#include <RBSegmentRelax.hh>

Inheritance diagram for protocols::rbsegment_relax::RBSegmentRelax:

Collaboration diagram for protocols::rbsegment_relax::RBSegmentRelax:

Public Member Functions
	RBSegmentRelax ()

	RBSegmentRelax (core::scoring::ScoreFunctionOP scorefxn, utility::vector1< RBSegment > const &RBSegment_input, protocols::loops::Loops const &Loops_input)

	~RBSegmentRelax ()

void	initialize (utility::vector1< core::fragment::FragSetOP > const &frag_libs, core::Real rnd=0.0)
	setup_RBSegmentRelax; initialize movesets to defaults More...

void	apply (core::pose::Pose &pose)
	apply method More...

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

void	add_helixMover (RBSegmentMoverOP newMover)

void	add_strandMover (RBSegmentMoverOP newMover)

void	add_genericRBMover (RBSegmentMoverOP newMover)

void	add_compositeSegmentMover (RBSegmentMoverOP newMover)

void	add_wholeStructureMover (protocols::moves::MoverOP newMover)

void	clear_movesets ()

void	set_temperature (core::Real start, core::Real final)

void	set_helicalMoveStepsize (core::Real onAxisTrans, core::Real onAxisRot, core::Real offAxisTrans, core::Real offAxisRot)

void	set_genericRBMoveStepsize (core::Real trans, core::Real rot)

void	set_ncycles (int ncycles)

void	set_cst_weight (core::Real wt)

void	set_cst_width (core::Real width)

void	set_randomize (core::Size rand)

void	set_bootstrap (bool boot)

void	set_skip_lr (bool skip)

void	set_fix_ligands (bool fix)

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

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...

virtual 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...

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

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	set_default_movemap ()

Private Attributes
core::Real	cst_weight_

core::Real	cst_width_

core::Real	cst_stdev_

core::Size	cst_seqwidth_

core::scoring::ScoreFunctionOP	scorefxn_

protocols::moves::MonteCarloOP	mc_

core::Size	cycles_

core::Real	init_temp

core::Real	final_temp

core::Real	helical_sigT

core::Real	helical_sigR

core::Real	helical_sigOffAxisT

core::Real	helical_sigOffAxisR

core::Real	strand_sigT

core::Real	strand_sigR

core::Real	strand_sigOffAxisT

core::Real	strand_sigOffAxisR

core::Real	genericRB_sigT

core::Real	genericRB_sigR

core::Real	randomness_

core::Size	rand_

bool	no_lr_

bool	bootstrap_

bool	fix_ligands_

utility::vector1< RBSegment >	rbsegs_input_

utility::vector1< RBSegment >	rbsegs_remap_

protocols::loops::Loops	loops_input_

utility::vector1 < core::fragment::FragSetOP >	frag_libs_

std::vector < protocols::moves::MoverOP >	WholeStructureMoveSet_

std::vector< RBSegmentMoverOP >	HelixMoveSet_

std::vector< RBSegmentMoverOP >	StrandMoveSet_

std::vector< RBSegmentMoverOP >	GenericRBMoveSet_

std::vector< RBSegmentMoverOP >	CompositeSegmentMoveSet_

Additional Inherited Members
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

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...

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

Definition at line 56 of file RBSegmentRelax.hh.

Constructor & Destructor Documentation

protocols::rbsegment_relax::RBSegmentRelax::RBSegmentRelax ( )

Definition at line 76 of file RBSegmentRelax.cc.

protocols::rbsegment_relax::RBSegmentRelax::RBSegmentRelax	(	core::scoring::ScoreFunctionOP	scorefxn,
		utility::vector1< RBSegment > const &	RBSegment_input,
		protocols::loops::Loops const &	Loops_input
	)

Definition at line 79 of file RBSegmentRelax.cc.

References bootstrap_, cst_seqwidth_, cst_stdev_, cst_weight_, cst_width_, cycles_, final_temp, genericRB_sigR, genericRB_sigT, helical_sigOffAxisR, helical_sigOffAxisT, helical_sigR, helical_sigT, init_temp, no_lr_, rand_, strand_sigOffAxisR, strand_sigOffAxisT, strand_sigR, and strand_sigT.

protocols::rbsegment_relax::RBSegmentRelax::~RBSegmentRelax ( )

Definition at line 77 of file RBSegmentRelax.cc.

Member Function Documentation

void protocols::rbsegment_relax::RBSegmentRelax::add_compositeSegmentMover ( RBSegmentMoverOP newMover)

Definition at line 528 of file RBSegmentRelax.cc.

References CompositeSegmentMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::add_genericRBMover ( RBSegmentMoverOP newMover)

Definition at line 520 of file RBSegmentRelax.cc.

References GenericRBMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::add_helixMover ( RBSegmentMoverOP newMover)

Definition at line 504 of file RBSegmentRelax.cc.

References HelixMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::add_strandMover ( RBSegmentMoverOP newMover)

Definition at line 512 of file RBSegmentRelax.cc.

References StrandMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::add_wholeStructureMover ( protocols::moves::MoverOP newMover)

Definition at line 535 of file RBSegmentRelax.cc.

References WholeStructureMoveSet_.

void protocols::rbsegment_relax::RBSegmentRelax::apply ( core::pose::Pose & pose)

virtual

apply method

Implements protocols::moves::Mover.

Definition at line 186 of file RBSegmentRelax.cc.

Referenced by protocols::RBSegmentRelaxImpl::apply().

void protocols::rbsegment_relax::RBSegmentRelax::clear_movesets ( )

Definition at line 543 of file RBSegmentRelax.cc.

References CompositeSegmentMoveSet_, GenericRBMoveSet_, HelixMoveSet_, StrandMoveSet_, and WholeStructureMoveSet_.

std::string protocols::rbsegment_relax::RBSegmentRelax::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Definition at line 497 of file RBSegmentRelax.cc.

void protocols::rbsegment_relax::RBSegmentRelax::initialize	(	utility::vector1< core::fragment::FragSetOP > const &	frag_libs,
		core::Real	rnd = `0.0`
	)

setup_RBSegmentRelax; initialize movesets to defaults

Definition at line 122 of file RBSegmentRelax.cc.

References CompositeSegmentMoveSet_, frag_libs_, genericRB_sigR, genericRB_sigT, GenericRBMoveSet_, helical_sigOffAxisR, helical_sigOffAxisT, helical_sigR, helical_sigT, HelixMoveSet_, randomness_, strand_sigOffAxisR, strand_sigOffAxisT, strand_sigR, strand_sigT, and StrandMoveSet_.

Referenced by protocols::RBSegmentRelaxImpl::apply().

void protocols::rbsegment_relax::RBSegmentRelax::set_bootstrap ( bool boot)

inline

Definition at line 92 of file RBSegmentRelax.hh.

References bootstrap_.

void protocols::rbsegment_relax::RBSegmentRelax::set_cst_weight ( core::Real wt)

Definition at line 172 of file RBSegmentRelax.cc.

References cst_weight_.

void protocols::rbsegment_relax::RBSegmentRelax::set_cst_width ( core::Real width)

Definition at line 177 of file RBSegmentRelax.cc.

References cst_width_.

void protocols::rbsegment_relax::RBSegmentRelax::set_default_movemap ( )

private

void protocols::rbsegment_relax::RBSegmentRelax::set_fix_ligands ( bool fix)

inline

Definition at line 94 of file RBSegmentRelax.hh.

References fix_ligands_.

void protocols::rbsegment_relax::RBSegmentRelax::set_genericRBMoveStepsize	(	core::Real	trans,
		core::Real	rot
	)

Definition at line 160 of file RBSegmentRelax.cc.

References genericRB_sigR, genericRB_sigT, rot(), and trans().

void protocols::rbsegment_relax::RBSegmentRelax::set_helicalMoveStepsize	(	core::Real	onAxisTrans,
		core::Real	onAxisRot,
		core::Real	offAxisTrans,
		core::Real	offAxisRot
	)