protocols::hybridization::BackboneTorsionSampler Class Reference

#include <BackboneTorsionSampler.hh>

Inheritance diagram for protocols::hybridization::BackboneTorsionSampler:

Public Member Functions
	BackboneTorsionSampler ()
	empty constructor fills values with the expected defaults More...
	~BackboneTorsionSampler ()
void	init ()
void	set_scorefunction (core::scoring::ScoreFunctionOP const scorefxn)
void	local_perturb (core::pose::Pose pose, core::Real max_delta_torsion)
void	perturb (core::pose::Pose &pose, core::Size level, core::Real max_delta_torsion, core::Size local, bool rama_biased, bool repack, bool minimize)
void	apply (core::pose::Pose &pose)
void	task_factory (core::pack::task::TaskFactoryCOP tf)
void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &datamap, Filters_map const &filters, moves::Movers_map const &movers, Pose const &pose)
	parse XML (specifically in the context of the parser/scripting scheme) More...
virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...
virtual protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...
std::string	get_name () const
	Each derived class must specify its name. The class name. More...
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual	~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...
	Mover (Mover const &other)
Mover &	operator= (Mover const &other)
	assignment operator More...
virtual core::Real	last_proposal_density_ratio ()
std::string const &	type () const
void	set_type (std::string const &setting)
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	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)
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...
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
core::scoring::ScoreFunctionOP	scorefxn_
core::Real	increase_cycles_
core::Real	temperature_
bool	recover_low_
core::Size	local_
bool	dump_snapshots_
std::string	snapshot_prefix_
core::Size	snapshot_interval_
core::Size	n_nested_
core::Size	perturbed_res_
utility::vector1< core::Size >	residue_list_
protocols::simple_moves::PackRotamersMoverOP	pack_full_repack_
core::optimization::AtomTreeMinimizerOP	minimizer_
core::pose::PoseOP	native_
core::optimization::MinimizerOptionsOP	options_
core::kinematics::MoveMap	mm_
core::pack::task::TaskFactoryCOP	task_factory_

Additional Inherited Members
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::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::hybridization::BackboneTorsionSampler::BackboneTorsionSampler

(

)

empty constructor fills values with the expected defaults

References init().

Referenced by clone().

protocols::hybridization::BackboneTorsionSampler::~BackboneTorsionSampler

(

)

Member Function Documentation

void protocols::hybridization::BackboneTorsionSampler::apply ( core::pose::Pose &  pose )

virtual

Implements protocols::moves::Mover.

References core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::dump_pdb(), dump_snapshots_, core::chemical::element::F, protocols::hybridization::get_gdtmm(), core::chemical::element::I, increase_cycles_, local_, minimizer_, mm_, n_nested_, native_, options_, pack_full_repack_, perturb(), perturbed_res_, recover_low_, protocols::hybridization::score, scorefxn_, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), core::kinematics::MoveMap::set_jump(), snapshot_interval_, snapshot_prefix_, task_factory_, temperature_, core::pose::Pose::total_residue(), and protocols::hybridization::TR().

moves::MoverOP protocols::hybridization::BackboneTorsionSampler::clone ( ) const

virtual

Return a clone of the Mover object.

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.

References BackboneTorsionSampler().

moves::MoverOP protocols::hybridization::BackboneTorsionSampler::fresh_instance ( ) const

virtual

Generates a new Mover object freshly created with the default ctor.

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.

std::string protocols::hybridization::BackboneTorsionSampler::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::hybridization::BackboneTorsionSampler::init

(

void

)

References core::scoring::ScoreFunctionFactory::create_score_function(), dump_snapshots_, increase_cycles_, local_, recover_low_, set_scorefunction(), snapshot_interval_, and temperature_.

Referenced by BackboneTorsionSampler().

void protocols::hybridization::BackboneTorsionSampler::local_perturb	(	core::pose::Pose	pose,
		core::Real	max_delta_torsion
	)

References perturbed_res_, core::pose::Pose::phi(), core::pose::Pose::psi(), core::scoring::rg, core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

void protocols::hybridization::BackboneTorsionSampler::parse_my_tag ( TagCOP  tag, basic::datacache::DataMap &  datamap, Filters_map const &  filters, moves::Movers_map const &  movers, Pose const &  pose  )

virtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References dump_snapshots_, increase_cycles_, local_, n_nested_, native_, protocols::rosetta_scripts::parse_task_operations(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), recover_low_, residue_list_, set_scorefunction(), snapshot_interval_, snapshot_prefix_, task_factory(), temperature_, and core::pose::Pose::total_residue().

void protocols::hybridization::BackboneTorsionSampler::perturb	(	core::pose::Pose &	pose,
		core::Size	level,
		core::Real	max_delta_torsion,
		core::Size	local,
		bool	rama_biased,
		bool	repack,
		bool	minimize
	)

References core::chemical::ResidueType::aa(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::conformation::Residue::has_property(), core::chemical::ResidueType::is_protein(), minimizer_, mm_, options_, pack_full_repack_, perturbed_res_, core::pose::Pose::phi(), core::pose::Pose::psi(), core::scoring::rama, core::scoring::Ramachandran::random_phipsi_from_rama(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, scorefxn_, core::kinematics::MoveMap::set_bb(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::hybridization::BackboneTorsionSampler::set_scorefunction ( core::scoring::ScoreFunctionOP const  scorefxn )

inline

References scorefxn_.

Referenced by init(), and parse_my_tag().

void protocols::hybridization::BackboneTorsionSampler::task_factory

(

core::pack::task::TaskFactoryCOP

tf

)

References task_factory_.

Referenced by parse_my_tag().

Member Data Documentation

bool protocols::hybridization::BackboneTorsionSampler::dump_snapshots_

private

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

core::Real protocols::hybridization::BackboneTorsionSampler::increase_cycles_

private

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

core::Size protocols::hybridization::BackboneTorsionSampler::local_

private

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

core::optimization::AtomTreeMinimizerOP protocols::hybridization::BackboneTorsionSampler::minimizer_

private

Referenced by apply(), and perturb().

core::kinematics::MoveMap protocols::hybridization::BackboneTorsionSampler::mm_

private

Referenced by apply(), and perturb().

core::Size protocols::hybridization::BackboneTorsionSampler::n_nested_

private

Referenced by apply(), and parse_my_tag().

core::pose::PoseOP protocols::hybridization::BackboneTorsionSampler::native_

private

Referenced by apply(), and parse_my_tag().

core::optimization::MinimizerOptionsOP protocols::hybridization::BackboneTorsionSampler::options_

private

Referenced by apply(), and perturb().

protocols::simple_moves::PackRotamersMoverOP protocols::hybridization::BackboneTorsionSampler::pack_full_repack_

private

Referenced by apply(), and perturb().

core::Size protocols::hybridization::BackboneTorsionSampler::perturbed_res_

private

Referenced by apply(), local_perturb(), and perturb().

bool protocols::hybridization::BackboneTorsionSampler::recover_low_

private

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

utility::vector1< core::Size > protocols::hybridization::BackboneTorsionSampler::residue_list_

private

Referenced by parse_my_tag().

core::scoring::ScoreFunctionOP protocols::hybridization::BackboneTorsionSampler::scorefxn_

private

Referenced by apply(), perturb(), and set_scorefunction().

core::Size protocols::hybridization::BackboneTorsionSampler::snapshot_interval_

private

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

std::string protocols::hybridization::BackboneTorsionSampler::snapshot_prefix_

private

Referenced by apply(), and parse_my_tag().

core::pack::task::TaskFactoryCOP protocols::hybridization::BackboneTorsionSampler::task_factory_

private

Referenced by apply(), and task_factory().

core::Real protocols::hybridization::BackboneTorsionSampler::temperature_

private

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

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

• src/protocols/hybridization/BackboneTorsionSampler.hh
• src/protocols/hybridization/BackboneTorsionSampler.cc