler::RotamerBase
	RotamerBase ()

virtual	~RotamerBase ()

virtual bool	random () const
	Check if is random sampling. 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 MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::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
	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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Protected Member Functions
utility::vector1< core::Size >	id2list (core::Size const id) const
	Convert input id number to the individual id_list for each stored rotamer sampler. More...

core::Size	list2id (utility::vector1< core::Size > const &id_list) const
	Convert id_list for each stored rotamer sampler stored to the global id number. More...

Protected Member Functions inherited from protocols::rotamer_sampler::RotamerBase
bool	is_init () const
	Check if the sampler has been initialized. More...

void	set_init (bool const setting)
	Set the initialization state. More...

template<class T >
void	set_and_reinit (T &params, T const &setting)
	Set value of a parameter, return to pre-init state. 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...

Protected Attributes
utility::vector1< core::Size >	id_list_

utility::vector1< RotamerSizedOP >	rotamer_list_

Protected Attributes inherited from protocols::rotamer_sampler::RotamerSized
core::Size	id_

Private Member Functions
void	update_rotamer_ids ()

Private Attributes
core::Size	size_

utility::vector1< core::Size >	size_list_

Additional Inherited Members
Public Types inherited from protocols::rotamer_sampler::RotamerBase
typedef utility::vector1 < core::Real >	TorsionList

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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...

Constructor & Destructor Documentation

protocols::rotamer_sampler::RotamerSizedComb::RotamerSizedComb ( )

protocols::rotamer_sampler::RotamerSizedComb::RotamerSizedComb	(	RotamerSizedOP	outer_loop_rotamer,
		RotamerSizedOP	inner_loop_rotamer
	)

References add_rotamer(), and init().

protocols::rotamer_sampler::RotamerSizedComb::~RotamerSizedComb ( )

virtual

Member Function Documentation

virtual void protocols::rotamer_sampler::RotamerSizedComb::add_rotamer ( RotamerSizedOP const & rotamer )

inlinevirtual

Add one more rotamer sampler to this sampler.

References rotamer_list_, and protocols::rotamer_sampler::RotamerBase::set_init().

Referenced by protocols::rotamer_sampler::RotamerOneValueComb::add_rotamer(), and RotamerSizedComb().

void protocols::rotamer_sampler::RotamerSizedComb::apply ( core::pose::Pose & pose )

virtual

Apply the current rotamer to pose.

Reimplemented from protocols::rotamer_sampler::RotamerSized.

Reimplemented in protocols::rotamer_sampler::rigid_body::RigidBodyRotamer.

References protocols::rotamer_sampler::RotamerSized::id_.

void protocols::rotamer_sampler::RotamerSizedComb::apply	(	core::pose::Pose &	pose,
		Size const	id
	)

virtual

Apply the i-th rotamer to pose.

Implements protocols::rotamer_sampler::RotamerSized.

Reimplemented in protocols::rotamer_sampler::rigid_body::RigidBodyRotamer.

References id2list(), protocols::rotamer_sampler::RotamerBase::is_init(), rotamer_list_, and runtime_assert.

virtual void protocols::rotamer_sampler::RotamerSizedComb::clear_rotamer ( )

inlinevirtual

Clear all rotamer samplers stored in this sampler.

References id_list_, rotamer_list_, protocols::rotamer_sampler::RotamerBase::set_init(), and size_list_.

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::init().

void protocols::rotamer_sampler::RotamerSizedComb::fast_forward ( Size const sampler_number )

Move sampler to end.

References protocols::rotamer_sampler::RotamerSized::id_, id_list_, list2id(), rotamer_list_, and runtime_assert.

virtual std::string protocols::rotamer_sampler::RotamerSizedComb::get_name ( ) const

inlinevirtual

Name of the class.

Reimplemented from protocols::rotamer_sampler::RotamerSized.

Reimplemented in protocols::rotamer_sampler::copy_dofs::ResidueAlternativeRotamerComb, and protocols::rotamer_sampler::RotamerOneValueComb.

utility::vector1< Size > protocols::rotamer_sampler::RotamerSizedComb::id2list ( core::Size const id ) const

protected

Convert input id number to the individual id_list for each stored rotamer sampler.

References protocols::rotamer_sampler::RotamerSized::id(), id_list_, protocols::rotamer_sampler::RotamerBase::is_init(), runtime_assert, and size_list_.

Referenced by apply(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::get_stub(), protocols::rotamer_sampler::RotamerOneValueComb::get_value_list(), and operator++().

void protocols::rotamer_sampler::RotamerSizedComb::init ( void )

virtual

Initialization.

Reimplemented from protocols::rotamer_sampler::RotamerSized.

Reimplemented in protocols::rotamer_sampler::rigid_body::RigidBodyRotamer.

References id_list_, rotamer_list_, runtime_assert, protocols::rotamer_sampler::RotamerBase::set_init(), size_, size_list_, and protocols::TR.

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::init(), and RotamerSizedComb().

core::Size protocols::rotamer_sampler::RotamerSizedComb::list2id ( utility::vector1< core::Size > const & id_list ) const

protected

Convert id_list for each stored rotamer sampler stored to the global id number.

References protocols::rotamer_sampler::RotamerSized::id(), protocols::rotamer_sampler::RotamerBase::is_init(), runtime_assert, and size_list_.

Referenced by fast_forward().

void protocols::rotamer_sampler::RotamerSizedComb::operator++ ( )

virtual

Move to next rotamer.

Reimplemented from protocols::rotamer_sampler::RotamerSized.

References id2list(), protocols::rotamer_sampler::RotamerSized::id_, id_list_, protocols::rotamer_sampler::RotamerSized::not_end(), protocols::rotamer_sampler::RotamerBase::random(), numeric::random::RandomGenerator::random_range(), protocols::RG, runtime_assert, size(), and update_rotamer_ids().

void protocols::rotamer_sampler::RotamerSizedComb::reset ( void )

virtual

Reset to the first (or random if random()) rotamer.

Reimplemented from protocols::rotamer_sampler::RotamerSized.

References protocols::rotamer_sampler::RotamerSized::id_, id_list_, protocols::rotamer_sampler::RotamerBase::is_init(), protocols::rotamer_sampler::RotamerBase::random(), runtime_assert, and update_rotamer_ids().

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::apply().

void protocols::rotamer_sampler::RotamerSizedComb::set_random ( bool const setting )

virtual

Set the random sampling state.

Reimplemented from protocols::rotamer_sampler::RotamerBase.

References rotamer_list_, and protocols::rotamer_sampler::RotamerBase::set_random().

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_FloatingBaseSampler::initialize_rigid_body_sampler().

virtual core::Size protocols::rotamer_sampler::RotamerSizedComb::size ( ) const

inlinevirtual

Get the total number of rotamers in sampler.

Implements protocols::rotamer_sampler::RotamerSized.

References protocols::rotamer_sampler::RotamerBase::is_init(), runtime_assert, and size_.

Referenced by operator++().

virtual RotamerType protocols::rotamer_sampler::RotamerSizedComb::type ( ) const

inlinevirtual

Type of class (see enum in RotamerTypes.hh)

Reimplemented from protocols::rotamer_sampler::RotamerSized.

Reimplemented in protocols::rotamer_sampler::rigid_body::RigidBodyRotamer, protocols::rotamer_sampler::copy_dofs::ResidueAlternativeRotamerComb, and protocols::rotamer_sampler::RotamerOneValueComb.

References protocols::rotamer_sampler::SIZED_COMB.

void protocols::rotamer_sampler::RotamerSizedComb::update_rotamer_ids ( )

private

References id_list_, and rotamer_list_.

Referenced by operator++(), and reset().

Member Data Documentation

utility::vector1<core::Size> protocols::rotamer_sampler::RotamerSizedComb::id_list_

protected

Referenced by clear_rotamer(), fast_forward(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::get_stub(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::get_values(), id2list(), init(), operator++(), reset(), and update_rotamer_ids().

utility::vector1<RotamerSizedOP> protocols::rotamer_sampler::RotamerSizedComb::rotamer_list_

protected

Referenced by add_rotamer(), apply(), clear_rotamer(), fast_forward(), protocols::rotamer_sampler::RotamerOneValueComb::get_value_list(), init(), set_random(), and update_rotamer_ids().

core::Size protocols::rotamer_sampler::RotamerSizedComb::size_

private

Referenced by init(), and size().

utility::vector1<core::Size> protocols::rotamer_sampler::RotamerSizedComb::size_list_

private

Referenced by clear_rotamer(), id2list(), init(), and list2id().

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

symlinks/rosetta/src/protocols/rotamer_sampler/RotamerSizedComb.hh
symlinks/rosetta/src/protocols/rotamer_sampler/RotamerSizedComb.cc

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation