protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover Class Reference

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:

Collaboration diagram for protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover:

List of all members.

Public Types
typedef SidechainMoverBase	Parent
typedef utility::vector1 < core::pack::dunbrack::DunbrackRotamerSampleData >	RotamerList
Public Member Functions
	PerturbRotamerSidechainMover ()
	default constructor
	PerturbRotamerSidechainMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
	constructor with user provided rotamer library
	PerturbRotamerSidechainMover (PerturbRotamerSidechainMover const &mover)
virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected.
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.
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.
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
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
void	compute_rotdensities (RotamerList const &, ChiVector const &old_chi, ChiVector const &new_chi, core::Real &within_rot_density) const
Protected Member Functions
void	set_defaults ()

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Detailed Description

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

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Member Typedef Documentation

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

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

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

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Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::PerturbRotamerSidechainMover

(

)

default constructor

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

Referenced by clone().

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().

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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 protocols::swa::phi(), protocols::swa::psi(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::rotamer_library(), and core::conformation::Residue::type().

Referenced by compute_proposal_density(), protocols::simple_moves::sidechain_moves::SidechainMoverBase::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]

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::JumpRotamerSidechainMover.

References PerturbRotamerSidechainMover().

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 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(), and protocols::simple_moves::RG().

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

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

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_defaults

(

)

[protected]

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

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

Referenced by PerturbRotamerSidechainMover().

void protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::set_temperature

(

core::Real

setting

)

[inline]

core::Real protocols::simple_moves::sidechain_moves::PerturbRotamerSidechainMover::temperature

(

)

const [inline]

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

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

• src/protocols/simple_moves/sidechain_moves/PerturbRotamerSidechainMover.hh
• src/protocols/simple_moves/sidechain_moves/PerturbRotamerSidechainMover.cc