#include <MedalMover.hh>

Inheritance diagram for protocols::medal::MedalMover:

[legend]

Public Member Functions
	MedalMover ()

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

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

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 Types
typedef utility::vector1< core::Real >	Probabilities

Protected Member Functions
void	do_loop_closure (core::pose::Pose *pose, core::util::ChainbreakUtil const &chainbreak_util) const
	Closes chainbreaks in <pose> More...

void	compute_per_residue_probabilities (const unsigned num_residues, const core::sequence::SequenceAlignment &alignment, const protocols::loops::Loops &chunks, const core::kinematics::FoldTree &tree, const core::fragment::FragSet &fragments, Probabilities *probs) const
	Computes per-residue sampling probabilities. More...

void	decompose_structure (const core::pose::Pose &pose, protocols::loops::LoopsOP &chunks) const
	Partitions the structure into non-overlapping chunks. More...

protocols::moves::MoverOP	create_fragment_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
	Configures a mover for biased fragment insertion. More...

protocols::moves::MoverOP	create_fragment_and_rigid_mover (const core::pose::Pose &pose, core::pose::PoseOP native, core::scoring::ScoreFunctionOP score, core::fragment::FragSetOP fragments, const Probabilities &probs, const std::string &policy, unsigned library_size) const
	Configures a mover for alternating biased fragment insertion and rigid body moves. More...

protocols::moves::MoverOP	create_small_mover (core::pose::PoseOP native, core::scoring::ScoreFunctionOP score) const
	Configures a mover for performing alternating small and shear moves. More...

core::scoring::ScoreFunctionOP	score_function () const
	Configures a basic score functions which callers can then specialize. 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
core::fragment::FragSetOP	fragments_sm_

core::fragment::FragSetOP	fragments_lg_

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

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...

Member Typedef Documentation

◆ Probabilities

typedef utility::vector1<core::Real> protocols::medal::MedalMover::Probabilities

protected

Constructor & Destructor Documentation

◆ MedalMover()

protocols::medal::MedalMover::MedalMover ( )

References fragments_lg_, and fragments_sm_.

Member Function Documentation

◆ apply()

void protocols::medal::MedalMover::apply ( core::pose::Pose & )

overridevirtual

◆ clone()

protocols::moves::MoverOP protocols::medal::MedalMover::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.

◆ compute_per_residue_probabilities()

void protocols::medal::MedalMover::compute_per_residue_probabilities	(	const unsigned	num_residues,
		const core::sequence::SequenceAlignment &	alignment,
		const protocols::loops::Loops &	chunks,
		const core::kinematics::FoldTree &	tree,
		const core::fragment::FragSet &	fragments,
		Probabilities *	probs
	)		const

protected

Computes per-residue sampling probabilities.

References core::scoring::alignment, protocols::medal::alignment_probabilities(), protocols::medal::chunk_probabilities(), protocols::medal::cutpoint_probabilities(), protocols::medal::end_bias_probabilities(), protocols::medal::invalidate_residues_spanning_cuts(), core::fragment::FragSet::max_frag_length(), core::pack::dunbrack::product(), and protocols::medal::TR().

Referenced by apply().

◆ create_fragment_and_rigid_mover()

protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_and_rigid_mover	(	const core::pose::Pose &	pose,
		core::pose::PoseOP	native,
		core::scoring::ScoreFunctionOP	score,
		core::fragment::FragSetOP	fragments,
		const Probabilities &	probs,
		const std::string &	policy,
		unsigned	library_size
	)		const

protected

Configures a mover for alternating biased fragment insertion and rigid body moves.

References core::pose::Pose::fold_tree(), protocols::medal::on_pose_accept(), and protocols::hybridization::score.

Referenced by apply().

◆ create_fragment_mover()

protocols::moves::MoverOP protocols::medal::MedalMover::create_fragment_mover	(	core::pose::PoseOP	native,
		core::scoring::ScoreFunctionOP	score,
		core::fragment::FragSetOP	fragments,
		const Probabilities &	probs,
		const std::string &	policy,
		unsigned	library_size
	)		const

protected

Configures a mover for biased fragment insertion.

References protocols::medal::on_pose_accept(), and protocols::hybridization::score.

◆ create_small_mover()

protocols::moves::MoverOP protocols::medal::MedalMover::create_small_mover	(	core::pose::PoseOP	native,
		core::scoring::ScoreFunctionOP	score
	)		const

protected

Configures a mover for performing alternating small and shear moves.

References protocols::medal::on_pose_accept(), and protocols::hybridization::score.

Referenced by apply().

◆ decompose_structure()

void protocols::medal::MedalMover::decompose_structure	(	const core::pose::Pose &	pose,
		protocols::loops::LoopsOP &	chunks
	)		const

protected

Partitions the structure into non-overlapping chunks.

References protocols::nonlocal::chunks_by_CA_CA_distance().

Referenced by apply().

◆ do_loop_closure()

void protocols::medal::MedalMover::do_loop_closure	(	core::pose::Pose *	pose,
		core::util::ChainbreakUtil const &	chainbreak_util
	)		const

protected

Closes chainbreaks in <pose>

References protocols::relax::loop::LoopRelaxMover::apply(), protocols::relax::loop::LoopRelaxMover::cmd_line_csts(), core::pose::Pose::fold_tree(), protocols::relax::loop::LoopRelaxMover::frag_libs(), fragments_sm_, core::util::ChainbreakUtil::has_chainbreak(), protocols::relax::loop::LoopRelaxMover::intermedrelax(), protocols::relax::loop::LoopRelaxMover::loops(), protocols::relax::loop::LoopRelaxMover::refine(), protocols::relax::loop::LoopRelaxMover::relax(), protocols::relax::loop::LoopRelaxMover::remodel(), and core::pose::Pose::size().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::medal::MedalMover::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::medal::MedalMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ score_function()

core::scoring::ScoreFunctionOP protocols::medal::MedalMover::score_function ( ) const

protected

Configures a basic score functions which callers can then specialize.

@detail Configures the score function used during the simulation. Precedence:

User-specified patch file (i.e. -rigid:patch)
User-specified options (e.g. -jumps:increase_chainbreak)
Default values

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::hbond_lr_bb, core::scoring::hbond_sr_bb, core::scoring::linear_chainbreak, and protocols::hybridization::score.

Referenced by apply().

Member Data Documentation

◆ fragments_lg_

core::fragment::FragSetOP protocols::medal::MedalMover::fragments_lg_

protected

Referenced by MedalMover().

◆ fragments_sm_

core::fragment::FragSetOP protocols::medal::MedalMover::fragments_sm_

protected

Referenced by apply(), do_loop_closure(), and MedalMover().

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

src/protocols/medal/MedalMover.hh
src/protocols/medal/MedalMover.cc

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Additional Inherited Members

Member Typedef Documentation

◆ Probabilities

Constructor & Destructor Documentation

◆ MedalMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ compute_per_residue_probabilities()

◆ create_fragment_and_rigid_mover()

◆ create_fragment_mover()

◆ create_small_mover()

◆ decompose_structure()

◆ do_loop_closure()

◆ fresh_instance()

◆ get_name()

◆ score_function()

Member Data Documentation

◆ fragments_lg_

◆ fragments_sm_