A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and 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::SmallMover:

[legend]

Public Member Functions
	SmallMover ()

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

	~SmallMover () override

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...

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

void	set_angles (core::Real angle_in) override

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

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

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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 (BackboneMover const &src)
	Copy constructor. More...

	~BackboneMover () override

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

void	show (std::ostream &output=std::cout) const override
	Outputs details about the Mover, including current settings. More...

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

void	test_move (core::pose::Pose &) override
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	clear ()

bool	check_rama ()

void	temperature (core::Real const temperature_in)

core::Real	temperature () const

void	nmoves (core::Size const nmoves_in)

core::Size	nmoves () const

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

void	movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory)

core::kinematics::MoveMapCOP	movemap (core::pose::Pose const &pose)
	Get the movemap for this pose. More...

core::select::residue_selector::ResidueSelectorCOP	selector () const
	Return the residue selector that can be used to dynamically select residues to perturb at runtime. More...

void	selector (core::select::residue_selector::ResidueSelectorCOP selector)

core::scoring::ScoreFunctionOP	scorefxn () const
	If set, this scorefunction will be used instead of the original rama method (default = not set). More...

void	scorefxn (core::scoring::ScoreFunctionOP sfxn)

void	angle_max (core::Real const angle)
	Set the maximum angle of perturbation, independent of secondary structure. new_angle = old_angle +/- ( angle_max/2 ) 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'.) new_angle = old_angle +/- ( angle_max/2 ) 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'. new_angle = old_angle +/- ( angle_max/2 ) 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...

void	set_residue_selector (core::select::residue_selector::ResidueSelectorCOP selector)
	Set the ResidueSelector that this mover will use. More...

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

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

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

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()
	Default constructor. More...

	~ThermodynamicMover () override
	Default destructor. More...

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 are attempted. More...

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

core::Real	last_proposal_density_ratio () override
	Return the proposal density ratio for 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 are completed. More...

virtual bool	is_multi_trial ()
	Return true if the move performs multiple trials on each apply. More...

virtual core::Real	last_inner_score_delta_over_temperature ()
	If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	If this is a multi-trial move, return the MetropolisHastingsMover being used internally. More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	If this is a multi-trial move, set the MetropolisHastingsMover to be used internally. 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 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	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	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. 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::simple_moves::BackboneMover
static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_backbone_mover (utility::tag::XMLSchemaDefinition &xsd)

static std::string	backbone_mover_complex_type_namer (std::string tag_name)

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...

Private Member Functions
bool	move_with_scorefxn (core::pose::Pose &pose) override

bool	move_with_rama (core::pose::Pose &pose) override

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

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

Protected Member Functions inherited from protocols::simple_moves::BackboneMover
core::select::residue_selector::ResidueSubset	compute_selected_residues (core::pose::Pose const &pose) const
	Set the ResidueSelector that this mover will use. More...

utility::vector1 < core::id::TorsionID >	get_mainchain_TorsionIDs (core::conformation::Conformation const &conf, core::uint const seqpos) const
	Return a list of TorsionIDs for the standard main-chain torsions of this residue. More...

bool	are_torsions_allowed (utility::vector1< core::id::TorsionID > torsions, core::kinematics::MoveMapCOP mm) const
	Is this set of torsions allowed to move by the MoveMap? 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
std::map< char, core::Real >	angle_max_

core::uint	resnum_

core::Real	big_angle_

core::Real	small_angle_

utility::vector1 < core::id::TorsionID >	moving_torsions_

utility::vector1< std::tuple < core::uint, utility::vector1 < core::id::TorsionID > , core::Real > >	move_pos_list_

core::Real	old_rama_score_

core::Real	new_rama_score_

Detailed Description

A mover that makes independent random perturbations of the phi and psi torsion angles of residue i. It selects residue i at random among movable residues (set by its MoveMap), and 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: SmallMover.apply SmallMover.angle_max

Constructor & Destructor Documentation

protocols::simple_moves::SmallMover::SmallMover ( )

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

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

Constructs a SmallMover smallmover = SmallMover( 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

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

protocols::simple_moves::SmallMover::~SmallMover ( )

overridedefault

Member Function Documentation

protocols::moves::MoverOP protocols::simple_moves::SmallMover::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.

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

overridevirtual

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

Implements protocols::simple_moves::BackboneMover.

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

protocols::moves::MoverOP protocols::simple_moves::SmallMover::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.

std::string protocols::simple_moves::SmallMover::get_name ( ) const

overridevirtual

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

Reimplemented from protocols::simple_moves::BackboneMover.

References mover_name().

bool protocols::simple_moves::SmallMover::move_with_rama ( core::pose::Pose & pose )