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

#include <SidechainMoverBase.hh>

Public Types
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
	SidechainMoverBase ()
	default constructor More...

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

	SidechainMoverBase (SidechainMoverBase const &mover)

	~SidechainMoverBase ()

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...

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 void	make_chi_move (core::conformation::Residue const &residue, ChiVector const &old_chi, ChiVector &new_chi)=0

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...

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 =0

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_temperature_delta ()
	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 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

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...

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
	Return a clone of the Mover object. 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
	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...

Private Member Functions
void	set_defaults ()

void	init_from_options ()

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...

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

Member Typedef Documentation

typedef utility::vector1< core::Real > protocols::simple_moves::sidechain_moves::SidechainMoverBase::ChiVector

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::SidechainMoverBase::SidechainMoverBase ( )

default constructor

References init_from_options(), and set_defaults().

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

constructor with user provided rotamer library

References init_from_options(), and set_defaults().

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

References canonical_sampling, task_, and task_factory_.

protocols::simple_moves::sidechain_moves::SidechainMoverBase::~SidechainMoverBase ( )

Member Function Documentation

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

virtual

apply a sidechain move to a Pose object

Detailed:

Implements protocols::moves::Mover.

References change_chi_without_replacing_residue(), numeric::conversions::degrees(), have_mutated_residue(), init_task(), make_move(), numeric::conversions::radians(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::set_chi(), and suggest_residue_number().

bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.

References change_chi_without_replacing_residue_.

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

virtual core::Real protocols::simple_moves::sidechain_moves::SidechainMoverBase::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

pure virtual

Implemented in protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover, and protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover.

Referenced by make_move().

utility::vector1< id::DOF_ID_Range > protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.

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

std::string protocols::simple_moves::sidechain_moves::SidechainMoverBase::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::JumpRotamerSidechainMover, protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, and protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.

virtual bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::have_mutated_residue ( ) const

inlinevirtual

return true if your last move has mutated residue — make sure the residue is replaced entirely

Referenced by apply().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::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

References aa_pro, core::pose::Pose::chi(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), 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::SidechainMoverBase::init_from_options ( )

private

References option, core::pack::task::TaskFactory::push_back(), set_task_factory(), and user.

Referenced by SidechainMoverBase().

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

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

Referenced by apply(), dof_id_ranges(), idealize_sidechains(), and initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::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 are attempted.

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References idealize_sidechains(), and init_task().

Real protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio ( )

virtual

get the ratio of proposal densities for the last move

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References last_proposal_density_ratio_.

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

pure virtual

Implemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover, protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, and protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.

Referenced by make_move().

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

virtual

References core::conformation::Residue::chi(), compute_proposal_density(), numeric::conversions::degrees(), protocols::comparative_modeling::features::E, last_proposal_density_ratio_, make_chi_move(), core::conformation::Residue::nchi(), preserve_detailed_balance_, numeric::conversions::radians(), core::conformation::Residue::seqpos(), core::conformation::Residue::set_chi(), protocols::simple_moves::tr, and core::conformation::Residue::type().

Referenced by apply().

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

get the residues that can be changed by this mover

References packed_residues_.

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::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::moves::Mover.

Reimplemented in protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover, protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, and protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.

References change_chi_without_replacing_residue(), end, basic::datacache::DataMap::get(), basic::datacache::DataMap::has(), preserve_detailed_balance(), core::pack::task::TaskFactory::push_back(), set_change_chi_without_replacing_residue(), set_preserve_detailed_balance(), utility::string_split(), and task_factory_.

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

virtual

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

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance_.

Referenced by parse_my_tag(), and set_preserve_detailed_balance().

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

get a vector indicating whether each residue can be packed

References residue_packed_.

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

get the rotamer library

References rotamer_library_.

Referenced by protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list().

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

References change_chi_without_replacing_residue(), and change_chi_without_replacing_residue_.

Referenced by parse_my_tag().

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

private

References change_chi_without_replacing_residue_, and last_proposal_density_ratio_.

Referenced by SidechainMoverBase().

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::set_preserve_detailed_balance ( bool setting )

virtual

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

Implements protocols::canonical_sampling::ThermodynamicMover.

References preserve_detailed_balance(), and preserve_detailed_balance_.

Referenced by parse_my_tag().

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

set the task

References aa_pro, packed_residues_, residue_packed_, task(), and task_.

Referenced by init_task().

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

set the task factory

References task_factory(), and task_factory_.

Referenced by init_from_options().

core::Size protocols::simple_moves::sidechain_moves::SidechainMoverBase::suggest_residue_number ( core::pose::Pose const & pose ) const

virtual

References core::conformation::Residue::name1(), packed_residues_, numeric::random::RandomGenerator::random_range(), core::pose::Pose::residue(), and protocols::simple_moves::RG.

Referenced by apply().

pack::task::PackerTaskCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task ( ) const

get the packer task

References task_.

Referenced by set_task().

pack::task::TaskFactoryCOP protocols::simple_moves::sidechain_moves::SidechainMoverBase::task_factory ( ) const

get the task factory

References task_factory_.

Referenced by set_task_factory().

utility::vector1< id::TorsionID_Range > protocols::simple_moves::sidechain_moves::SidechainMoverBase::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.

Member Data Documentation

bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::change_chi_without_replacing_residue_

private

Referenced by change_chi_without_replacing_residue(), set_change_chi_without_replacing_residue(), and set_defaults().

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

private

core::Size protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_nchi_

private

core::Real protocols::simple_moves::sidechain_moves::SidechainMoverBase::last_proposal_density_ratio_

private

Referenced by last_proposal_density_ratio(), make_move(), and set_defaults().

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

private

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

bool protocols::simple_moves::sidechain_moves::SidechainMoverBase::preserve_detailed_balance_

private

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

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

private

Referenced by residue_packed(), and set_task().

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

private

Referenced by rotamer_library().

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

private

Referenced by dof_id_ranges(), idealize_sidechains(), init_task(), set_task(), SidechainMoverBase(), and task().

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

private

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

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

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

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

core::pack::task::TaskFactoryCOP	task_factory_

core::pack::task::PackerTaskCOP	task_

utility::vector1< core::Size >	packed_residues_

utility::vector1< bool >	residue_packed_

bool	preserve_detailed_balance_

bool	change_chi_without_replacing_residue_

utility::vector1< core::Real >	last_chi_angles_

core::Size	last_nchi_

core::Real	last_proposal_density_ratio_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation