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

#include <SidechainMoverBase.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::SidechainMoverBase:

Collaboration diagram for protocols::simple_moves::sidechain_moves::SidechainMoverBase:

Public Types
typedef utility::vector1 < core::Real >	ChiVector
Public Member Functions
	SidechainMoverBase ()
	default constructor
	SidechainMoverBase (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
	constructor with user provided rotamer library
	SidechainMoverBase (SidechainMoverBase const &mover)
	~SidechainMoverBase ()
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.
void	init_task (core::pose::Pose const &pose)
	initialize the packer task if necessary
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
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
virtual std::string	get_name () const
	Each derived class must specify its name. The class name.
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
	all angles in degree
void	idealize_sidechains (core::pose::Pose &pose)
	idealize sidechains that might be altered
core::pack::dunbrack::RotamerLibrary const &	rotamer_library () const
	get the rotamer library
core::pack::task::TaskFactoryCOP	task_factory () const
	get the task factory
void	set_task_factory (core::pack::task::TaskFactoryCOP task_factory)
	set the task factory
core::pack::task::PackerTaskCOP	task () const
	get the packer task
void	set_task (core::pack::task::PackerTaskCOP task)
	set the task
bool	preserve_detailed_balance () const
	get whether detailed balance is preserved (i.e. proposal density ratio calculated)
void	set_preserve_detailed_balance (bool setting)
	set whether detailed balance is preserved (i.e. proposal density ratio calculated)
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.
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.
virtual bool	have_mutated_residue () const
	return true if your last move has mutated residue --- make sure the residue is replaced entirely
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
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
utility::vector1< core::Size > const &	packed_residues () const
	get the residues that can be changed by this mover
utility::vector1< bool > const &	residue_packed () const
	get a vector indicating whether each residue can be packed
virtual core::Real	last_proposal_density_ratio ()
	get the ratio of proposal densities for the last move

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

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

constructor with user provided rotamer library

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

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(), have_mutated_residue(), init_task(), make_move(), 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.

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

Real protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::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]`

all angles in degree

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

References protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::build_rotamer_list(), core::conformation::Residue::chi(), and protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::compute_rotdensities().

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

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 [inline, virtual]

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 core::chemical::aa_pro, core::pose::Pose::chi(), core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), init_task(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), and core::pose::Pose::set_chi().

Referenced by initialize_simulation().

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(), and core::pose::Pose::total_residue().

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

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.

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 compute_proposal_density(), protocols::comparative_modeling::features::E, make_chi_move(), and protocols::simple_moves::tr().

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

void protocols::simple_moves::sidechain_moves::SidechainMoverBase::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::JumpRotamerSidechainMover, protocols::simple_moves::sidechain_moves::PerturbChiSidechainMover, and protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover.

References change_chi_without_replacing_residue(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), preserve_detailed_balance(), set_change_chi_without_replacing_residue(), and set_preserve_detailed_balance().

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.

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

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

get the 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().

Referenced by parse_my_tag().

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().

Referenced by parse_my_tag().

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

set the task

References core::chemical::aa_pro, 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().

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

References core::conformation::Residue::name1(), 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

Referenced by set_task().

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

get the 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.

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

Public Types

Public Member Functions

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation