a particular gaussian mover from the original paper More...

#include <BBGaussianMover.hh>

Public Member Functions
virtual protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...

	BBG8T3AMover ()

	~BBG8T3AMover ()

void	apply (Pose &)

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

void	factorA (core::Real const fA)

void	factorB (core::Real const fB)

virtual void	parse_my_tag (TagCOP, basic::datacache::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

Public Member Functions inherited from protocols::simple_moves::BBGaussianMover
	BBGaussianMover (Size, Size, Size)

	~BBGaussianMover ()

core::kinematics::MoveMapCOP	movemap ()

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

Real	last_proposal_density_ratio () const
	get the ratio of proposal densities for the last move 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...

virtual core::Real	last_proposal_density_ratio ()

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)

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

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

Protected Member Functions
void	get_VdRdPhi (Pose const &)

void	get_G ()

void	get_A ()

Real	get_L_move (Pose &)

Real	get_L_prime ()

Protected Member Functions inherited from protocols::simple_moves::BBGaussianMover
void	setup_list (Pose const &)

Vector	get_dRdPhi (Vector const &r1, Vector const &r2, Vector const &r)

Vector	get_dRdTheta (Vector const &r1, Vector const &r2, Vector const &r3, Vector const &r)

Real	cholesky_fw (Matrix &, Size, utility::vector1< Real > &, utility::vector1< Real > &, Size from=1, Size to=0, Real scale=1.0)

Real	cholesky_bw (Matrix &, Size, utility::vector1< Real > &, utility::vector1< Real > &, Size from=1, Size to=0, Real scale=1.0)

void	pivot_range_randomly (Pose &, Size, Size)
	randomly rotate the dih angle in this range for avoiding the fixed ends 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...

Private Attributes
utility::vector1< std::string >	end_atom_list_

utility::vector1< Real >	dphi

Real	factorA_

Real	factorB_

Real	last_delta_square_

Additional Inherited Members
Public Types inherited from protocols::simple_moves::BBGaussianMover
typedef core::Vector	Vector

typedef core::Real	Real

typedef core::Size	Size

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::pose::PoseCOP	PoseCOP

typedef core::conformation::Residue	Residue

typedef utility::vector1< Vector >	VdRdPhi

typedef utility::vector1< VdRdPhi >	VMatrix

typedef utility::vector1 < utility::vector1< Real > >	Matrix

typedef numeric::xyzMatrix< Real >	xyzMatrix

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

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 Attributes inherited from protocols::simple_moves::BBGaussianMover
Size	n_end_atom_

Size	n_dof_angle_

Size	n_pert_res_

Size	resnum_

utility::vector1< std::pair < Size, Size > >	available_seg_list_

Matrix	matrix_G

Matrix	matrix_A

VMatrix	matrix_dRdPhi

Real	last_proposal_density_ratio_

core::kinematics::MoveMapCOP	movemap_

Detailed Description

a particular gaussian mover from the original paper

Note: using 8 torsion angles as DOF, 3 atoms (Ca,C,O) as end

Constructor & Destructor Documentation

protocols::simple_moves::BBG8T3AMover::BBG8T3AMover ( )

References end_atom_list_, bbg::factorA, factorA_, bbg::factorB, factorB_, option, and protocols::moves::Mover::type().

protocols::simple_moves::BBG8T3AMover::~BBG8T3AMover ( )

Member Function Documentation

void protocols::simple_moves::BBG8T3AMover::apply ( Pose & pose )

virtual

Implements protocols::moves::Mover.

References protocols::simple_moves::BBGaussianMover::available_seg_list_, get_A(), get_G(), get_L_move(), get_L_prime(), get_VdRdPhi(), protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio_, left, protocols::simple_moves::BBGaussianMover::n_pert_res_, protocols::simple_moves::BBGaussianMover::pivot_range_randomly(), protocols::simple_moves::BBGaussianMover::resnum_, protocols::simple_moves::RG, protocols::simple_moves::BBGaussianMover::setup_list(), and numeric::random::RandomGenerator::uniform().

Referenced by protocols::enzdes::BackboneSampler::apply(), and protocols::protein_interface_design::movers::BackrubDDMover::apply().

protocols::moves::MoverOP protocols::simple_moves::BBG8T3AMover::clone ( ) const

virtual

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.

References protocols::simple_moves::BBGaussianMover::movemap_.

void protocols::simple_moves::BBG8T3AMover::factorA ( core::Real const fA )

Referenced by protocols::enzdes::BackboneSampler::apply(), and protocols::protein_interface_design::movers::BackrubDDMover::apply().

void protocols::simple_moves::BBG8T3AMover::factorB ( core::Real const fB )

Referenced by protocols::enzdes::BackboneSampler::apply(), and protocols::protein_interface_design::movers::BackrubDDMover::apply().

void protocols::simple_moves::BBG8T3AMover::get_A ( )

protectedvirtual

Implements protocols::simple_moves::BBGaussianMover.

References factorA_, factorB_, j, protocols::simple_moves::BBGaussianMover::matrix_A, protocols::simple_moves::BBGaussianMover::matrix_G, and protocols::simple_moves::BBGaussianMover::n_dof_angle_.

Referenced by apply().

void protocols::simple_moves::BBG8T3AMover::get_G ( )

protectedvirtual

Implements protocols::simple_moves::BBGaussianMover.

References end_atom_list_, j, protocols::simple_moves::BBGaussianMover::matrix_dRdPhi, protocols::simple_moves::BBGaussianMover::matrix_G, and protocols::simple_moves::BBGaussianMover::n_dof_angle_.

Referenced by apply().

core::Real protocols::simple_moves::BBG8T3AMover::get_L_move ( Pose & pose )

protectedvirtual

Implements protocols::simple_moves::BBGaussianMover.

References protocols::simple_moves::BBGaussianMover::cholesky_fw(), dphi, numeric::random::RandomGenerator::gaussian(), protocols::simple_moves::BBGaussianMover::matrix_A, protocols::simple_moves::BBGaussianMover::n_dof_angle_, basic::periodic_range(), core::pose::Pose::phi(), core::pose::Pose::psi(), protocols::simple_moves::BBGaussianMover::resnum_, protocols::simple_moves::RG, core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by apply().

core::Real protocols::simple_moves::BBG8T3AMover::get_L_prime ( )

protectedvirtual

Implements protocols::simple_moves::BBGaussianMover.

References protocols::simple_moves::BBGaussianMover::cholesky_bw(), dphi, protocols::simple_moves::BBGaussianMover::matrix_A, and protocols::simple_moves::BBGaussianMover::n_dof_angle_.

Referenced by apply().

std::string protocols::simple_moves::BBG8T3AMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::simple_moves::BBG8T3AMover::get_VdRdPhi ( Pose const & pose )

protectedvirtual

Implements protocols::simple_moves::BBGaussianMover.

References end_atom_list_, protocols::simple_moves::BBGaussianMover::get_dRdPhi(), protocols::simple_moves::BBGaussianMover::matrix_dRdPhi, core::pose::Pose::residue(), and protocols::simple_moves::BBGaussianMover::resnum_.

Referenced by apply().

void protocols::simple_moves::BBG8T3AMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		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 factorA_, factorB_, protocols::simple_moves::BBGaussianMover::movemap(), protocols::rosetta_scripts::parse_movemap(), and core::kinematics::MoveMap::set_bb().