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

#include <BBGaussianMover.hh>

Inheritance diagram for protocols::simple_moves::BBGaussianMover:

Public Types
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< Real >	Vector

typedef numeric::xyzVector< Real >	xyzVector

typedef utility::vector1 < xyzVector >	VdRdPhi

typedef utility::vector1< VdRdPhi >	VMatrix

typedef utility::vector1< Vector >	Matrix

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
	BBGaussianMover ()

	BBGaussianMover (core::Size, core::Size, core::Size)

	~BBGaussianMover () override

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

void	apply (Pose &pose) override
	Main Method. More...

void	init ()

void	resize (core::Size, core::Size, core::Size)

void	factorA (Real const fA)

void	factorB (Real const fB)

void	get_G ()

void	get_A ()

Real	get_L_prime ()

Real	get_L_move (Pose &)

void	get_VdRdPhi (Pose const &)

core::kinematics::MoveMapCOP	movemap (core::pose::Pose const &) const
	Generates the movemap used by this mover for the given pose. More...

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

void	movemap_factory (core::select::movemap::MoveMapFactoryCOP new_movemap_factory)
	The movemap_factory will be used to generate a movemap, if an explcit one hasn't already been set. More...

void	update_counting_last_PDR (Real)

Real	last_proposal_density_ratio () override
	get the ratio of proposal densities for the last move 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::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &) override
	dummy More...

void	init_kic_loop (core::Size looplength, core::kinematics::MoveMapCOP mm)

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

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::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	Return a list specifying which degrees of freedom 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 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...

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

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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
void	setup_list (Pose const &)

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

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

void	parse_my_tag (TagCOP, basic::datacache::DataMap &) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

Real	cholesky_fw (Matrix &, core::Size, Vector &, Vector &, core::Size from=1, core::Size to=0, Real scale=1.0)

Real	cholesky_bw (Matrix &, core::Size, Vector &, Vector &, core::Size from=1, core::Size to=0, Real scale=1.0)

void	pivot_range_randomly (Pose &, core::Size, core::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
core::Size	n_end_atom_

core::Size	n_dof_angle_

core::Size	n_pert_res_

core::Size	resnum_

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

utility::vector1< std::pair < core::Size, std::string > >	end_atom_list_

Matrix	matrix_G

Matrix	matrix_A

VMatrix	matrix_dRdPhi

Real	last_proposal_density_ratio_

bool	preserve_detailed_balance_

core::kinematics::MoveMapCOP	movemap_

core::select::movemap::MoveMapFactoryCOP	movemap_factory_

Vector	dphi_

Real	factorA_

Real	factorB_

core::Size	N_auto_all

core::Size	N_auto_small

bool	use_all_pivot_res_

bool	auto_adjust_factorA_

bool	fix_short_segment_

bool	shrink_frag_ends_

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)

Member Typedef Documentation

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

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

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

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

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

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

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

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

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

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

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

Constructor & Destructor Documentation

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

References init().

Referenced by clone().

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

References init().

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

override

References factorA_, and protocols::simple_moves::TR().

Member Function Documentation

void protocols::simple_moves::BBGaussianMover::apply ( Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References available_seg_list_, get_A(), get_G(), get_L_move(), get_L_prime(), get_VdRdPhi(), last_proposal_density_ratio_, core::sequence::left, n_pert_res_, pivot_range_randomly(), resnum_, core::scoring::rg, setup_list(), and use_all_pivot_res_.

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

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

protected

References core::simple_metrics::metrics::sum.

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

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

protected

References core::simple_metrics::metrics::sum.

Referenced by protocols::simple_moves::BBConRotMover::get_L_move(), and get_L_move().

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

overridevirtual

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.

Reimplemented in protocols::simple_moves::BBG8T3AMover.

References BBGaussianMover(), factorA_, factorB_, movemap_, and movemap_factory_.

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

References factorA_.

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

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

References factorB_.

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

void protocols::simple_moves::BBGaussianMover::get_A ( )

References factorA_, factorB_, matrix_A, matrix_G, and n_dof_angle_.

Referenced by apply().

xyzVector protocols::simple_moves::BBGaussianMover::get_dRdPhi	(	xyzVector const &	r1,
		xyzVector const &	r2,
		xyzVector const &	r
	)

inlineprotected

Referenced by protocols::simple_moves::BBConRotMover::get_VdRdPhi(), and get_VdRdPhi().

xyzVector protocols::simple_moves::BBGaussianMover::get_dRdTheta	(	xyzVector const &	r1,
		xyzVector const &	r2,
		xyzVector const &	r3,
		xyzVector const &	r
	)

inlineprotected

Referenced by protocols::simple_moves::BBConRotMover::get_VdRdPhi().

void protocols::simple_moves::BBGaussianMover::get_G ( )

References end_atom_list_, matrix_dRdPhi, matrix_G, and n_dof_angle_.

Referenced by apply().

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

Note: calculate L matrix and update pose

References available_seg_list_, cholesky_fw(), dphi_, core::sequence::left, matrix_A, n_dof_angle_, n_pert_res_, core::pose::Pose::phi(), core::pose::Pose::psi(), resnum_, core::scoring::rg, core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), shrink_frag_ends_, and use_all_pivot_res_.

Referenced by apply().

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

Note: calculate L', update last_proposal_density

References cholesky_bw(), dphi_, matrix_A, and n_dof_angle_.

Referenced by apply().

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

overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::BBG8T3AMover.

References mover_name().

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

References core::conformation::Residue::atom(), available_seg_list_, end_atom_list_, get_dRdPhi(), core::sequence::left, matrix_dRdPhi, n_dof_angle_, n_pert_res_, core::pose::Pose::residue(), resnum_, shrink_frag_ends_, use_all_pivot_res_, and core::conformation::Atom::xyz().

Referenced by apply().

void protocols::simple_moves::BBGaussianMover::init ( void )

References auto_adjust_factorA_, end_atom_list_, factorA_, factorB_, fix_short_segment_, last_proposal_density_ratio_, N_auto_all, N_auto_small, n_end_atom_, preserve_detailed_balance_, shrink_frag_ends_, protocols::moves::Mover::type(), and use_all_pivot_res_.

Referenced by BBGaussianMover().

void protocols::simple_moves::BBGaussianMover::init_kic_loop	(	core::Size	looplength,
		core::kinematics::MoveMapCOP	mm
	)

References auto_adjust_factorA_, end_atom_list_, factorA_, factorB_, fix_short_segment_, movemap(), n_dof_angle_, n_end_atom_, n_pert_res_, resize(), shrink_frag_ends_, protocols::simple_moves::TR(), and use_all_pivot_res_.

core::Real protocols::simple_moves::BBGaussianMover::last_proposal_density_ratio ( )

overridevirtual

get the ratio of proposal densities for the last move

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References auto_adjust_factorA_, last_proposal_density_ratio_, and update_counting_last_PDR().

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

Generates the movemap used by this mover for the given pose.

References movemap_, and movemap_factory_.

Referenced by protocols::enzdes::BackboneSampler::apply(), protocols::protein_interface_design::movers::BackrubDDMover::apply(), protocols::simple_moves::BBG8T3AMover::BBG8T3AMover(), and init_kic_loop().

void protocols::simple_moves::BBGaussianMover::movemap ( core::kinematics::MoveMapCOP new_movemap )

References available_seg_list_, and movemap_.

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

The movemap_factory will be used to generate a movemap, if an explcit one hasn't already been set.

References available_seg_list_, and movemap_factory_.

Referenced by parse_my_tag().

std::string protocols::simple_moves::BBGaussianMover::mover_name ( )

static

Referenced by get_name(), protocols::simple_moves::BBGaussianMoverCreator::keyname(), and provide_xml_schema().

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

overrideprotectedvirtual

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 auto_adjust_factorA_, end_atom_list_, factorA_, factorB_, fix_short_segment_, movemap_factory(), n_dof_angle_, n_end_atom_, n_pert_res_, protocols::rosetta_scripts::parse_movemap_factory_legacy(), resize(), shrink_frag_ends_, protocols::simple_moves::TR(), and use_all_pivot_res_.