class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions More...

#include <PerturbRotamerSidechainMover.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover:

Public Types
typedef SidechainMoverBase	Parent

typedef utility::vector1 < core::pack::dunbrack::DunbrackRotamerSampleData >	RotamerList

Public Types inherited from protocols::simple_moves::sidechain_moves::SidechainMoverBase
typedef utility::vector1 < core::Real >	ChiVector

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
	PerturbRotamerSidechainMover ()
	default constructor More...

	PerturbRotamerSidechainMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
	constructor with user provided rotamer library More...

	PerturbRotamerSidechainMover (PerturbRotamerSidechainMover const &mover)

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

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...

virtual void	make_chi_move (core::conformation::Residue const &residue, ChiVector const &old_chi, ChiVector &new_chi)

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

virtual core::Real	compute_proposal_density (core::conformation::Residue const &new_residue, core::Size const resnum, core::chemical::ResidueType const &old_res_type, ChiVector const &old_chi) const
	all angles in degree More...

void	set_temperature (core::Real setting)

core::Real	temperature () const

void	build_rotamer_list (core::conformation::Residue const &, bool filter, RotamerList &) const
	all angles in degree More...

void	compute_rotdensities (RotamerList const &, ChiVector const &old_chi, ChiVector const &new_chi, core::Real &within_rot_density) const

Public Member Functions inherited from protocols::simple_moves::sidechain_moves::SidechainMoverBase
	SidechainMoverBase ()
	default constructor More...

	SidechainMoverBase (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
	constructor with user provided rotamer library More...

	SidechainMoverBase (SidechainMoverBase const &mover)

	~SidechainMoverBase ()

void	init_task (core::pose::Pose const &pose)
	initialize the packer task if necessary 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 core::conformation::ResidueOP	make_move (core::conformation::ResidueOP res)

virtual core::Size	suggest_residue_number (core::pose::Pose const &) const

virtual void	apply (core::pose::Pose &pose)
	apply a sidechain move to a Pose object More...

void	idealize_sidechains (core::pose::Pose &pose)
	idealize sidechains that might be altered More...

core::pack::dunbrack::RotamerLibrary const &	rotamer_library () const
	get the rotamer library More...

core::pack::task::TaskFactoryCOP	task_factory () const
	get the task factory More...

void	set_task_factory (core::pack::task::TaskFactoryCOP task_factory)
	set the task factory More...

core::pack::task::PackerTaskCOP	task () const
	get the packer task More...

void	set_task (core::pack::task::PackerTaskCOP task)
	set the task More...

bool	preserve_detailed_balance () const
	get whether detailed balance is preserved (i.e. proposal density ratio calculated) More...

void	set_preserve_detailed_balance (bool setting)
	set whether detailed balance is preserved (i.e. proposal density ratio calculated) More...

bool	change_chi_without_replacing_residue () const
	perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. More...

void	set_change_chi_without_replacing_residue (bool setting)
	perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. More...

virtual bool	have_mutated_residue () const
	return true if your last move has mutated residue — make sure the residue is replaced entirely More...

virtual utility::vector1 < core::id::TorsionID_Range >	torsion_id_ranges (core::pose::Pose &pose)
	get the TorsionIDs perturbed by the mover during moves, along with their ranges More...

virtual utility::vector1 < core::id::DOF_ID_Range >	dof_id_ranges (core::pose::Pose &pose)
	get the DOF_IDs perturbed by the mover during moves, along with their ranges More...

utility::vector1< core::Size > const &	packed_residues () const
	get the residues that can be changed by this mover More...

utility::vector1< bool > const &	residue_packed () const
	get a vector indicating whether each residue can be packed More...

virtual core::Real	last_proposal_density_ratio ()
	get the ratio of proposal densities for the last move More...

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()
	Default constructor. More...

virtual	~ThermodynamicMover ()
	Default destructor. 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...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~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...

	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)

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	set_defaults ()

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
core::Real	temperature_

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...

Detailed Description

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

Member Typedef Documentation

typedef SidechainMoverBase protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::Parent

typedef utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::RotamerList

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::PerturbRotamerSidechainMover ( )

default constructor

References protocols::moves::Mover::type().

protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::PerturbRotamerSidechainMover ( core::pack::dunbrack::RotamerLibrary const & rotamer_library )

constructor with user provided rotamer library

References set_defaults(), and protocols::moves::Mover::type().

protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::PerturbRotamerSidechainMover ( PerturbRotamerSidechainMover const & mover )

References set_defaults().

Member Function Documentation

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list	(	core::conformation::Residue const &	residue,
		bool	filter,
		RotamerList &	rotamers
	)		const

all angles in degree

References core::conformation::Residue::type().

Referenced by protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_proposal_density(), compute_proposal_density(), make_chi_move(), and protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::make_chi_move().

protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::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.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

Real protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_proposal_density	(	core::conformation::Residue const &	new_residue,
		core::Size const	resnum,
		core::chemical::ResidueType const &	old_res_type,
		ChiVector const &	old_chi
	)		const

virtual

all angles in degree

Implements protocols::simple_moves::sidechain_moves::SidechainMoverBase.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

References build_rotamer_list(), core::conformation::Residue::chi(), and compute_rotdensities().

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::compute_rotdensities	(	RotamerList const &	rotamers,
		ChiVector const &	old_chi,
		ChiVector const &	new_chi,
		core::Real &	within_rot_density
	)		const

References protocols::simple_moves::bb_sampler::probability, and temperature().

Referenced by compute_proposal_density().

std::string protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::sidechain_moves::SidechainMoverBase.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::make_chi_move	(	core::conformation::Residue const &	residue,
		ChiVector const &	old_chi,
		ChiVector &	new_chi
	)

virtual

Implements protocols::simple_moves::sidechain_moves::SidechainMoverBase.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

References build_rotamer_list(), protocols::simple_moves::bb_sampler::probability, core::scoring::rg, and temperature_.

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::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::simple_moves::sidechain_moves::SidechainMoverBase.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_defaults ( )

protected

References temperature_.

Referenced by PerturbRotamerSidechainMover().

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_temperature ( core::Real setting )

inline

References temperature_.

core::Real protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::temperature ( ) const

inline

References temperature_.