#include <StepWiseSamplerSizedComb.hh>

Inheritance diagram for protocols::stepwise::sampler::StepWiseSamplerSizedComb:

Public Member Functions
	StepWiseSamplerSizedComb ()

	StepWiseSamplerSizedComb (StepWiseSamplerSizedOP outer_loop_rotamer, StepWiseSamplerSizedOP inner_loop_rotamer)

	~StepWiseSamplerSizedComb () override

void	init () override
	Initialization. More...

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

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

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

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

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

virtual void	add_external_loop_rotamer (StepWiseSamplerSizedOP const &rotamer)
	Add one more rotamer sampler to this sampler. This one is 'external' to any previously existing rotamers, i.e., this new only gets incremented when all previous existing rotamers complete their cycle. More...

virtual void	add_internal_loop_rotamer (StepWiseSamplerSizedOP const &rotamer)
	Add one more rotamer sampler to this sampler. This one is 'internal' to existing rotamers, i.e., when this one completes its cycle, the existing. More...

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

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

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

toolbox::SamplerPlusPlusType	type () const override
	Type of class (see enum in SamplerPlusPlusTypes.hh) More...

void	set_random (bool const setting) override
	Set the random modeler state. More...

void	show (std::ostream &out, core::Size const indent=0) const override
	output summary of class More...

Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSamplerSized
	StepWiseSamplerSized ()

	~StepWiseSamplerSized () override

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

core::Size const &	id () const

virtual void	fast_forward ()

virtual void	set_id (core::Size const setting)

Public Member Functions inherited from protocols::stepwise::sampler::StepWiseSampler
	StepWiseSampler ()

	~StepWiseSampler () override

virtual bool	random () const
	Check if is random modeler. More...

Public Member Functions inherited from protocols::toolbox::SamplerPlusPlus
	SamplerPlusPlus ()

	~SamplerPlusPlus () override

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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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::toolbox::SamplerPlusPlus
bool	is_init () const
	return OP to the subsampler that controls exactly this torsion_id (assume only one). This is worked out in recces/sampler/MC_Sampler & derived classes – wouldn't be too hard to generalize to stepwise/sampler/ classes, too. 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 < StepWiseSamplerSizedOP >	rotamer_list_

Protected Attributes inherited from protocols::stepwise::sampler::StepWiseSamplerSized
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::toolbox::SamplerPlusPlus
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 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::stepwise::sampler::StepWiseSamplerSizedComb::StepWiseSamplerSizedComb ( )

protocols::stepwise::sampler::StepWiseSamplerSizedComb::StepWiseSamplerSizedComb	(	StepWiseSamplerSizedOP	outer_loop_rotamer,
		StepWiseSamplerSizedOP	inner_loop_rotamer
	)

References init(), and rotamer_list_.

protocols::stepwise::sampler::StepWiseSamplerSizedComb::~StepWiseSamplerSizedComb ( )

overridedefault

Member Function Documentation

virtual void protocols::stepwise::sampler::StepWiseSamplerSizedComb::add_external_loop_rotamer ( StepWiseSamplerSizedOP const & rotamer )

inlinevirtual

Add one more rotamer sampler to this sampler. This one is 'external' to any previously existing rotamers, i.e., this new only gets incremented when all previous existing rotamers complete their cycle.

References rotamer_list_, and protocols::toolbox::SamplerPlusPlus::set_init().

Referenced by protocols::stepwise::sampler::StepWiseSamplerOneValueComb::add_external_loop_rotamer().

virtual void protocols::stepwise::sampler::StepWiseSamplerSizedComb::add_internal_loop_rotamer ( StepWiseSamplerSizedOP const & rotamer )

inlinevirtual

Add one more rotamer sampler to this sampler. This one is 'internal' to existing rotamers, i.e., when this one completes its cycle, the existing.

References rotamer_list_, and protocols::toolbox::SamplerPlusPlus::set_init().

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::apply ( core::pose::Pose & pose )

overridevirtual

Apply the current rotamer to pose.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References protocols::stepwise::sampler::StepWiseSamplerSized::id_.

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::apply	(	core::pose::Pose &	pose,
		core::Size const	id
	)

overridevirtual

Apply the i-th rotamer to pose.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

References id2list(), protocols::toolbox::SamplerPlusPlus::is_init(), and rotamer_list_.

virtual void protocols::stepwise::sampler::StepWiseSamplerSizedComb::clear_rotamer ( )

inlinevirtual

Clear all rotamer samplers stored in this sampler.

References id_list_, rotamer_list_, protocols::toolbox::SamplerPlusPlus::set_init(), and size_list_.

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::init().

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::fast_forward ( core::Size const sampler_number )

Move sampler to end.

References protocols::stepwise::sampler::StepWiseSamplerSized::id_, id_list_, list2id(), and rotamer_list_.

std::string protocols::stepwise::sampler::StepWiseSamplerSizedComb::get_name ( ) const

inlineoverridevirtual

Name of the class.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

utility::vector1< core::Size > protocols::stepwise::sampler::StepWiseSamplerSizedComb::id2list ( core::Size const id ) const

protected

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

References protocols::stepwise::sampler::StepWiseSamplerSized::id(), id_list_, protocols::toolbox::SamplerPlusPlus::is_init(), and size_list_.

Referenced by apply(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::get_stub(), protocols::stepwise::sampler::StepWiseSamplerOneValueComb::get_value_list(), and operator++().

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::init ( void )

overridevirtual

Initialization.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References id_list_, rotamer_list_, protocols::toolbox::SamplerPlusPlus::set_init(), size_, size_list_, and protocols::TR().

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::init(), and StepWiseSamplerSizedComb().

core::Size protocols::stepwise::sampler::StepWiseSamplerSizedComb::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::stepwise::sampler::StepWiseSamplerSized::id(), protocols::toolbox::SamplerPlusPlus::is_init(), and size_list_.

Referenced by fast_forward().

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::operator++ ( )

overridevirtual

Move to next rotamer.

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References id2list(), protocols::stepwise::sampler::StepWiseSamplerSized::id_, id_list_, protocols::stepwise::sampler::StepWiseSamplerSized::not_end(), protocols::stepwise::sampler::StepWiseSampler::random(), core::scoring::rg, size(), and update_rotamer_ids().

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::reset ( void )

overridevirtual

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

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References protocols::stepwise::sampler::StepWiseSamplerSized::id_, id_list_, protocols::toolbox::SamplerPlusPlus::is_init(), protocols::stepwise::sampler::StepWiseSampler::random(), and update_rotamer_ids().

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::set_random ( bool const setting )

overridevirtual

Set the random modeler state.

Reimplemented from protocols::stepwise::sampler::StepWiseSampler.

References rotamer_list_, and protocols::stepwise::sampler::StepWiseSampler::set_random().

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::show	(	std::ostream &	out,
		core::Size const	indent = `0`
	)		const

overridevirtual

output summary of class

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References rotamer_list_, and protocols::stepwise::sampler::StepWiseSamplerSized::show().

core::Size protocols::stepwise::sampler::StepWiseSamplerSizedComb::size ( ) const

inlineoverridevirtual

Get the total number of rotamers in sampler.

Implements protocols::stepwise::sampler::StepWiseSamplerSized.

References protocols::toolbox::SamplerPlusPlus::is_init(), and size_.

Referenced by operator++().

toolbox::SamplerPlusPlusType protocols::stepwise::sampler::StepWiseSamplerSizedComb::type ( ) const

inlineoverridevirtual

Type of class (see enum in SamplerPlusPlusTypes.hh)

Reimplemented from protocols::stepwise::sampler::StepWiseSamplerSized.

References protocols::toolbox::SIZED_COMB.

void protocols::stepwise::sampler::StepWiseSamplerSizedComb::update_rotamer_ids ( )

private

References id_list_, and rotamer_list_.

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

Member Data Documentation

utility::vector1<core::Size> protocols::stepwise::sampler::StepWiseSamplerSizedComb::id_list_

protected

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

utility::vector1<StepWiseSamplerSizedOP> protocols::stepwise::sampler::StepWiseSamplerSizedComb::rotamer_list_

protected

Referenced by add_external_loop_rotamer(), add_internal_loop_rotamer(), apply(), clear_rotamer(), fast_forward(), protocols::stepwise::sampler::StepWiseSamplerOneValueComb::get_value_list(), init(), set_random(), show(), StepWiseSamplerSizedComb(), and update_rotamer_ids().

core::Size protocols::stepwise::sampler::StepWiseSamplerSizedComb::size_

private

Referenced by init(), and size().

utility::vector1<core::Size> protocols::stepwise::sampler::StepWiseSamplerSizedComb::size_list_

private

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

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

src/protocols/stepwise/sampler/StepWiseSamplerSizedComb.hh
src/protocols/stepwise/sampler/StepWiseSamplerSizedComb.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