A functor class which implements the classic Rosetta++ pose_relax protocol. More...

#include <ClassicRelax.hh>

Inheritance diagram for protocols::relax::ClassicRelax:

Collaboration diagram for protocols::relax::ClassicRelax:

Public Types
typedef RelaxProtocolBase	parent

Public Types inherited from protocols::relax::RelaxProtocolBase
typedef moves::Mover	parent

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

Public Member Functions
	ClassicRelax (core::scoring::ScoreFunctionOP scorefxn_in)

	ClassicRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::kinematics::MoveMapOP movemap)
	constructor taking both ScoreFunction and MoveMap More...

	ClassicRelax (ClassicRelax const &)

	ClassicRelax ()

virtual	~ClassicRelax ()

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

void	set_default (core::scoring::ScoreFunctionOP scorefxn_in)

virtual void	apply (core::pose::Pose &pose)

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

void	set_default (bool const use_default_movemap=true)

void	set_default_minimizer ()

void	set_default_moveset_phase1 ()

void	set_default_moveset_phase2 ()

void	set_default_moveset_phase3 ()

void	set_lj_ramp_cycles (int param)

void	set_lj_ramp_inner_cycles (int param)

void	set_start_rep_weight (core::Real param)

void	set_stage2_cycles (int cycles2)

void	set_stage2_repack_period (int repack2)

void	set_stage3_cycles (int cycles3)

void	set_tolerance (core::Real new_tolerance)

void	set_mc (moves::MonteCarloOP new_mc_)

void	set_full_repack (protocols::simple_moves::PackRotamersMoverOP new_pack_full_repack)

void	set_rottrial (protocols::simple_moves::RotamerTrialsMoverOP new_pack_rottrial)

void	setPoseExtraScores (core::pose::Pose &pose)

void	use_coarse_vdw ()

moves::MonteCarloOP	get_mc (core::pose::Pose &pose)

protocols::checkpoint::CheckPointer &	get_checkpoints ()

Public Member Functions inherited from protocols::relax::RelaxProtocolBase
	RelaxProtocolBase (core::scoring::ScoreFunctionOP)

	RelaxProtocolBase (std::string const &movername="RelaxProtocol")

	RelaxProtocolBase (std::string const &movername, core::scoring::ScoreFunctionOP)

	~RelaxProtocolBase ()

virtual protocols::moves::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_defaults ()

void	set_default_minimization_settings ()

void	set_default_coordinate_settings ()

void	set_default_movemap ()

void	minimize_bond_lengths (bool setting)

void	minimize_bond_angles (bool setting)

void	minimize_bondlength_subset (int setting)

void	minimize_bondangle_subset (int setting)

bool	minimize_bond_lengths () const

bool	minimize_bond_angles () const

int	minimize_bondlength_subset () const

int	minimize_bondangle_subset () const

bool	constrain_relax_to_native_coords () const

bool	constrain_relax_to_start_coords () const

bool	constrain_coords () const

bool	explicit_ramp_constraints () const

bool	ramp_down_constraints () const

bool	constrain_relax_segments () const

bool	limit_aroma_chi2 () const

void	constrain_relax_to_native_coords (bool constrain_relax_to_native_coords)

void	constrain_relax_to_start_coords (bool constrain_relax_to_start_coords)

void	constrain_coords (bool constrain_coords)

void	ramp_down_constraints (bool ramp_down_constraints)

void	constrain_relax_segments (bool constrain_relax_segments)

void	cartesian (bool newval)

bool	cartesian () const

core::kinematics::MoveMapOP	get_movemap ()

void	set_movemap (core::kinematics::MoveMapOP movemap)

void	set_min_type (std::string min_type)

void	set_scorefxn (core::scoring::ScoreFunctionOP score)

const core::scoring::ScoreFunctionCOP	get_scorefxn () const

void	set_task_factory (core::pack::task::TaskFactoryOP taskf)

core::pack::task::TaskFactoryOP const &	get_task_factory () const

void	set_dry_run (bool setting)

bool	dry_run () const

void	apply_disulfides (core::pose::Pose &pose)

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...

virtual core::Real	last_proposal_density_ratio ()

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

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 void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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
	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...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Static Public Member Functions
static void	register_options ()

Static Public Member Functions inherited from protocols::relax::RelaxProtocolBase
static void	register_options ()

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...

Private Member Functions
void	check_default_mc (core::pose::Pose &pose)

void	check_default_full_repacker (core::pose::Pose &pose, core::kinematics::MoveMap &movemap)

void	check_default_rottrial (core::pose::Pose &pose, core::kinematics::MoveMap &movemap)

Private Attributes
protocols::simple_moves::MinMoverOP	min_mover_

protocols::checkpoint::CheckPointer	checkpoints_

moves::MonteCarloOP	mc_

bool	use_default_mc_

protocols::simple_moves::PackRotamersMoverOP	pack_full_repack_

bool	use_default_pack_full_repack_

protocols::simple_moves::RotamerTrialsMoverOP	pack_rottrial_

bool	use_default_pack_rottrial_

core::Real	m_Temperature

core::Size	nmoves_

core::Real	energycut

std::string	min_type

bool	nb_list

core::Real	min_tolerance

moves::MoverOP	moveset_phase1_

moves::MoverOP	moveset_phase2_

moves::MoverOP	moveset_phase3_

int	lj_ramp_cycles

int	lj_ramp_inner_cycles

core::Real	start_rep_weight

core::Real	end_rep_weight

core::scoring::ScoreType	st_rep_

core::scoring::ScoreType	st_atr_

core::scoring::ScoreType	st_sol_

int	stage2_repack_period

int	stage2_cycles

int	stage3_cycles

float	score_stage2_beginning

float	score_stage2_quarter

float	score_stage2_half

float	score_stage2_end

float	filter_stage2_beginning

float	filter_stage2_quarter

float	filter_stage2_half

float	filter_stage2_end

Additional Inherited Members
Protected Member Functions inherited from protocols::relax::RelaxProtocolBase
void	initialize_movemap (core::pose::Pose const &pose, core::kinematics::MoveMap &movemap)

core::scoring::ScoreFunctionOP	get_scorefxn ()

void	set_up_constraints (core::pose::Pose &pose, core::kinematics::MoveMap &local_movemap)

void	output_debug_structure (core::pose::Pose &pose, std::string prefix)

Protected Attributes inherited from protocols::relax::RelaxProtocolBase
bool	constrain_relax_to_native_coords_

bool	constrain_relax_to_start_coords_

bool	constrain_coords_

bool	coord_constrain_sidechains_

bool	explicit_ramp_constraints_

bool	ramp_down_constraints_

bool	constrain_relax_segments_

std::string	min_type_

bool	cartesian_
	Do cartesian-space minimization? More...

bool	limit_aroma_chi2_

Detailed Description

A functor class which implements the classic Rosetta++ pose_relax protocol.

A functor class which implements the classic Rosetta++ pose_relax protocol

Todo:: Crank and Wobble Moves - however there's little evidence that they are essential

Member Typedef Documentation

typedef RelaxProtocolBase protocols::relax::ClassicRelax::parent

Constructor & Destructor Documentation

protocols::relax::ClassicRelax::ClassicRelax ( core::scoring::ScoreFunctionOP scorefxn_in)

References set_default(), use_default_mc_, use_default_pack_full_repack_, and use_default_pack_rottrial_.

protocols::relax::ClassicRelax::ClassicRelax	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		core::kinematics::MoveMapOP	movemap
	)

constructor taking both ScoreFunction and MoveMap

References set_default(), protocols::relax::RelaxProtocolBase::set_movemap(), use_default_mc_, use_default_pack_full_repack_, and use_default_pack_rottrial_.

protocols::relax::ClassicRelax::ClassicRelax ( ClassicRelax const & other)

protocols::relax::ClassicRelax::ClassicRelax ( )

References set_default(), use_default_mc_, use_default_pack_full_repack_, and use_default_pack_rottrial_.

Referenced by clone().

protocols::relax::ClassicRelax::~ClassicRelax ( )

virtual

Member Function Documentation

void protocols::relax::ClassicRelax::apply ( core::pose::Pose & pose)

virtual

Central Apply function

Implements protocols::moves::Mover.

References core::scoring::angle_constraint, protocols::relax::RelaxProtocolBase::apply_disulfides(), core::scoring::atom_pair_constraint, core::scoring::CA_rmsd(), check_default_full_repacker(), check_default_mc(), check_default_rottrial(), protocols::checkpoint::CheckPointer::checkpoint(), checkpoints_, core::pose::Pose::conformation(), core::scoring::coordinate_constraint, core::pose::Pose::data(), core::scoring::dihedral_constraint, end_rep_weight, core::scoring::fa_rep, filter_stage2_beginning, filter_stage2_quarter, protocols::moves::Mover::get_current_tag(), protocols::relax::RelaxProtocolBase::get_movemap(), protocols::moves::Mover::get_native_pose(), protocols::relax::RelaxProtocolBase::get_scorefxn(), protocols::relax::RelaxProtocolBase::initialize_movemap(), core::pose::symmetry::is_symmetric(), lj_ramp_cycles, lj_ramp_inner_cycles, core::pose::symmetry::make_symmetric_movemap(), mc_, min_mover_, moveset_phase2_, moveset_phase3_, protocols::jd2::ScoreMap::nonzero_energies(), pack_full_repack_, pack_rottrial_, protocols::relax::RelaxProtocolBase::ramp_down_constraints_, protocols::checkpoint::CheckPointer::recover_checkpoint(), core::pose::Pose::residue(), score_stage2_beginning, score_stage2_end, score_stage2_half, score_stage2_quarter, protocols::relax::RelaxProtocolBase::set_up_constraints(), setPoseExtraScores(), stage2_cycles, stage2_repack_period, stage3_cycles, start_rep_weight, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), and protocols::relax::TR().

void protocols::relax::ClassicRelax::check_default_full_repacker	(	core::pose::Pose &	pose,
		core::kinematics::MoveMap &	movemap
	)

private

References core::kinematics::MoveMap::get_chi(), protocols::relax::RelaxProtocolBase::get_scorefxn(), pack_full_repack_, core::pose::Pose::total_residue(), and use_default_pack_full_repack_.

Referenced by apply().

void protocols::relax::ClassicRelax::check_default_mc ( core::pose::Pose & pose)

private

References protocols::relax::RelaxProtocolBase::get_scorefxn(), mc_, and use_default_mc_.

Referenced by apply(), and get_mc().

void protocols::relax::ClassicRelax::check_default_rottrial	(	core::pose::Pose &	pose,
		core::kinematics::MoveMap &	movemap
	)

private

References energycut, core::kinematics::MoveMap::get_chi(), protocols::relax::RelaxProtocolBase::get_scorefxn(), mc_, pack_rottrial_, core::pose::Pose::total_residue(), and use_default_pack_full_repack_.

Referenced by apply().

protocols::moves::MoverOP protocols::relax::ClassicRelax::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.

References ClassicRelax().

protocols::checkpoint::CheckPointer& protocols::relax::ClassicRelax::get_checkpoints ( )

inline

moves::MonteCarloOP protocols::relax::ClassicRelax::get_mc ( core::pose::Pose & pose)

Accessors

References check_default_mc(), and mc_.

std::string protocols::relax::ClassicRelax::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::relax::ClassicRelax::register_options ( )

static

registering of options that are relevant for AbrelaxApplication

References protocols::relax::RelaxProtocolBase::register_options().

void protocols::relax::ClassicRelax::set_default ( core::scoring::ScoreFunctionOP scorefxn_in)

References protocols::relax::RelaxProtocolBase::set_scorefxn().

Referenced by ClassicRelax().

void protocols::relax::ClassicRelax::set_default ( bool const use_default_movemap = true)

void protocols::relax::ClassicRelax::set_default_minimizer ( )

References protocols::relax::RelaxProtocolBase::get_movemap(), protocols::relax::RelaxProtocolBase::get_scorefxn(), min_mover_, min_tolerance, min_type, and nb_list.

Referenced by set_default(), and set_tolerance().

void protocols::relax::ClassicRelax::set_default_moveset_phase1 ( )

At stage 1 we're only doing small and shear moves

References protocols::relax::RelaxProtocolBase::get_movemap(), m_Temperature, moveset_phase1_, and nmoves_.

Referenced by set_default().

void protocols::relax::ClassicRelax::set_default_moveset_phase2 ( )

At stage 2 we're doing small, shear, wobble and crank moves (the latter two are works in progress)

References protocols::relax::RelaxProtocolBase::get_movemap(), m_Temperature, moveset_phase2_, and nmoves_.

Referenced by set_default().

void protocols::relax::ClassicRelax::set_default_moveset_phase3 ( )

At stage 3 we're only doing small and shear moves

References protocols::relax::RelaxProtocolBase::get_movemap(), m_Temperature, moveset_phase3_, and nmoves_.

Referenced by set_default().

void protocols::relax::ClassicRelax::set_full_repack ( protocols::simple_moves::PackRotamersMoverOP new_pack_full_repack)

References pack_full_repack_, and use_default_pack_full_repack_.

void protocols::relax::ClassicRelax::set_lj_ramp_cycles ( int param)

inline

Set options from outside

References lj_ramp_cycles.

void protocols::relax::ClassicRelax::set_lj_ramp_inner_cycles ( int param)

inline

References lj_ramp_inner_cycles.

void protocols::relax::ClassicRelax::set_mc ( moves::MonteCarloOP new_mc_)

References mc_, and use_default_mc_.

void protocols::relax::ClassicRelax::set_rottrial ( protocols::simple_moves::RotamerTrialsMoverOP new_pack_rottrial)

References pack_rottrial_, and use_default_pack_full_repack_.

void protocols::relax::ClassicRelax::set_stage2_cycles ( int cycles2)

inline

References stage2_cycles.

void protocols::relax::ClassicRelax::set_stage2_repack_period ( int repack2)

inline

References stage2_repack_period.

void protocols::relax::ClassicRelax::set_stage3_cycles ( int cycles3)

inline

References stage3_cycles.

void protocols::relax::ClassicRelax::set_start_rep_weight ( core::Real param)

inline

References start_rep_weight.

void protocols::relax::ClassicRelax::set_tolerance ( core::Real new_tolerance)

References min_tolerance, set_default_minimizer(), and protocols::relax::TR().

void protocols::relax::ClassicRelax::setPoseExtraScores ( core::pose::Pose & pose)

References score_stage2_beginning, score_stage2_end, score_stage2_half, score_stage2_quarter, and core::pose::setPoseExtraScores().

Referenced by protocols::abinitio::AbrelaxMover::apply(), apply(), protocols::abinitio::AbrelaxApplication::do_distributed_rerun(), and protocols::abinitio::AbrelaxApplication::fold().

void protocols::relax::ClassicRelax::use_coarse_vdw ( )

inline

References core::scoring::coarse_fa_atr, core::scoring::coarse_fa_rep, core::scoring::coarse_fa_sol, st_atr_, st_rep_, and st_sol_.

Member Data Documentation

protocols::checkpoint::CheckPointer protocols::relax::ClassicRelax::checkpoints_

private

Referenced by apply().

core::Real protocols::relax::ClassicRelax::end_rep_weight

private

Referenced by apply(), and set_default().

core::Real protocols::relax::ClassicRelax::energycut

private

Referenced by check_default_rottrial(), and set_default().

float protocols::relax::ClassicRelax::filter_stage2_beginning

private

Referenced by apply(), and set_default().

float protocols::relax::ClassicRelax::filter_stage2_end

private

Referenced by set_default().

float protocols::relax::ClassicRelax::filter_stage2_half

private

Referenced by set_default().

float protocols::relax::ClassicRelax::filter_stage2_quarter

private

Referenced by apply(), and set_default().

int protocols::relax::ClassicRelax::lj_ramp_cycles

private

Referenced by apply(), set_default(), and set_lj_ramp_cycles().

int protocols::relax::ClassicRelax::lj_ramp_inner_cycles

private

Referenced by apply(), set_default(), and set_lj_ramp_inner_cycles().

core::Real protocols::relax::ClassicRelax::m_Temperature

private

Referenced by set_default(), set_default_moveset_phase1(), set_default_moveset_phase2(), and set_default_moveset_phase3().

moves::MonteCarloOP protocols::relax::ClassicRelax::mc_

private

Referenced by apply(), check_default_mc(), check_default_rottrial(), get_mc(), and set_mc().

protocols::simple_moves::MinMoverOP protocols::relax::ClassicRelax::min_mover_

private

Referenced by apply(), and set_default_minimizer().

core::Real protocols::relax::ClassicRelax::min_tolerance

private

Referenced by set_default(), set_default_minimizer(), and set_tolerance().

std::string protocols::relax::ClassicRelax::min_type

private

Referenced by set_default(), and set_default_minimizer().

moves::MoverOP protocols::relax::ClassicRelax::moveset_phase1_

private

Referenced by set_default_moveset_phase1().

moves::MoverOP protocols::relax::ClassicRelax::moveset_phase2_

private

Referenced by apply(), and set_default_moveset_phase2().

moves::MoverOP protocols::relax::ClassicRelax::moveset_phase3_

private

Referenced by apply(), and set_default_moveset_phase3().

bool protocols::relax::ClassicRelax::nb_list

private

Referenced by set_default(), and set_default_minimizer().

core::Size protocols::relax::ClassicRelax::nmoves_

private

Referenced by set_default(), set_default_moveset_phase1(), set_default_moveset_phase2(), and set_default_moveset_phase3().

protocols::simple_moves::PackRotamersMoverOP protocols::relax::ClassicRelax::pack_full_repack_

private

Referenced by apply(), check_default_full_repacker(), and set_full_repack().

protocols::simple_moves::RotamerTrialsMoverOP protocols::relax::ClassicRelax::pack_rottrial_

private

Referenced by apply(), check_default_rottrial(), and set_rottrial().

float protocols::relax::ClassicRelax::score_stage2_beginning

private

Referenced by apply(), set_default(), and setPoseExtraScores().

float protocols::relax::ClassicRelax::score_stage2_end

private

Referenced by apply(), set_default(), and setPoseExtraScores().

float protocols::relax::ClassicRelax::score_stage2_half

private

Referenced by apply(), set_default(), and setPoseExtraScores().

float protocols::relax::ClassicRelax::score_stage2_quarter

private

Referenced by apply(), set_default(), and setPoseExtraScores().

core::scoring::ScoreType protocols::relax::ClassicRelax::st_atr_

private

Referenced by set_default(), and use_coarse_vdw().

core::scoring::ScoreType protocols::relax::ClassicRelax::st_rep_

private

Referenced by set_default(), and use_coarse_vdw().

core::scoring::ScoreType protocols::relax::ClassicRelax::st_sol_

private

Referenced by set_default(), and use_coarse_vdw().

int protocols::relax::ClassicRelax::stage2_cycles

private

Referenced by apply(), set_default(), and set_stage2_cycles().

int protocols::relax::ClassicRelax::stage2_repack_period

private

Referenced by apply(), set_default(), and set_stage2_repack_period().

int protocols::relax::ClassicRelax::stage3_cycles

private

Referenced by apply(), set_default(), and set_stage3_cycles().

core::Real protocols::relax::ClassicRelax::start_rep_weight

private

Referenced by apply(), set_default(), and set_start_rep_weight().

bool protocols::relax::ClassicRelax::use_default_mc_

private

Referenced by check_default_mc(), ClassicRelax(), and set_mc().

bool protocols::relax::ClassicRelax::use_default_pack_full_repack_

private

Referenced by check_default_full_repacker(), check_default_rottrial(), ClassicRelax(), set_full_repack(), and set_rottrial().

bool protocols::relax::ClassicRelax::use_default_pack_rottrial_

private

Referenced by ClassicRelax().

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

src/protocols/relax/ClassicRelax.hh
src/protocols/relax/ClassicRelax.cc

Public Types

Public Member Functions

Static 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