#include <FastRelax.hh>

Inheritance 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_script_from_lines (std::vector< std::string > const filelines)
	replace schedule by providing lines of commands explicitly More...

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

void	dualspace (bool val)
	Use the dualspace (Dihedral + Cartesian) relax protocol (Default false) More...

bool	dualspace ()

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

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

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	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...

void	set_enable_design (bool const val)
	sets the enable_design option. Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.) 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
	Generates a new Mover object freshly created with the default ctor. More...

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

void	set_defaults ()

void	set_default_minimization_settings ()

void	set_default_coordinate_settings ()

void	set_default_movemap ()

core::kinematics::MoveMapOP	get_movemap ()

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

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

bool	cartesian () const

std::string	min_type () const

Size	max_iter () const

bool	dry_run () 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	minimize_bond_lengths () const

bool	minimize_bond_angles () const

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

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

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

void	cartesian (bool newval)
	Use cartesian (minimization step) More...

void	min_type (std::string min_type)

void	max_iter (Size max_iter)

void	dry_run (bool setting)

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	constrain_relax_segments (bool constrain_relax_segments)

void	ramp_down_constraints (bool ramp_down_constraints)

void	minimize_bond_lengths (bool minimize_bond_lengths)

void	minimize_bond_angles (bool minimize_bond_angles)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	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

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...

virtual 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
	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...

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...

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)

virtual void	set_constraint_weight (core::scoring::ScoreFunctionOP local_scorefxn, core::scoring::EnergyMap const &full_weights, core::Real const weight, core::pose::Pose &pose) const
	Use for constraint scaling – sets the coordinate constraint weight given a scorefxn, energy map, and weight. TL - Derived classes which may want to scale more than coordinate constraints can override this without forking apply() More...

void	do_md (core::pose::Pose &pose, core::Real nstep, core::Real temp0, core::kinematics::MoveMapOP local_movemap, core::scoring::ScoreFunctionOP local_scorefxn)

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

bool	fix_omega () const

int	minimize_bondlength_subset () const

int	minimize_bondangle_subset () const

bool	limit_aroma_chi2 () const

std::string	cst_files (core::Size const i) const

void	fix_omega (bool fix_omega)

void	minimize_bondangle_subset (int minimize_bondangle_subset)

void	minimize_bondlength_subset (int minimize_bondlength_subset)

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

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

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

void	add_cst_files (std::string const cstfile)

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...

Protected Attributes
bool	script_file_specified_

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

void	check_nonideal_mintype ()
	Make sure correct mintype for cartesian or dualspace during apply. More...

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

bool	delete_virtual_residues_after_FastRelax_
	If true, delete virtual residues at the end of FastRelax for smooth rmsd calculation later. 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	dna_move_
	Allow DNA to move? default is False. If True will setup DNA-specific relax settings. 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...

bool	dualspace_
	Use dualspace (Dihedral + Cartesian) Relax? More...

bool	enable_design_
	Enable design – if false, a RestrictToRepacking task will be added to the TaskFactory. 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::TagCOP	movemap_tag_

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

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

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. More...

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::comparative_modeling::LoopRelaxMover::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::forge::remodel::RemodelLoopMover::fa_relax_stage(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::fascore(), protocols::residue_optimization::MetapatchEnumeration::final_sampling(), protocols::residue_optimization::MetapatchEnumeration::initial_sampling(), protocols::abinitio::AbrelaxApplication::relax(), protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys(), and protocols::mpi_refinement::WorkUnit_Relax::run().

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().

void protocols::relax::FastRelax::check_nonideal_mintype ( )

private

Make sure correct mintype for cartesian or dualspace during apply.

References protocols::relax::RelaxProtocolBase::cartesian(), dualspace(), protocols::relax::RelaxProtocolBase::min_type(), protocols::relax::RelaxProtocolBase::minimize_bond_angles(), and protocols::relax::RelaxProtocolBase::minimize_bond_lengths().

Referenced by apply(), and batch_apply().

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_my_tag().

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, protocols::hybridization::score, symmetric_rmsd_, and protocols::relax::TR().

void protocols::relax::FastRelax::do_md	(	core::pose::Pose &	pose,
		core::Real	nstep,
		core::Real	temp0,
		core::kinematics::MoveMapOP	local_movemap,
		core::scoring::ScoreFunctionOP	local_scorefxn
	)

protected

References protocols::md::CartesianMD::apply(), protocols::md::MDBase::set_nstep(), and protocols::md::MDBase::set_temperature().

Referenced by apply().

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::Pose::conformation(), core::conformation::Conformation::is_membrane(), core::pose::symmetry::is_symmetric(), protocols::relax::RelaxProtocolBase::max_iter(), and protocols::relax::RelaxProtocolBase::min_type().

Referenced by apply(), and batch_apply().

void protocols::relax::FastRelax::dualspace ( bool val )

Use the dualspace (Dihedral + Cartesian) relax protocol (Default false)

Sets to use the lbfgs_armijo_nonmonotone if true or FR default if false Recommended to set max_iter to 200. Recommended to set minimize_bond_angles to true as well. Requires scorefunction setup for non-ideal minimization.

References dualspace_, and protocols::hybridization::val.

bool protocols::relax::FastRelax::dualspace ( )

References dualspace_.

Referenced by check_nonideal_mintype(), and parse_my_tag().

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

virtual

Return the name of this mover.

Implements protocols::moves::Mover.

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

virtual

Parses the FastRelaxTags.

Reimplemented from protocols::moves::Mover.

void protocols::relax::FastRelax::read_script_file	(	const std::string &	script_file,
		core::Size	standard_repeats = `5`
	)

private

References dualspace_, script_, set_script_from_lines(), and protocols::relax::TR().

Referenced by FastRelax(), and parse_my_tag().

void protocols::relax::FastRelax::set_constraint_weight	(	core::scoring::ScoreFunctionOP	local_scorefxn,
		core::scoring::EnergyMap const &	full_weights,
		core::Real const	weight,
		core::pose::Pose &	pose
	)		const

protectedvirtual

Use for constraint scaling – sets the coordinate constraint weight given a scorefxn, energy map, and weight. TL - Derived classes which may want to scale more than coordinate constraints can override this without forking apply()

References core::scoring::coordinate_constraint.

Referenced by apply().

void protocols::relax::FastRelax::set_enable_design ( bool const val )

inline

sets the enable_design option. Note - (Only used by ParseMyTag! Class will respect the passed TF otherwise, as it should.)

References enable_design_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::relax::FastRelax::set_force_nonideal ( bool val )

inline

Force us to batchrelax with nonideal geometry (using additional memory)

References force_nonideal_, and protocols::hybridization::val.

Referenced by protocols::hybridization::HybridizeProtocol::apply().