#include <BackboneTorsionPerturbation.hh>

Inheritance diagram for protocols::hybridization::BackboneTorsionPerturbation:

[legend]

Public Member Functions
	BackboneTorsionPerturbation ()
	empty constructor fills values with the expected defaults More...

	~BackboneTorsionPerturbation () override

void	init ()

void	set_scorefunction (core::scoring::ScoreFunctionOP const scorefxn)

void	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) override
	Main Method. More...

void	task_factory (core::pack::task::TaskFactoryCOP tf)

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &datamap) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

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

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 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...

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

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 std::list< std::string >	Strings

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

◆ BackboneTorsionPerturbation()

protocols::hybridization::BackboneTorsionPerturbation::BackboneTorsionPerturbation ( )

empty constructor fills values with the expected defaults

References core::init::init().

◆ ~BackboneTorsionPerturbation()

protocols::hybridization::BackboneTorsionPerturbation::~BackboneTorsionPerturbation ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::pose::Pose::conformation(), core::pack::task::TaskFactory::create_packer_task(), core::scoring::ScoreFunctionFactory::create_score_function(), core::conformation::Conformation::detect_disulfides(), core::pose::Pose::dump_pdb(), core::chemical::element::F, protocols::hybridization::get_gdtmm(), core::scoring::get_score_function(), core::chemical::element::I, protocols::hybridization::score, core::pose::Pose::size(), and protocols::hybridization::TR().

◆ clone()

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

overridevirtual

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.

◆ fresh_instance()

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

overridevirtual

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.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

◆ init()

void protocols::hybridization::BackboneTorsionPerturbation::init ( void )

◆ mover_name()

std::string protocols::hybridization::BackboneTorsionPerturbation::mover_name ( )

static

Referenced by protocols::hybridization::BackboneTorsionPerturbationCreator::keyname().

◆ parse_my_tag()

void protocols::hybridization::BackboneTorsionPerturbation::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References core::pack::task::parse_task_operations(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::hybridization::TR().

◆ perturb() [1/2]

void protocols::hybridization::BackboneTorsionPerturbation::perturb	(	core::pose::Pose &	pose,
		core::Real	max_delta_torsion
	)

References protocols::hybridization::add_constraints(), core::scoring::atom_pair_constraint, core::pose::Pose::dump_pdb(), core::chemical::element::I, protocols::hybridization::optimize(), core::pose::Pose::phi(), protocols::hybridization::pick_pivots(), core::pose::Pose::psi(), core::pose::Pose::remove_constraints(), core::scoring::rg, core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

◆ perturb() [2/2]

void protocols::hybridization::BackboneTorsionPerturbation::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::ResidueTypeBase::aa(), core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::conformation::Residue::has_property(), core::chemical::ResidueTypeBase::is_protein(), protocols::antibody::design::minimize, core::pose::Pose::phi(), core::pose::Pose::psi(), core::scoring::rama, protocols::antibody::design::repack, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::scoring::rg, core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::size().

◆ provide_xml_schema()

void protocols::hybridization::BackboneTorsionPerturbation::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::hybridization::BackboneTorsionPerturbationCreator::provide_xml_schema().

◆ set_scorefunction()

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

inline

References scorefxn_.

◆ task_factory()

void protocols::hybridization::BackboneTorsionPerturbation::task_factory ( core::pack::task::TaskFactoryCOP tf )

Member Data Documentation

◆ dump_snapshots_

bool protocols::hybridization::BackboneTorsionPerturbation::dump_snapshots_

private

◆ increase_cycles_

core::Real protocols::hybridization::BackboneTorsionPerturbation::increase_cycles_

private

◆ local_

core::Size protocols::hybridization::BackboneTorsionPerturbation::local_

private

◆ minimizer_

core::optimization::AtomTreeMinimizerOP protocols::hybridization::BackboneTorsionPerturbation::minimizer_

private

◆ mm_

core::kinematics::MoveMap protocols::hybridization::BackboneTorsionPerturbation::mm_

private

◆ native_

core::pose::PoseOP protocols::hybridization::BackboneTorsionPerturbation::native_

private

◆ options_

core::optimization::MinimizerOptionsOP protocols::hybridization::BackboneTorsionPerturbation::options_

private

◆ pack_full_repack_

protocols::minimization_packing::PackRotamersMoverOP protocols::hybridization::BackboneTorsionPerturbation::pack_full_repack_

private

◆ perturbed_res_

core::Size protocols::hybridization::BackboneTorsionPerturbation::perturbed_res_

private

◆ recover_low_

bool protocols::hybridization::BackboneTorsionPerturbation::recover_low_

private

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::hybridization::BackboneTorsionPerturbation::scorefxn_

private

Referenced by set_scorefunction().

◆ snapshot_counter_

core::Size protocols::hybridization::BackboneTorsionPerturbation::snapshot_counter_

private

◆ snapshot_interval_

core::Size protocols::hybridization::BackboneTorsionPerturbation::snapshot_interval_

private

◆ snapshot_prefix_

std::string protocols::hybridization::BackboneTorsionPerturbation::snapshot_prefix_

private

◆ task_factory_

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

private

◆ temperature_

core::Real protocols::hybridization::BackboneTorsionPerturbation::temperature_

private

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

src/protocols/hybridization/BackboneTorsionPerturbation.hh
src/protocols/hybridization/BackboneTorsionPerturbation.cc

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	snapshot_counter_

core::Size	perturbed_res_

protocols::minimization_packing::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_

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ BackboneTorsionPerturbation()

◆ ~BackboneTorsionPerturbation()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ init()

◆ mover_name()

◆ parse_my_tag()

◆ perturb() [1/2]

◆ perturb() [2/2]

◆ provide_xml_schema()

◆ set_scorefunction()

◆ task_factory()

Member Data Documentation

◆ dump_snapshots_

◆ increase_cycles_

◆ local_

◆ minimizer_

◆ mm_

◆ native_

◆ options_

◆ pack_full_repack_

◆ perturbed_res_

◆ recover_low_

◆ scorefxn_

◆ snapshot_counter_

◆ snapshot_interval_

◆ snapshot_prefix_

◆ task_factory_

◆ temperature_