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

#include <BackboneMover.hh>

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 protocols::filters::Filters_map	Filters_map

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 ()

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

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

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

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

virtual void	set_angles (core::Real)=0

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

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::TagCOP tag, basic::datacache::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...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)=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...

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

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

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

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

virtual void	finalize_simulation (core::pose::Pose &pose, 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_temperature_delta ()
	If this is a multi-trial move, return the change in internal score/temperature caused by the last call to apply(). More...

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

virtual void	set_metropolis_hastings_mover (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	~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

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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

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
	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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Protected Attributes
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_

Additional Inherited Members
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 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...

Detailed Description

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

Todo:: change this to some kind of 'protocol' so the MC is managed separately from conformational moves

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

References angle_max(), canonical_sampling, movemap(), movemap_, core::kinematics::MoveMap::set_bb(), 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(), canonical_sampling, and protocols::moves::Mover::type().

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

Member Function Documentation

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

Sets the maximum angle of perturbation, independent of secondary structure.

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

Referenced by protocols::ncbb::NcbbDockDesignProtocol::apply(), protocols::ncbb::oop::OopDockDesignProtocol::apply(), protocols::ncbb::oop::OopCreatorMover::apply(), protocols::grafting::AnchoredGraftMover::apply(), protocols::anchored_design::AnchoredPerturbMover::apply(), BackboneMover(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::abinitio::KinematicAbinitio::create_bb_moves(), parse_my_tag(), protocols::grafting::GraftMoverBase::perturb_backbone_for_test(), protocols::relax::ClassicRelax::set_default_moveset_phase1(), protocols::relax::ClassicRelax::set_default_moveset_phase2(), protocols::relax::ClassicRelax::set_default_moveset_phase3(), protocols::surface_docking::FullatomRelaxMover::set_smallmovesize(), protocols::surface_docking::CentroidRelaxMover::setup_movers(), protocols::simple_moves::ShakeStructureMover::setup_movers(), protocols::flexpep_docking::FlexPepDockingProtocol::shear_moves(), protocols::forge::remodel::RemodelLoopMover::small_move_stage(), protocols::flexpep_docking::FlexPepDockingProtocol::small_moves(), and protocols::flexpep_docking::FlexPepDockingAbInitio::torsions_monte_carlo().

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'.)

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

See also: ShearMover SmallMover

References angle_max_.

Referenced by show().

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

virtual

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.

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

pure virtual

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

Referenced by apply().

core::kinematics::MoveMapCOP protocols::simple_moves::BackboneMover::movemap ( ) const

References movemap_.

Referenced by protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover(), protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), BackboneMover(), parse_my_tag(), show(), and protocols::simple_moves::SmallMover::test_move().

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

References movemap_.

core::Real protocols::simple_moves::BackboneMover::new_phi ( )

References new_phi_.

core::Real protocols::simple_moves::BackboneMover::new_psi ( )

References new_psi_.

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

References nmoves_.

Referenced by protocols::canonical_sampling::MetropolisHastingsMover::add_shear_mover(), protocols::canonical_sampling::MetropolisHastingsMover::add_small_mover(), and protocols::protein_interface_design::movers::BackrubDDMover::apply().

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

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,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References angle_max(), movemap(), nmoves(), nmoves_, protocols::rosetta_scripts::parse_movemap(), preserve_detailed_balance_, set_preserve_detailed_balance(), temperature(), and temperature_.