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

#include <SidechainMover.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::SidechainMover:

Collaboration diagram for protocols::simple_moves::sidechain_moves::SidechainMover:

Public Member Functions
	SidechainMover ()
	default constructor More...

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

	SidechainMover (SidechainMover const &mover)

	~SidechainMover ()

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::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...

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 More...

core::conformation::ResidueOP	make_move (core::conformation::ResidueOP res)

bool	task_initialized ()

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

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

core::Real	proposal_density (core::conformation::Residue const &proposed_residue, core::Size const proposed_resnum, core::chemical::ResidueType const &initial_residue_type, utility::vector1< core::Real > const &initial_chi_angles) const

void	test_move (core::pose::Pose &)
	test the backrub move 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...

core::Real	prob_uniform () const
	get the probability of uniformly sampling chi angles More...

void	set_prob_uniform (core::Real prob_uniform)
	set the probability of uniformly sampling chi angles 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 preserve_detailed_balance)
	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 const change_chi_without_replacing_residue)
	perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain. 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...

core::Real	prob_withinrot () const
	get the probability of sampling within the same rotamer More...

void	set_prob_withinrot (core::Real prob_withinrot)
	set the probability of sampling within the same rotamer More...

core::Real	prob_random_pert_current () const

void	set_prob_random_pert_current (core::Real prob_pert)

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...

core::Size	next_resnum () const
	get the next residue to be changed, 0 means a random will be chosen More...

void	next_resnum (core::Size resnum)
	set the next residue to be changed, 0 means a random will be chosen More...

core::Size	last_nchi () const
	get the number of chi angles sampled in the last move More...

bool	last_mutation () const
	get whether the last move mutated the residue More...

bool	last_uniform () const
	get whether the last move used uniform chi sampling More...

bool	last_withinrot () const
	get whether the last move sampled within the same rotamer More...

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

void	update_type ()
	update string describing the move type More...

void	set_sampling_temperature (core::Real temp)
	set temperature for bias sampling at dunbrack distribution More...

core::Real	sampling_temperature ()

Public Member Functions inherited from protocols::canonical_sampling::ThermodynamicMover
	ThermodynamicMover ()

virtual	~ThermodynamicMover ()

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 More...

virtual bool	is_multi_trial ()
	determine whether the move performs multiple trials on a single apply More...

virtual core::Real	last_inner_score_temperature_delta ()
	get change in internal score/temperature for last apply method of multiple trial movers More...

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	get the MetropolisHastingsMover for multiple trial movers More...

virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	set the MetropolisHastingsMover for multiple trial movers 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...

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

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
	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 Attributes
core::Real	temperature0_

core::Real	sampling_temperature_

Private Member Functions
void	make_rotwell_jump (utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const &rotamer_sample_data)

void	preturb_rot_and_dunbrack_eval (core::conformation::ResidueOP input_residue)

void	perturb_rot_within_well (utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const &rotamer_sample_data, utility::vector1< core::Real > const &previous_chi_angles)

bool	dunbrack_accept (numeric::random::RandomGenerator &Rand, core::conformation::Residue &res, utility::vector1< core::Real > const &previous_chi_angles, utility::vector1< core::Real > const &new_chi_angles)

void	perturb_chi (numeric::random::RandomGenerator Rand, core::Real max_deviation, utility::vector1< core::Real > &current_chi, utility::vector1< core::Real > &new_chi)

Private Attributes
core::pack::dunbrack::RotamerLibrary const &	rotamer_library_

core::pack::task::TaskFactoryCOP	task_factory_

core::pack::task::PackerTaskCOP	task_

core::pose::PoseOP	pose_

utility::vector1< core::Size >	packed_residues_

utility::vector1< bool >	residue_packed_

core::Real	prob_uniform_

core::Real	prob_withinrot_

core::Real	prob_random_pert_to_current_

bool	preserve_detailed_balance_

bool	accept_according_to_dunbrack_

bool	sample_rotwells_unif_

bool	change_chi_without_replacing_residue_

core::Size	next_resnum_

utility::vector1< core::Real >	last_chi_angles_

core::Size	last_nchi_

bool	last_mutation_

bool	last_uniform_

bool	last_withinrot_

bool	last_pertrot_

core::Real	last_proposal_density_ratio_

bool	task_initialized_

core::pack::dunbrack::RotamerLibraryScratchSpaceOP	scratch_

Additional Inherited Members
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

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...

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...

Detailed Description

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

Definition at line 52 of file SidechainMover.hh.

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::SidechainMover::SidechainMover ( )

default constructor

Definition at line 87 of file SidechainMover.cc.

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

constructor with user provided rotamer library

Definition at line 104 of file SidechainMover.cc.

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

Definition at line 123 of file SidechainMover.cc.

References pose_, scratch_, task_, and task_factory_.

protocols::simple_moves::sidechain_moves::SidechainMover::~SidechainMover ( )

Definition at line 156 of file SidechainMover.cc.

Member Function Documentation

void protocols::simple_moves::sidechain_moves::SidechainMover::apply ( core::pose::Pose & pose)

virtual

apply a sidechain move to a Pose object

Detailed:

Implements protocols::moves::Mover.

Definition at line 599 of file SidechainMover.cc.

References change_chi_without_replacing_residue(), core::conformation::Residue::chi(), init_task(), last_mutation_, make_move(), core::chemical::ResidueType::name(), core::chemical::ResidueType::nchi(), next_resnum_, packed_residues_, core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), protocols::simple_moves::RG(), core::pose::Pose::set_chi(), protocols::simple_moves::sidechain_moves::TR(), and core::conformation::Residue::type().

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply().

bool protocols::simple_moves::sidechain_moves::SidechainMover::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.

Definition at line 925 of file SidechainMover.cc.

References change_chi_without_replacing_residue_.

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

protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::SidechainMover::clone ( ) const

virtual

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

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::SidechainMCMover.

Definition at line 159 of file SidechainMover.cc.

utility::vector1< core::id::DOF_ID_Range > protocols::simple_moves::sidechain_moves::SidechainMover::dof_id_ranges ( core::pose::Pose & pose)

virtual

get the DOF_IDs perturbed by the mover during moves, along with their ranges

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Definition at line 947 of file SidechainMover.cc.

References core::id::CHI, core::pose::Pose::conformation(), core::conformation::Conformation::dof_id_from_torsion_id(), init_task(), core::chemical::ResidueType::name3(), core::chemical::ResidueType::nchi(), packed_residues_, core::pose::Pose::residue_type(), and task_.

bool protocols::simple_moves::sidechain_moves::SidechainMover::dunbrack_accept	(	numeric::random::RandomGenerator &	Rand,
		core::conformation::Residue &	res,
		utility::vector1< core::Real > const &	previous_chi_angles,
		utility::vector1< core::Real > const &	new_chi_angles
	)

private

Definition at line 261 of file SidechainMover.cc.

References core::pack::dunbrack::RotamerLibrary::rotamer_energy(), rotamer_library_, sampling_temperature_, scratch_, core::conformation::Residue::set_all_chi(), and temperature0_.

Referenced by preturb_rot_and_dunbrack_eval().

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

virtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

Definition at line 654 of file SidechainMover.cc.

void protocols::simple_moves::sidechain_moves::SidechainMover::idealize_sidechains ( core::pose::Pose & pose)

idealize sidechains that might be altered

Detailed:: all sidechains that might be changed are replaced with ideal coordinates that have the original chi angles

Definition at line 774 of file SidechainMover.cc.

References core::chemical::aa_pro, core::pose::Pose::chi(), core::pose::Pose::conformation(), init_task(), packed_residues_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_chi(), and task_.

Referenced by initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMover::init_task ( core::pose::Pose const & pose)

initialize the packer task if necessary

Detailed:: Check to make sure that a packer task exists and matches the numer of residues in the given pose. If that isn't the case, create a new one with the task factory. Exits with an error if no task factory exists.

Definition at line 208 of file SidechainMover.cc.

References pose_, set_task(), task_, task_factory_, and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::sidechain_moves::SidechainMCMover::apply(), apply(), dof_id_ranges(), and idealize_sidechains().

void protocols::simple_moves::sidechain_moves::SidechainMover::initialize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	cycle
	)

virtual

callback executed before any Monte Carlo trials

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

Definition at line 231 of file SidechainMover.cc.

References idealize_sidechains().

Referenced by protocols::simple_moves::sidechain_moves::SidechainMCMover::initialize_simulation().

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_mutation ( ) const

get whether the last move mutated the residue

Definition at line 1022 of file SidechainMover.cc.

References last_mutation_.

core::Size protocols::simple_moves::sidechain_moves::SidechainMover::last_nchi ( ) const

get the number of chi angles sampled in the last move

Definition at line 1016 of file SidechainMover.cc.

References last_nchi_.

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::last_proposal_density_ratio ( )

virtual

get the ratio of proposal densities for the last move

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

Definition at line 1040 of file SidechainMover.cc.

References last_proposal_density_ratio_.

Referenced by protocols::simple_moves::sidechain_moves::SidechainMCMover::apply().

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_uniform ( ) const

get whether the last move used uniform chi sampling

Definition at line 1028 of file SidechainMover.cc.

References last_uniform_.

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_withinrot ( ) const

get whether the last move sampled within the same rotamer

Definition at line 1034 of file SidechainMover.cc.

References last_withinrot_.

core::conformation::ResidueOP protocols::simple_moves::sidechain_moves::SidechainMover::make_move ( core::conformation::ResidueOP res)

void protocols::simple_moves::sidechain_moves::SidechainMover::make_rotwell_jump ( utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const & rotamer_sample_data)

private

Definition at line 477 of file SidechainMover.cc.

References last_chi_angles_, protocols::simple_moves::RG(), sample_rotwells_unif_, sampling_temperature_, temperature0_, and protocols::simple_moves::sidechain_moves::TR().

Referenced by make_move().

core::Size protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum ( ) const

get the next residue to be changed, 0 means a random will be chosen

Definition at line 1001 of file SidechainMover.cc.

References next_resnum_.

void protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum ( core::Size resnum)

set the next residue to be changed, 0 means a random will be chosen

Definition at line 1007 of file SidechainMover.cc.

References next_resnum_, and residue_packed_.

utility::vector1< core::Size > const & protocols::simple_moves::sidechain_moves::SidechainMover::packed_residues ( ) const

get the residues that can be changed by this mover

Definition at line 989 of file SidechainMover.cc.

References packed_residues_.

Referenced by protocols::simple_moves::sidechain_moves::SidechainMCMover::apply().

void protocols::simple_moves::sidechain_moves::SidechainMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::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::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::SidechainMCMover.

Definition at line 165 of file SidechainMover.cc.

References change_chi_without_replacing_residue(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), preserve_detailed_balance(), prob_random_pert_current(), prob_uniform(), prob_withinrot(), set_change_chi_without_replacing_residue(), set_preserve_detailed_balance(), set_prob_random_pert_current(), set_prob_uniform(), set_prob_withinrot(), and task_factory_.

void protocols::simple_moves::sidechain_moves::SidechainMover::perturb_chi	(	numeric::random::RandomGenerator	Rand,
		core::Real	max_deviation,
		utility::vector1< core::Real > &	current_chi,
		utility::vector1< core::Real > &	new_chi
	)

private

Definition at line 241 of file SidechainMover.cc.

Referenced by preturb_rot_and_dunbrack_eval().

void protocols::simple_moves::sidechain_moves::SidechainMover::perturb_rot_within_well	(	utility::vector1< core::pack::dunbrack::DunbrackRotamerSampleData > const &	rotamer_sample_data,
		utility::vector1< core::Real > const &	previous_chi_angles
	)

private

Definition at line 562 of file SidechainMover.cc.

References last_chi_angles_, last_withinrot_, protocols::simple_moves::RG(), and protocols::simple_moves::sidechain_moves::TR().

Referenced by make_move().

bool protocols::simple_moves::sidechain_moves::SidechainMover::preserve_detailed_balance ( ) const

virtual

get whether detailed balance is preserved (i.e. proposal density ratio calculated)

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 911 of file SidechainMover.cc.

References preserve_detailed_balance_.

Referenced by parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), and set_preserve_detailed_balance().

void protocols::simple_moves::sidechain_moves::SidechainMover::preturb_rot_and_dunbrack_eval ( core::conformation::ResidueOP input_residue)

private

Definition at line 527 of file SidechainMover.cc.

References accept_according_to_dunbrack_, dunbrack_accept(), last_chi_angles_, last_pertrot_, perturb_chi(), preserve_detailed_balance_, protocols::simple_moves::RG(), and protocols::simple_moves::sidechain_moves::TR().

Referenced by make_move().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_random_pert_current ( ) const

Definition at line 898 of file SidechainMover.cc.

References prob_random_pert_to_current_.

Referenced by parse_my_tag(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_uniform ( ) const

get the probability of uniformly sampling chi angles

Definition at line 870 of file SidechainMover.cc.

References prob_uniform_.

Referenced by parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), and set_prob_uniform().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_withinrot ( ) const

get the probability of sampling within the same rotamer

Definition at line 884 of file SidechainMover.cc.

References prob_withinrot_.

Referenced by parse_my_tag(), protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag(), and set_prob_withinrot().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::proposal_density	(	core::conformation::Residue const &	proposed_residue,
		core::Size const	proposed_resnum,
		core::chemical::ResidueType const &	initial_residue_type,
		utility::vector1< core::Real > const &	initial_chi_angles
	)		const

Definition at line 660 of file SidechainMover.cc.

References core::chemical::ResidueType::aa(), core::conformation::Residue::chi(), core::pack::dunbrack::RotamerLibrary::get_rsd_library(), core::conformation::Residue::nchi(), protocols::swa::phi(), prob_uniform_, prob_withinrot_, protocols::swa::psi(), rotamer_library_, sample_rotwells_unif_, task_, and core::conformation::Residue::type().

Referenced by make_move().

utility::vector1< bool > const & protocols::simple_moves::sidechain_moves::SidechainMover::residue_packed ( ) const

get a vector indicating whether each residue can be packed

Definition at line 995 of file SidechainMover.cc.

References residue_packed_.

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

get the rotamer library

Definition at line 814 of file SidechainMover.cc.

References rotamer_library_.

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::sampling_temperature ( )

inline

Definition at line 267 of file SidechainMover.hh.

References sampling_temperature_.

void protocols::simple_moves::sidechain_moves::SidechainMover::set_change_chi_without_replacing_residue ( bool const change_chi_without_replacing_residue)

perform direct chi manipulations rather than using replace_residue to effect rotamer changes; useful if things are kinematically dependent on a sidechain.

Definition at line 931 of file SidechainMover.cc.

References change_chi_without_replacing_residue(), and change_chi_without_replacing_residue_.

Referenced by parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_preserve_detailed_balance ( bool preserve_detailed_balance)

virtual

set whether detailed balance is preserved (i.e. proposal density ratio calculated)

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 917 of file SidechainMover.cc.

References preserve_detailed_balance(), and preserve_detailed_balance_.

Referenced by parse_my_tag(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_random_pert_current ( core::Real prob_pert)

Definition at line 903 of file SidechainMover.cc.

References prob_random_pert_to_current_.

Referenced by parse_my_tag(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_uniform ( core::Real prob_uniform)

set the probability of uniformly sampling chi angles

Definition at line 876 of file SidechainMover.cc.

References prob_uniform(), and prob_uniform_.

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply(), parse_my_tag(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_withinrot ( core::Real prob_withinrot)

set the probability of sampling within the same rotamer

Definition at line 890 of file SidechainMover.cc.

References prob_withinrot(), and prob_withinrot_.

Referenced by parse_my_tag(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_sampling_temperature ( core::Real temp)

inline

set temperature for bias sampling at dunbrack distribution

Definition at line 262 of file SidechainMover.hh.

References sampling_temperature_.

void protocols::simple_moves::sidechain_moves::SidechainMover::set_task ( core::pack::task::PackerTaskCOP task)

set the task

Definition at line 840 of file SidechainMover.cc.

References core::chemical::aa_pro, packed_residues_, residue_packed_, task(), and task_.

Referenced by init_task(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMover::set_task_factory ( core::pack::task::TaskFactoryCOP task_factory)

set the task factory

Definition at line 826 of file SidechainMover.cc.

References task_factory(), and task_factory_.

Referenced by protocols::protein_interface_design::movers::BackrubDDMover::apply(), and protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag().

core::pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMover::task ( ) const

get the packer task

Definition at line 834 of file SidechainMover.cc.

References task_.

Referenced by set_task().

core::pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMover::task_factory ( ) const

get the task factory

Definition at line 820 of file SidechainMover.cc.

References task_factory_.

Referenced by set_task_factory().

bool protocols::simple_moves::sidechain_moves::SidechainMover::task_initialized ( )

Definition at line 593 of file SidechainMover.cc.

References task_initialized_.

void protocols::simple_moves::sidechain_moves::SidechainMover::test_move ( core::pose::Pose & )

virtual

test the backrub move

Detailed:

Reimplemented from protocols::moves::Mover.

Definition at line 763 of file SidechainMover.cc.

utility::vector1< core::id::TorsionID_Range > protocols::simple_moves::sidechain_moves::SidechainMover::torsion_id_ranges ( core::pose::Pose & pose)

virtual

get the TorsionIDs perturbed by the mover during moves, along with their ranges

Implements protocols::canonical_sampling::ThermodynamicMover.

Definition at line 939 of file SidechainMover.cc.

void protocols::simple_moves::sidechain_moves::SidechainMover::update_type ( )

update string describing the move type

Detailed:: All move types are prefixed with "sc". Sections are divided by underscores. The next section indicates whether a mutation was made ("mut") or not ("chi"). The last section indicates wehter chi sampling was uniform ("unif"), used Dunbrack rotamer statistics ("rot"), or whether no chi angles existed in the placed residue ("none").

Definition at line 1052 of file SidechainMover.cc.

References last_mutation_, last_nchi_, last_pertrot_, last_uniform_, last_withinrot_, protocols::motifs::mt(), and protocols::moves::Mover::type().

Referenced by make_move().

Member Data Documentation

bool protocols::simple_moves::sidechain_moves::SidechainMover::accept_according_to_dunbrack_

private

Definition at line 317 of file SidechainMover.hh.

Referenced by preturb_rot_and_dunbrack_eval().

bool protocols::simple_moves::sidechain_moves::SidechainMover::change_chi_without_replacing_residue_

private

Definition at line 319 of file SidechainMover.hh.

Referenced by change_chi_without_replacing_residue(), and set_change_chi_without_replacing_residue().

utility::vector1<core::Real> protocols::simple_moves::sidechain_moves::SidechainMover::last_chi_angles_

private

Definition at line 321 of file SidechainMover.hh.

Referenced by make_move(), make_rotwell_jump(), perturb_rot_within_well(), and preturb_rot_and_dunbrack_eval().

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_mutation_

private

Definition at line 323 of file SidechainMover.hh.

Referenced by apply(), last_mutation(), make_move(), and update_type().

core::Size protocols::simple_moves::sidechain_moves::SidechainMover::last_nchi_

private

Definition at line 322 of file SidechainMover.hh.

Referenced by last_nchi(), make_move(), and update_type().

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_pertrot_

private

Definition at line 326 of file SidechainMover.hh.

Referenced by make_move(), preturb_rot_and_dunbrack_eval(), and update_type().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::last_proposal_density_ratio_

private

Definition at line 327 of file SidechainMover.hh.

Referenced by last_proposal_density_ratio(), and make_move().

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_uniform_

private

Definition at line 324 of file SidechainMover.hh.

Referenced by last_uniform(), make_move(), and update_type().

bool protocols::simple_moves::sidechain_moves::SidechainMover::last_withinrot_

private

Definition at line 325 of file SidechainMover.hh.

Referenced by last_withinrot(), make_move(), perturb_rot_within_well(), and update_type().

core::Size protocols::simple_moves::sidechain_moves::SidechainMover::next_resnum_

private

Definition at line 320 of file SidechainMover.hh.

Referenced by apply(), and next_resnum().

utility::vector1<core::Size> protocols::simple_moves::sidechain_moves::SidechainMover::packed_residues_

private

Definition at line 311 of file SidechainMover.hh.

Referenced by apply(), dof_id_ranges(), idealize_sidechains(), packed_residues(), and set_task().

core::pose::PoseOP protocols::simple_moves::sidechain_moves::SidechainMover::pose_

private

Definition at line 310 of file SidechainMover.hh.

Referenced by init_task(), make_move(), and SidechainMover().

bool protocols::simple_moves::sidechain_moves::SidechainMover::preserve_detailed_balance_

private

Definition at line 316 of file SidechainMover.hh.

Referenced by make_move(), preserve_detailed_balance(), preturb_rot_and_dunbrack_eval(), and set_preserve_detailed_balance().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_random_pert_to_current_

private

Definition at line 315 of file SidechainMover.hh.

Referenced by make_move(), prob_random_pert_current(), and set_prob_random_pert_current().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_uniform_

private

Definition at line 313 of file SidechainMover.hh.

Referenced by make_move(), prob_uniform(), proposal_density(), and set_prob_uniform().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::prob_withinrot_

private

Definition at line 314 of file SidechainMover.hh.

Referenced by make_move(), prob_withinrot(), proposal_density(), and set_prob_withinrot().

utility::vector1<bool> protocols::simple_moves::sidechain_moves::SidechainMover::residue_packed_

private

Definition at line 312 of file SidechainMover.hh.

Referenced by next_resnum(), residue_packed(), and set_task().

core::pack::dunbrack::RotamerLibrary const& protocols::simple_moves::sidechain_moves::SidechainMover::rotamer_library_

private

Definition at line 307 of file SidechainMover.hh.

Referenced by dunbrack_accept(), make_move(), proposal_density(), and rotamer_library().

bool protocols::simple_moves::sidechain_moves::SidechainMover::sample_rotwells_unif_

private

Definition at line 318 of file SidechainMover.hh.

Referenced by make_rotwell_jump(), and proposal_density().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::sampling_temperature_

protected

Definition at line 333 of file SidechainMover.hh.

Referenced by dunbrack_accept(), make_rotwell_jump(), sampling_temperature(), and set_sampling_temperature().

core::pack::dunbrack::RotamerLibraryScratchSpaceOP protocols::simple_moves::sidechain_moves::SidechainMover::scratch_

private

Definition at line 329 of file SidechainMover.hh.

Referenced by dunbrack_accept(), and SidechainMover().

core::pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMover::task_

private

Definition at line 309 of file SidechainMover.hh.

Referenced by dof_id_ranges(), idealize_sidechains(), init_task(), make_move(), proposal_density(), set_task(), SidechainMover(), and task().

core::pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMover::task_factory_

private

Definition at line 308 of file SidechainMover.hh.

Referenced by init_task(), parse_my_tag(), set_task_factory(), SidechainMover(), and task_factory().

bool protocols::simple_moves::sidechain_moves::SidechainMover::task_initialized_

private

Definition at line 328 of file SidechainMover.hh.

Referenced by task_initialized().

core::Real protocols::simple_moves::sidechain_moves::SidechainMover::temperature0_

protected

Definition at line 332 of file SidechainMover.hh.

Referenced by dunbrack_accept(), and make_rotwell_jump().

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

src/protocols/simple_moves/sidechain_moves/SidechainMover.hh
src/protocols/simple_moves/sidechain_moves/SidechainMover.cc

Public Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation