#include <RigidBodyRotamerWithResidueAlternatives.hh>

Public Member Functions
	RigidBodyRotamerWithResidueAlternatives (ResidueAlternativeRotamerCombOP residue_alternative_rotamer, RigidBodyRotamerOP rigid_body_rotamer)

	~RigidBodyRotamerWithResidueAlternatives ()

void	fast_forward ()

void	fast_forward_to_next_rigid_body ()

void	fast_forward_to_next_translation ()

void	fast_forward_to_next_euler_gamma ()

ValueList const &	get_rigid_body_values ()

core::kinematics::Stub	get_stub ()

core::conformation::Residue const &	get_residue_at_origin ()

core::conformation::Residue const &	get_residue_at_origin (Size const seqpos)

ResidueAlternativeRotamerCombOP	residue_alternatives_rotamer ()

RigidBodyRotamerOP	rigid_body_rotamer ()

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

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

void	apply_rigid_body_only (pose::Pose &pose)

void	fast_forward_to_next_residue_pair (Size const i, Size const j)

void	fast_forward_to_next_residue (Size const i)

Vector	get_xyz (Size const seqpos, std::string const atom_name)

conformation::ResidueCOP	get_residue (Size const seqpos)

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

virtual	~RotamerComb ()

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

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

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

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

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

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...

Private Attributes
ResidueAlternativeRotamerCombOP	residue_alternatives_rotamer_

RigidBodyRotamerOP	rigid_body_rotamer_

std::map< Size, conformation::ResidueOP >	transformed_residues

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...

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...

Constructor & Destructor Documentation

protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::RigidBodyRotamerWithResidueAlternatives	(	ResidueAlternativeRotamerCombOP	residue_alternative_rotamer,
		RigidBodyRotamerOP	rigid_body_rotamer
	)

References protocols::rotamer_sampler::RotamerComb::add_rotamer(), residue_alternatives_rotamer_, and rigid_body_rotamer_.

protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::~RigidBodyRotamerWithResidueAlternatives ( )

Member Function Documentation

void protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::apply_rigid_body_only ( pose::Pose & pose )

References rigid_body_rotamer_.

Referenced by protocols::stepwise::screener::SampleApplier::get_update().

void protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::fast_forward ( )

References residue_alternatives_rotamer_, and rigid_body_rotamer_.

Referenced by protocols::stepwise::screener::IntegrationTestBreaker::fast_forward().

void protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::fast_forward_to_next_euler_gamma ( )

References residue_alternatives_rotamer_, and rigid_body_rotamer_.

void protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::fast_forward_to_next_residue ( Size const i )

References residue_alternatives_rotamer_.

void protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::fast_forward_to_next_residue_pair	(	Size const	i,
		Size const	j
	)

References residue_alternatives_rotamer_.

void protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::fast_forward_to_next_rigid_body ( )

References residue_alternatives_rotamer_.

void protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::fast_forward_to_next_translation ( )

References residue_alternatives_rotamer_, and rigid_body_rotamer_.

Referenced by protocols::stepwise::screener::StubDistanceScreener::fast_forward(), and protocols::stepwise::screener::CentroidDistanceScreener::fast_forward().

virtual std::string protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_name ( ) const

inlinevirtual

Name of the class.

Reimplemented from protocols::rotamer_sampler::RotamerComb.

conformation::ResidueCOP protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_residue ( Size const seqpos )

References core::conformation::Residue::clone(), get_residue_at_origin(), rigid_body_rotamer_, and transformed_residues.

Referenced by protocols::stepwise::sampling::rna::legacy::rigid_body::StepWiseRNA_RigidBodyConnectionSampler::initialize_residue_level_screeners().

core::conformation::Residue const & protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_residue_at_origin ( )

References rigid_body_rotamer_.

Referenced by get_residue(), and get_xyz().

core::conformation::Residue const & protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_residue_at_origin ( Size const seqpos )

References residue_alternatives_rotamer_, and rigid_body_rotamer_.

ValueList const & protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_rigid_body_values ( )

References rigid_body_rotamer_.

Referenced by protocols::stepwise::screener::BaseBinMapUpdater::get_update().

core::kinematics::Stub protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_stub ( )

References rigid_body_rotamer_.

Referenced by protocols::stepwise::screener::StubApplier::get_update().

Vector protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::get_xyz	(	Size const	seqpos,
		std::string const	atom_name
	)

References get_residue_at_origin(), rigid_body_rotamer_, core::conformation::Residue::xyz(), and protocols::kinmatch::xyz().

ResidueAlternativeRotamerCombOP protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::residue_alternatives_rotamer ( )

References residue_alternatives_rotamer_.

Referenced by protocols::stepwise::StepWiseSampleAndScreen::early_exit_check(), and protocols::stepwise::StepWiseSampleAndScreen::set_ok_to_increment().

RigidBodyRotamerOP protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::rigid_body_rotamer ( )

References rigid_body_rotamer_.

Referenced by protocols::stepwise::StepWiseSampleAndScreen::early_exit_check().

virtual RotamerType protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::type ( ) const

inlinevirtual

Type of class (see enum in RotamerTypes.hh)

Reimplemented from protocols::rotamer_sampler::RotamerComb.

References protocols::rotamer_sampler::RIGID_BODY_WITH_RESIDUE_ALTERNATIVES.

Member Data Documentation

ResidueAlternativeRotamerCombOP protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::residue_alternatives_rotamer_

private

Referenced by fast_forward(), fast_forward_to_next_euler_gamma(), fast_forward_to_next_residue(), fast_forward_to_next_residue_pair(), fast_forward_to_next_rigid_body(), fast_forward_to_next_translation(), get_residue_at_origin(), residue_alternatives_rotamer(), and RigidBodyRotamerWithResidueAlternatives().

RigidBodyRotamerOP protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::rigid_body_rotamer_

private

Referenced by apply_rigid_body_only(), fast_forward(), fast_forward_to_next_euler_gamma(), fast_forward_to_next_translation(), get_residue(), get_residue_at_origin(), get_rigid_body_values(), get_stub(), get_xyz(), rigid_body_rotamer(), and RigidBodyRotamerWithResidueAlternatives().

std::map< Size, conformation::ResidueOP > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternatives::transformed_residues

private

Referenced by get_residue().

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

symlinks/rosetta/src/protocols/rotamer_sampler/rigid_body/RigidBodyRotamerWithResidueAlternatives.hh
symlinks/rosetta/src/protocols/rotamer_sampler/rigid_body/RigidBodyRotamerWithResidueAlternatives.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation