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 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 (BackboneMover const &src)
	Copy constructor. More...

	~BackboneMover () override

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

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)

core::select::residue_selector::ResidueSelectorCOP	selector () const
	returns the residue selector which 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)
	Sets 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...

core::Real	new_phi ()

core::Real	new_psi ()

core::Real	new_omega ()

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...

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 ()

	~Mover () override

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 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

void	set_type (std::string const &setting)

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	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

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...

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_
	max allowed angle-change as a function of ss type More...

int	resnum_

core::Real	big_angle_

core::Real	small_angle_

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

core::Real	old_phi_

core::Real	new_phi_

core::Real	old_psi_

core::Real	new_psi_

core::Real	old_omega_

core::Real	new_omega_

core::Real	old_rama_score_

core::Real	new_rama_score_

Private Attributes
core::kinematics::MoveMapOP	movemap_

core::scoring::ScoreFunctionOP	scorefxn_

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

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

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.).

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(), movemap(), movemap_, 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 movemap(), movemap_, scorefxn_, and selector_.

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

overridedefault

Member Function Documentation

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

Sets 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().

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.

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

inline

References movemap_.

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

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

inline

References movemap_.

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

inline

References new_omega_.

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

inline

References new_phi_.

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

inline

References new_psi_.

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

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 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(), protocols::rosetta_scripts::parse_residue_selector(), protocols::rosetta_scripts::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 protocols::simple_moves::SmallMover::make_move(), protocols::simple_moves::ShearMover::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

returns the residue selector which 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_.

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(), movemap(), 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

Properties set/get functions.

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().

Member Data Documentation

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

protected

max allowed angle-change as a function of ss type

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::make_move(), protocols::simple_moves::ShearMover::make_move(), protocols::simple_moves::SmallMover::set_angles(), and protocols::simple_moves::ShearMover::set_angles().

core::kinematics::MoveMapOP protocols::simple_moves::BackboneMover::movemap_

private

Referenced by apply(), BackboneMover(), and movemap().

core::Real protocols::simple_moves::BackboneMover::new_omega_

protected

Referenced by protocols::simple_moves::SmallMover::make_move(), protocols::simple_moves::SmallMover::move_with_rama(), protocols::simple_moves::SmallMover::move_with_scorefxn(), and new_omega().

core::Real protocols::simple_moves::BackboneMover::new_phi_

protected

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

core::Real protocols::simple_moves::BackboneMover::new_psi_

protected

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

core::Real protocols::simple_moves::BackboneMover::new_rama_score_

protected

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

Size protocols::simple_moves::BackboneMover::nmoves_

private

number of positions at which to make moves

Referenced by apply(), nmoves(), and parse_my_tag().

core::Real protocols::simple_moves::BackboneMover::old_omega_

protected

Referenced by protocols::simple_moves::SmallMover::make_move().

core::Real protocols::simple_moves::BackboneMover::old_phi_

protected

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

core::Real protocols::simple_moves::BackboneMover::old_psi_

protected

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

core::Real protocols::simple_moves::BackboneMover::old_rama_score_

protected

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

utility::vector1< std::pair< int, core::Real > > protocols::simple_moves::BackboneMover::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().

bool protocols::simple_moves::BackboneMover::preserve_detailed_balance_

private

Referenced by check_rama(), parse_my_tag(), preserve_detailed_balance(), and set_preserve_detailed_balance().

int protocols::simple_moves::BackboneMover::resnum_

protected

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

core::scoring::ScoreFunctionOP protocols::simple_moves::BackboneMover::scorefxn_

private

Referenced by BackboneMover(), and scorefxn().

core::select::residue_selector::ResidueSelectorCOP protocols::simple_moves::BackboneMover::selector_

private

Referenced by BackboneMover(), compute_selected_residues(), selector(), and set_residue_selector().

core::Real protocols::simple_moves::BackboneMover::small_angle_

protected

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

core::Real protocols::simple_moves::BackboneMover::temperature_

private

controls bias w/which uphill moves are accepted

Referenced by check_rama(), parse_my_tag(), and temperature().

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

src/protocols/simple_moves/BackboneMover.hh
src/protocols/simple_moves/BackboneMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation