A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified. More...

#include <BackboneMover.hh>

Inheritance diagram for protocols::simple_moves::ShearMover:

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Collaboration diagram for protocols::simple_moves::ShearMover:

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Public Member Functions
	ShearMover ()

	ShearMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in)
	Constructs a ShearMover shearmover = ShearMover( movemap , kT , n_moves ) More...

	~ShearMover ()

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

protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	setup_list (core::pose::Pose &pose)

virtual void	set_angles (core::Real angle_in)

virtual bool	make_move (core::pose::Pose &pose)

virtual void	test_move (core::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 utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)
	get the TorsionIDs perturbed by the mover during moves, along with their ranges More...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	get the DOF_IDs perturbed by the mover during moves, along with their ranges More...

Public Member Functions inherited from protocols::simple_moves::BackboneMover
	BackboneMover ()

	BackboneMover (core::kinematics::MoveMapOP movemap_in, core::Real temperature_in, core::Size nmoves_in)

	~BackboneMover ()

virtual void	apply (core::pose::Pose &)
	virtual functions that get overridden or called from the inheriting classes More...

void	clear ()

bool	check_rama ()

void	temperature (core::Real const temperature_in)
	Properties set/get functions. More...

core::Real	temperature () const

void	nmoves (core::Size const nmoves_in)

core::Size	nmoves () const

core::kinematics::MoveMapCOP	movemap () const

void	movemap (core::kinematics::MoveMapOP new_movemap)

void	angle_max (core::Real const angle)
	Sets the maximum angle of perturbation, independent of secondary structure. More...

void	angle_max (char const type, core::Real const angle)
	Sets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) More...

void	angle_max (std::map< char, core::Real > angle_max_in)
	Sets the max angle of perturbation, for secondary structures 'H', 'E', and 'L'. More...

core::Real	get_angle_max (char const type) const
	Gets the max angle of perturbation for residues with <type> secondary structure. (<type> must be 'H', 'E', or 'L'.) More...

core::Real	new_phi ()

core::Real	new_psi ()

virtual void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

bool	preserve_detailed_balance () const
	get whether detailed balance is preserved (i.e. no Ramachandran biasing) More...

void	set_preserve_detailed_balance (bool preserve_detailed_balance)
	set whether detailed balance is preserved (i.e. no Ramachandran biasing) More...

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()

virtual	~ThermodynamicMover ()

virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	callback executed before any Monte Carlo trials More...

virtual void	observe_after_metropolis (protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	callback executed after the Metropolis criterion is evaluated More...

virtual core::Real	last_proposal_density_ratio ()
	callback for proposal density ratio of last apply method More...

virtual void	finalize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover)
	callback executed after all Monte Carlo trials More...

virtual bool	is_multi_trial ()
	determine whether the move performs multiple trials on a single apply More...

virtual core::Real	last_inner_score_temperature_delta ()
	get change in internal score/temperature for last apply method of multiple trial movers More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	get the MetropolisHastingsMover for multiple trial movers More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	set the MetropolisHastingsMover for multiple trial movers More...

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...

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

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
	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

Additional Inherited Members
Public Types inherited from protocols::simple_moves::BackboneMover
typedef core::Real	Real

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...

Protected Attributes inherited from protocols::simple_moves::BackboneMover
core::kinematics::MoveMapOP	movemap_

core::Real	temperature_
	controls bias w/which uphill moves are accepted More...

Size	nmoves_
	number of positions at which to make moves More...

std::map< char, core::Real >	angle_max_
	max allowed angle-change as a function of ss type More...

int	num_

int	resnum_

int	tries_

core::Real	big_angle_

core::Real	small_angle_

utility::vector1< std::pair < int, core::Real > >	pos_list_

utility::vector1< int >	already_moved_

core::Real	old_phi_

core::Real	new_phi_

core::Real	old_psi_

core::Real	new_psi_

core::Real	old_rama_score_

core::Real	new_rama_score_

bool	preserve_detailed_balance_

Detailed Description

A mover that perturbs the phi of residue i and the psi of residue i-1 such that they create a 'shearing' effect, minimizing the downstream consequences of this torsional perturbation. The final torsion angle is subject to a metropolis criterion using the rama score to ensure that only favorable backbone torsion angles are being selected. The number of perturbations, and the magnitude of perturbations, and the temperature in the rama check, can all be modified.

Common Methods: ShearMover.apply

Definition at line 269 of file BackboneMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::ShearMover::ShearMover ( )

Definition at line 434 of file BackboneMover.cc.

References protocols::moves::Mover::type().

protocols::simple_moves::ShearMover::ShearMover	(	core::kinematics::MoveMapOP	movemap_in,
		core::Real	temperature_in,
		core::Size	nmoves_in
	)

Constructs a ShearMover shearmover = ShearMover( movemap , kT , n_moves )

MoveMap movemap /object storing BB torsion movability Real (float) kT /used in rama Metropolis Criterion Size (int) n_moves /the number of perturbations for one move

Definition at line 436 of file BackboneMover.cc.

References protocols::moves::Mover::type().

protocols::simple_moves::ShearMover::~ShearMover ( )

Definition at line 447 of file BackboneMover.cc.

Member Function Documentation

protocols::moves::MoverOP protocols::simple_moves::ShearMover::clone ( ) const

virtual

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

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.

Definition at line 455 of file BackboneMover.cc.

utility::vector1< core::id::DOF_ID_Range > protocols::simple_moves::ShearMover::dof_id_ranges ( core::pose::Pose & pose)

virtual

get the DOF_IDs perturbed by the mover during moves, along with their ranges

Implements protocols::simple_moves::BackboneMover.

Definition at line 496 of file BackboneMover.cc.

References core::id::BB, protocols::simple_moves::BackboneMover::clear(), core::pose::Pose::conformation(), core::conformation::Conformation::dof_id_from_torsion_id(), core::id::phi_torsion(), protocols::simple_moves::BackboneMover::pos_list_, core::id::psi_torsion(), and setup_list().