#include <FastRelax.hh>

Inheritance diagram for protocols::relax::FastRelax:

Collaboration diagram for protocols::relax::FastRelax:

Public Member Functions
	FastRelax (core::Size standard_repeats=0)
	Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied. More...

	FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats=0)
	Initialize FastRelax using the default script with a varying number of rounds, defined by the standard_repeats repeats paramter. By default, 5. More...

	FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, std::string const &script_file)
	Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied. More...

	FastRelax (core::scoring::ScoreFunctionOP scorefxn_in, core::Size standard_repeats, const std::string &script_file)
	Initialize FastRelax with a specific script file, and allows fastrelax to only use a subset of the number of stages in the scriptfile. More...

void	set_script_to_batchrelax_default (core::Size standard_repeats=0)
	Override the stored script with the default script for batchrelax Ignores '-default_repeat' value. More...

void	set_force_nonideal (bool val)
	Force us to batchrelax with nonideal geometry (using additional memory) More...

virtual	~FastRelax ()
	virtual constructor to allow derivation More...

void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Parses the FastRelaxTags. More...

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)

void	set_to_default ()
	Initializes class using option system. This is called by the constructors. More...

virtual std::string	get_name () const
	Return the name of this mover. More...

virtual protocols::moves::MoverOP	clone () const
	return a fresh instance of this class in an owning pointer More...

virtual void	apply (core::pose::Pose &pose)
	Apply the FastRelax. Overloaded apply function from mover base class. More...

void	makeDnaRigid (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
	sets the movemap to not allow DNA to move during relax. More...

void	batch_apply (std::vector< core::io::silent::SilentStructOP > &input_structs, core::scoring::constraints::ConstraintSetOP input_csts=NULL, core::Real decay_rate=0.5)
	Batch Relax, a new even faster way to relax entire batches of structures. More...

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	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)

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

Protected Member Functions
void	cmd_accept_to_best (const core::scoring::ScoreFunctionOP local_scorefxn, core::pose::Pose &pose, core::pose::Pose &best_pose, const core::pose::Pose &start_pose, core::Real &best_score, core::Size &accept_count)

void	do_minimize (core::pose::Pose &pose, core::Real tolerance, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)

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 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...

Private Member Functions
void	read_script_file (const std::string &script_file, core::Size standard_repeats=5)

Private Attributes
core::Size	default_repeats_
	Number of repeats if using default script. More...

bool	ramady_
	Apply Ramady(tm) fix to residues with bad rama scores ? More...

core::Size	ramady_num_rebuild_
	Number of bad ramas to fix per call to 'fix_worst_bad_ramas'. More...

core::Real	ramady_rms_limit_
	Reject ramady changes perturbing structure more than this amount. More...

core::Real	ramady_cutoff_
	Cutoff for calling a rama 'bad'. More...

bool	ramady_force_
	Force ramady to be run (normally skip rate of 10%) More...

bool	repack_
	Allow Chi angles to move ? More...

bool	test_cycles_
	Do only a few test_cycles ? More...

bool	force_nonideal_
	[batch mode only] force structures to be nonideal? Default uses -out:silent_struct_type to decide More...

bool	dumpall_
	Dump pdb after repack, min, or ramp_repack_min? More...

core::Size	script_max_accept_
	Quit after this many accepts ?// limits themaximum number of accepts, default is 1000000. More...

bool	symmetric_rmsd_
	Do a symmetric RMSD calculation rather then a monomeric one. More...

protocols::checkpoint::CheckPointer	checkpoints_

std::vector< RelaxScriptCommand >	script_

utility::tag::TagPtr	movemap_tag_

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

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

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_

Constructor & Destructor Documentation

protocols::relax::FastRelax::FastRelax ( core::Size standard_repeats = 0)

Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied.

FastRelax main code:

References default_repeats_, protocols::relax::RelaxProtocolBase::explicit_ramp_constraints(), protocols::relax::RelaxProtocolBase::ramp_down_constraints(), read_script_file(), and set_to_default().

Referenced by clone().

protocols::relax::FastRelax::FastRelax	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		core::Size	standard_repeats = `0`
	)

Initialize FastRelax using the default script with a varying number of rounds, defined by the standard_repeats repeats paramter. By default, 5.

References default_repeats_, protocols::relax::RelaxProtocolBase::explicit_ramp_constraints(), protocols::relax::RelaxProtocolBase::ramp_down_constraints(), read_script_file(), and set_to_default().

protocols::relax::FastRelax::FastRelax	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		std::string const &	script_file
	)

Initialize FastRelax with a specific script file, which encodes the script of steps the is to be applied.

References read_script_file(), and set_to_default().

protocols::relax::FastRelax::FastRelax	(	core::scoring::ScoreFunctionOP	scorefxn_in,
		core::Size	standard_repeats,
		const std::string &	script_file
	)

Initialize FastRelax with a specific script file, and allows fastrelax to only use a subset of the number of stages in the scriptfile.

References default_repeats_, read_script_file(), and set_to_default().

protocols::relax::FastRelax::~FastRelax ( )

virtual

virtual constructor to allow derivation

destructor - this class has no dynamic allocation, so / nothing needs to be cleaned. C++ will take care of that for us.

Member Function Documentation

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

virtual

Apply the FastRelax. Overloaded apply function from mover base class.

Implements protocols::moves::Mover.

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), protocols::relax::MiniRelax::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::abinitio::AbrelaxApplication::relax(), and protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys().

void protocols::relax::FastRelax::batch_apply	(	std::vector< core::io::silent::SilentStructOP > &	input_structs,
		core::scoring::constraints::ConstraintSetOP	input_csts = `NULL`,
		core::Real	decay_rate = `0.5`
	)

Batch Relax, a new even faster way to relax entire batches of structures.

Referenced by protocols::loophash::Mover_LoopHashRefine::apply(), protocols::hybridization::HybridizeProtocol::apply(), and protocols::relax::WorkUnit_BatchRelax::run().

protocols::moves::MoverOP protocols::relax::FastRelax::clone ( ) const

virtual

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Reimplemented from protocols::moves::Mover.

References FastRelax().

Referenced by apply(), batch_apply(), and parse_def().

void protocols::relax::FastRelax::cmd_accept_to_best	(	const core::scoring::ScoreFunctionOP	local_scorefxn,
		core::pose::Pose &	pose,
		core::pose::Pose &	best_pose,
		const core::pose::Pose &	start_pose,
		core::Real &	best_score,
		core::Size &	accept_count
	)

protected

References core::scoring::CA_rmsd_symmetric(), protocols::moves::Mover::get_native_pose(), core::pose::symmetry::is_symmetric(), core::scoring::native_CA_rmsd(), core::scoring::rms, symmetric_rmsd_, and protocols::relax::TR().

void protocols::relax::FastRelax::do_minimize	(	core::pose::Pose &	pose,
		core::Real	tolerance,
		core::kinematics::MoveMapOP	local_movemap,
		core::scoring::ScoreFunctionOP	local_scorefxn
	)

protected

References protocols::relax::RelaxProtocolBase::cartesian_, core::pose::symmetry::is_symmetric(), and protocols::relax::RelaxProtocolBase::min_type_.

Referenced by apply(), and batch_apply().

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

virtual

Return the name of this mover.

Implements protocols::moves::Mover.

void protocols::relax::FastRelax::makeDnaRigid	(	core::pose::Pose &	pose,
		core::kinematics::MoveMapOP	mm
	)

sets the movemap to not allow DNA to move during relax.

References core::conformation::Residue::is_DNA(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::relax::TR().

void protocols::relax::FastRelax::parse_def	(	utility::lua::LuaObject const &	def,
		utility::lua::LuaObject const &	score_fxns,
		utility::lua::LuaObject const &	tasks,
		protocols::moves::MoverCacheSP	cache
	)

virtual

Reimplemented from protocols::moves::Mover.

References protocols::relax::RelaxProtocolBase::cartesian(), clone(), default_repeats_, protocols::elscripts::parse_movemapdef(), protocols::elscripts::parse_scoredef(), protocols::elscripts::parse_taskdef(), read_script_file(), protocols::relax::RelaxProtocolBase::set_movemap(), protocols::relax::RelaxProtocolBase::set_scorefxn(), set_script_to_batchrelax_default(), and protocols::relax::RelaxProtocolBase::set_task_factory().

void protocols::relax::FastRelax::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &	pose
	)