BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.). More...

#include <BackboneMover.hh>

Inheritance diagram for protocols::simple_moves::BackboneMover:

[legend]

Public Types
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 std::list< std::string >	Strings

Public Member Functions
	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...

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

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

virtual void	setup_list (core::pose::Pose &)=0

virtual void	set_angles (core::Real)=0

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

virtual bool	move_with_scorefxn (core::pose::Pose &pose)=0

virtual bool	move_with_rama (core::pose::Pose &pose)=0

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) 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...

utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose) override=0
	get the DOF_IDs perturbed by the mover during moves, along with their ranges 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...

virtual utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)=0
	Return a list specifying which torsions may be perturbed by apply(), and the in what range each perturbation may be. 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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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 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 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...

Protected Member Functions
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
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_

Private Attributes
core::select::movemap::MoveMapFactoryCOP	movemap_factory_

core::kinematics::MoveMapOP	movemap_

core::scoring::ScoreFunctionOP	scorefxn_

core::Real	temperature_

core::Size	nmoves_

bool	preserve_detailed_balance_

core::select::residue_selector::ResidueSelectorCOP	selector_

Detailed Description

BackboneMover class has elements of the MC temperature to do repetitions of bb moves (small, shear, wobble, etc.).

Member Typedef Documentation

typedef core::Real protocols::simple_moves::BackboneMover::Real

Constructor & Destructor Documentation

protocols::simple_moves::BackboneMover::BackboneMover ( )

References angle_max(), and protocols::moves::Mover::type().

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

References angle_max(), and protocols::moves::Mover::type().

protocols::simple_moves::BackboneMover::BackboneMover ( BackboneMover const & src )

Copy constructor.

References scorefxn_, and selector_.

protocols::simple_moves::BackboneMover::~BackboneMover ( )

overridedefault

Member Function Documentation

void protocols::simple_moves::BackboneMover::angle_max ( core::Real const angle )

Set the maximum angle of perturbation, independent of secondary structure. new_angle = old_angle +/- ( angle_max/2 )

Example: bbmover.angle_max(25) See also: ShearMover SmallMover

Referenced by BackboneMover(), parse_my_tag(), protocols::grafting::perturb_backbone_for_test(), and protocols::mpi_refinement::WorkUnit_RamaPerturber::run().

void protocols::simple_moves::BackboneMover::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 )

Example: bbmover.angle_max('H', 25)

See also: ShearMover SmallMover

References angle_max_.

Referenced by show().

utility::vector1< core::id::TorsionID > protocols::simple_moves::BackboneMover::get_mainchain_TorsionIDs	(	core::conformation::Conformation const &	conf,
		core::uint const	seqpos
	)		const

protected

Return a list of TorsionIDs for the standard main-chain torsions of this residue.

Every residue family has its own set of standard (usually named) main-chain torsions, which have a variety of TorsionIDs "under the hood". This function gets these IDs from the residue.

Remarks: Ultimately, I plan to finish a project to store each of these IDs in ResidueType. When and if that happens, this helper function can be replaced by a direct call to ResidueType::get_mainchain_TorsionIDs() instead. ~Labonte

Note: The Conformation is only needed for the carbohydrate case, as its main-chain torsions are not even a part of the Residue being queried from Rosetta's point of view.

Author: Labonte JWLab.nosp@m.onte.nosp@m.@jhu..nosp@m.edu

References core::id::BB, core::conformation::carbohydrates::get_glycosidic_TorsionIDs(), core::id::phi_torsion(), core::id::phi_torsion_oligourea(), core::id::psi_torsion(), core::id::psi_torsion_oligourea(), core::conformation::Conformation::residue(), and core::id::theta_torsion_oligourea().

Referenced by protocols::simple_moves::SmallMover::setup_list(), and protocols::simple_moves::ShearMover::setup_list().

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::ShearMover, and protocols::simple_moves::SmallMover.

bool protocols::simple_moves::BackboneMover::make_move ( core::pose::Pose & pose )

References move_with_rama(), move_with_scorefxn(), and scorefxn().

Referenced by apply().

virtual bool protocols::simple_moves::BackboneMover::move_with_rama ( core::pose::Pose & pose )

pure virtual

Implemented in protocols::simple_moves::ShearMover, and protocols::simple_moves::SmallMover.

Referenced by make_move().

virtual bool protocols::simple_moves::BackboneMover::move_with_scorefxn ( core::pose::Pose & pose )

pure virtual

Implemented in protocols::simple_moves::ShearMover, and protocols::simple_moves::SmallMover.

Referenced by make_move().

void protocols::simple_moves::BackboneMover::movemap ( core::kinematics::MoveMapOP new_movemap )

inline

References movemap_.

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply(), movemap(), protocols::simple_moves::SmallMover::setup_list(), protocols::simple_moves::ShearMover::setup_list(), and test_move().

core::kinematics::MoveMapCOP protocols::simple_moves::BackboneMover::movemap ( core::pose::Pose const & pose )

Get the movemap for this pose.

References movemap(), movemap_, and movemap_factory_.

void protocols::simple_moves::BackboneMover::movemap_factory ( core::select::movemap::MoveMapFactoryCOP new_movemap_factory )

inline

References movemap_factory_.

Referenced by parse_my_tag().

void protocols::simple_moves::BackboneMover::nmoves ( core::Size const nmoves_in )

inline

References nmoves_.

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply().

core::Size protocols::simple_moves::BackboneMover::nmoves ( ) const

inline

References nmoves_.

Referenced by parse_my_tag(), and show().

void protocols::simple_moves::BackboneMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References angle_max(), movemap_factory(), nmoves(), nmoves_, protocols::rosetta_scripts::parse_movemap_factory_legacy(), core::select::residue_selector::parse_residue_selector(), core::scoring::parse_score_function(), preserve_detailed_balance_, scorefxn(), selector(), set_preserve_detailed_balance(), temperature(), and temperature_.

bool protocols::simple_moves::BackboneMover::preserve_detailed_balance ( ) const

inlineoverridevirtual

get whether detailed balance is preserved (i.e. no Ramachandran biasing)

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance_.

Referenced by set_preserve_detailed_balance().

core::scoring::ScoreFunctionOP protocols::simple_moves::BackboneMover::scorefxn ( ) const

inline

If set, this scorefunction will be used instead of the original rama method (default = not set).

References scorefxn_.

Referenced by make_move(), protocols::simple_moves::SmallMover::move_with_scorefxn(), protocols::simple_moves::ShearMover::move_with_scorefxn(), and parse_my_tag().

void protocols::simple_moves::BackboneMover::scorefxn ( core::scoring::ScoreFunctionOP sfxn )

inline

References scorefxn_.

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::BackboneMover::selector ( ) const

inline

Return the residue selector that can be used to dynamically select residues to perturb at runtime.

References selector_.

Referenced by parse_my_tag().

void protocols::simple_moves::BackboneMover::selector ( core::select::residue_selector::ResidueSelectorCOP selector )

inline

References selector(), and selector_.

Referenced by selector().

virtual void protocols::simple_moves::BackboneMover::set_angles ( core::Real )

pure virtual

Implemented in protocols::simple_moves::ShearMover, and protocols::simple_moves::SmallMover.

Referenced by apply().

void protocols::simple_moves::BackboneMover::set_preserve_detailed_balance ( bool preserve_detailed_balance )

inlineoverridevirtual

set whether detailed balance is preserved (i.e. no Ramachandran biasing)

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance(), and preserve_detailed_balance_.

Referenced by parse_my_tag().

void protocols::simple_moves::BackboneMover::set_residue_selector ( core::select::residue_selector::ResidueSelectorCOP selector )

Set the ResidueSelector that this mover will use.

Clones the input.

References selector_.

Referenced by protocols::carbohydrates::GlycanTreeModeler::apply().

virtual void protocols::simple_moves::BackboneMover::setup_list ( core::pose::Pose & )

pure virtual

Implemented in protocols::simple_moves::ShearMover, and protocols::simple_moves::SmallMover.

Referenced by apply().

void protocols::simple_moves::BackboneMover::show ( std::ostream & output = std::cout ) const

overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

References get_angle_max(), nmoves(), protocols::moves::Mover::show(), and temperature().

Referenced by protocols::simple_moves::operator<<().

void protocols::simple_moves::BackboneMover::temperature ( core::Real const temperature_in )

inline

References temperature_.

core::Real protocols::simple_moves::BackboneMover::temperature ( ) const

inline

References temperature_.

Referenced by protocols::simple_moves::SmallMover::move_with_scorefxn(), parse_my_tag(), and show().

void protocols::simple_moves::BackboneMover::test_move ( core::pose::Pose & pose )

overridevirtual

: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying

Reimplemented from protocols::moves::Mover.

References apply(), and movemap().

Member Data Documentation

std::map< char, core::Real > protocols::simple_moves::BackboneMover::angle_max_

protected

Referenced by angle_max(), get_angle_max(), protocols::simple_moves::SmallMover::setup_list(), and protocols::simple_moves::ShearMover::setup_list().

core::Real protocols::simple_moves::BackboneMover::big_angle_

protected

Referenced by protocols::simple_moves::SmallMover::move_with_rama(), protocols::simple_moves::ShearMover::move_with_rama(), protocols::simple_moves::SmallMover::move_with_scorefxn(), protocols::simple_moves::ShearMover::move_with_scorefxn(), protocols::simple_moves::SmallMover::set_angles(), and protocols::simple_moves::ShearMover::set_angles().

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

protected

Referenced by apply(), clear(), protocols::simple_moves::SmallMover::dof_id_ranges(), protocols::simple_moves::ShearMover::dof_id_ranges(), protocols::simple_moves::SmallMover::setup_list(), and protocols::simple_moves::ShearMover::setup_list().