the basic class for implementing Gaussian Perturbation of bb More...

#include <BBGaussianMover.hh>

Inheritance diagram for protocols::simple_moves::BBGaussianMover:

Collaboration diagram for protocols::simple_moves::BBGaussianMover:

Public Types
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::TagPtr	TagPtr

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
	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 ()

virtual void	apply (Pose &)=0

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
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. 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
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

Protected Member Functions
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)

virtual void	get_VdRdPhi (Pose const &)=0

virtual void	get_G ()=0

virtual void	get_A ()=0

virtual Real	get_L_move (Pose &)=0

virtual Real	get_L_prime ()=0

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...

Protected Attributes
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_

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Detailed Description

the basic class for implementing Gaussian Perturbation of bb

Note: "Monte Carlo update for chain molecules: Biased Gaussian steps in torsional space" "The Journal of Chemical Physics, Vol. 114, No. 18. (2001), pp. 8154-8158." Two steps for perturbing the backbone and keeping the geometry constrain Step 1: Gaussian Biased steps in torsional space: the end atoms of the moving segment should be choosen by user and to keep the geometry constrain(6), the DOF of the moving segment > 6 Step 2: "pivot" update the bb conformation, or followed by a chainclosure method (BBConRot)

Definition at line 50 of file BBGaussianMover.hh.

Member Typedef Documentation

typedef utility::vector1< utility::vector1<Real> > protocols::simple_moves::BBGaussianMover::Matrix

Definition at line 62 of file BBGaussianMover.hh.

typedef core::pose::Pose protocols::simple_moves::BBGaussianMover::Pose

Definition at line 56 of file BBGaussianMover.hh.

typedef core::pose::PoseCOP protocols::simple_moves::BBGaussianMover::PoseCOP

Definition at line 58 of file BBGaussianMover.hh.

typedef core::pose::PoseOP protocols::simple_moves::BBGaussianMover::PoseOP

Definition at line 57 of file BBGaussianMover.hh.

typedef core::Real protocols::simple_moves::BBGaussianMover::Real

Definition at line 54 of file BBGaussianMover.hh.

typedef core::conformation::Residue protocols::simple_moves::BBGaussianMover::Residue

Definition at line 59 of file BBGaussianMover.hh.

typedef core::Size protocols::simple_moves::BBGaussianMover::Size

Definition at line 55 of file BBGaussianMover.hh.

typedef utility::vector1< Vector > protocols::simple_moves::BBGaussianMover::VdRdPhi

Definition at line 60 of file BBGaussianMover.hh.

typedef core::Vector protocols::simple_moves::BBGaussianMover::Vector

Definition at line 53 of file BBGaussianMover.hh.

typedef utility::vector1< VdRdPhi > protocols::simple_moves::BBGaussianMover::VMatrix

Definition at line 61 of file BBGaussianMover.hh.

typedef numeric::xyzMatrix<Real> protocols::simple_moves::BBGaussianMover::xyzMatrix

Definition at line 63 of file BBGaussianMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::BBGaussianMover::BBGaussianMover	(	Size	n_end_atom,
		Size	n_dof_angle,
		Size	n_pert_res
	)

Definition at line 61 of file BBGaussianMover.cc.

References movemap(), movemap_, and protocols::moves::Mover::type().

protocols::simple_moves::BBGaussianMover::~BBGaussianMover ( )

Definition at line 78 of file BBGaussianMover.cc.

Member Function Documentation

core::Real protocols::simple_moves::BBGaussianMover::cholesky_bw	(	Matrix &	a,
		Size	n,
		utility::vector1< Real > &	dphi,
		utility::vector1< Real > &	delta,
		Size	from = `1`,
		Size	to = `0`,
		Real	scale = `1.0`
	)

protected

Definition at line 225 of file BBGaussianMover.cc.

Referenced by protocols::simple_moves::BBConRotMover::get_L_prime(), and protocols::simple_moves::BBG8T3AMover::get_L_prime().

core::Real protocols::simple_moves::BBGaussianMover::cholesky_fw	(	Matrix &	a,
		Size	n,
		utility::vector1< Real > &	delta,
		utility::vector1< Real > &	dphi,
		Size	from = `1`,
		Size	to = `0`,
		Real	scale = `1.0`
	)