#include <FastRelax.hh>

Inheritance diagram for protocols::relax::FastRelax:

[legend]

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 ()

core::Size	default_repeats () const
	Return the number of repeats. More...

void	set_movemap_disables_packing_of_fixed_chi_positions (bool const setting)
	Set whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...

bool	movemap_disables_packing_of_fixed_chi_positions () const
	Get whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false. More...

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

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Parses the FastRelaxTags. More...

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

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

void	apply (core::pose::Pose &pose) override
	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=nullptr, 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...

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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 () override

protocols::moves::MoverOP	fresh_instance () const override
	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::MoveMapCOP	get_movemap () const

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

core::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	coord_constrain_sidechains () 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_movemap_factory (core::select::movemap::MoveMapFactoryOP mm_factory)

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 (core::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	coord_constrain_sidechains (bool coord_constrain_sidechains)

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)

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. More...

Public Member Functions inherited from protocols::moves::Mover
	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...

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...

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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

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...

Static Public Member Functions
static std::string	mover_name ()
	Return the name of this mover. More...

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_fast_relax (utility::tag::XMLSchemaDefinition &)

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...

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)

std::string	determine_default_relax_script ()
	default is currently MonomerDesign2019 or MonomerRelax2019, depending on the state of enable_design_ More...

core::pack::task::TaskFactoryOP	setup_local_tf (core::pose::Pose const &pose, core::kinematics::MoveMapOP const &local_movemap)
	helper function for apply(). Helps setup the task factory More...

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...

Private Member Functions
utility::vector1< std::string >	get_possible_relax_script_names (std::string const &prefix) const

void	read_script_file (std::string script_file, core::Size standard_repeats=5)

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

void	inner_loop_repack_command (core::Size const chk_counter, core::pose::Pose &pose, core::scoring::ScoreFunctionOP const &local_scorefxn, minimization_packing::PackRotamersMoverOP const &pack_full_repack, int &dump_counter)

void	inner_loop_min_command (RelaxScriptCommand const &cmd, core::pose::Pose &pose, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn, core::Size &chk_counter, int &dump_counter)

void	inner_loop_ramp_repack_min_command (RelaxScriptCommand const &cmd, int const total_repeat_count, bool const do_rama_repair, core::scoring::EnergyMap &full_weights, core::pose::Pose &pose, minimization_packing::PackRotamersMoverOP const &pack_full_repack, int const repeat_count, int const total_count, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn, core::Size &chk_counter, int &dump_counter)

void	inner_loop_dumpall_command (RelaxScriptCommand const &cmd)

void	inner_loop_md_command (RelaxScriptCommand const &cmd, core::Size &chk_counter, core::pose::Pose &pose, core::kinematics::MoveMapOP const &local_movemap, core::scoring::ScoreFunctionOP const &local_scorefxn)

void	inner_loop_reset_reference_command (core::scoring::ScoreFunctionOP const &local_scorefxn) const

void	inner_loop_reference_command (RelaxScriptCommand const &cmd, core::scoring::ScoreFunctionOP const &local_scorefxn) const

void	inner_loop_accept_to_best_command (core::scoring::ScoreFunctionOP const &local_scorefxn, core::pose::Pose &pose, core::Real &best_score, core::Size &accept_count, core::pose::Pose &best_pose, core::pose::Pose const &start_pose, std::vector< core::Real > &best_score_log, std::vector< core::Real > &curr_score_log, int const)

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

bool	movemap_disables_packing_of_fixed_chi_positions_ = false
	Option to have the MoveMap disable packing at positions where sidechain minimization is disabled. 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_

Friends
class	::FastRelaxTests

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 std::list< std::string >	Strings

Constructor & Destructor Documentation

◆ FastRelax() [1/4]

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_, read_script_file(), and set_to_default().

◆ FastRelax() [2/4]

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_, read_script_file(), and set_to_default().

◆ FastRelax() [3/4]

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().

◆ FastRelax() [4/4]

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().

◆ ~FastRelax()

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

overridedefault

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

◆ apply()

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

overridevirtual

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

Implements protocols::moves::Mover.

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), protocols::relax::loop::LoopRelaxMover::apply(), protocols::relax::MiniRelax::apply(), protocols::symmetric_docking::SymDockingHiRes::apply(), protocols::hybridization::HybridizeProtocol::apply(), protocols::normalmode::NormalModeRelaxMover::apply_on_pose(), protocols::evolution::NucleotideMutation::compute_folding_energies(), protocols::forge::remodel::RemodelMover::design_refine_seq_relax(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), 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::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains(), protocols::abinitio::AbrelaxApplication::relax(), protocols::relax::RepeatProteinRelax::relax_pose(), and protocols::relax::WorkUnit_BatchRelax_and_PostRescore::rescore_all_decoys().

◆ batch_apply()

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

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

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

◆ check_nonideal_mintype()

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().

◆ clone()

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

overridevirtual

return a fresh instance of this class in an owning pointer

Return a copy of ourselves.

Reimplemented from protocols::moves::Mover.

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

◆ cmd_accept_to_best()

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().

◆ complex_type_generator_for_fast_relax()

utility::tag::XMLSchemaComplexTypeGeneratorOP protocols::relax::FastRelax::complex_type_generator_for_fast_relax ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::rosetta_scripts::append_subelement_for_parse_movemap_factory_legacy(), core::select::movemap::attributes_for_parse_movemap_factory_default_attr_name(), core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations_w_factory(), and protocols::moves::complex_type_name_for_mover().

Referenced by provide_xml_schema().

◆ default_repeats()

core::Size protocols::relax::FastRelax::default_repeats ( ) const

inline

Return the number of repeats.

References default_repeats_.

◆ determine_default_relax_script()

std::string protocols::relax::FastRelax::determine_default_relax_script ( )

protected

default is currently MonomerDesign2019 or MonomerRelax2019, depending on the state of enable_design_

Author: Jack Maguire

References enable_design_.

Referenced by read_script_file().

◆ do_md()

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_temp0().

Referenced by inner_loop_md_command().

◆ do_minimize()

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(), protocols::relax::RelaxProtocolBase::max_iter(), and protocols::relax::RelaxProtocolBase::min_type().

Referenced by batch_apply(), inner_loop_min_command(), and inner_loop_ramp_repack_min_command().

◆ dualspace() [1/2]

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

References dualspace_.

Referenced by check_nonideal_mintype(), and parse_my_tag().

◆ dualspace() [2/2]

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.

◆ get_name()

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

overridevirtual

Return the name of this mover.

Implements protocols::moves::Mover.

References mover_name().

Referenced by provide_citation_info().

◆ get_possible_relax_script_names()

utility::vector1< std::string > protocols::relax::FastRelax::get_possible_relax_script_names ( std::string const & prefix ) const

private

References core::scoring::basename_for_score_function(), dualspace_, core::scoring::get_score_functionName(), and protocols::moves::Mover::name().

◆ inner_loop_accept_to_best_command()

void protocols::relax::FastRelax::inner_loop_accept_to_best_command	(	core::scoring::ScoreFunctionOP const &	local_scorefxn,
		core::pose::Pose &	pose,
		core::Real &	best_score,
		core::Size &	accept_count,
		core::pose::Pose &	best_pose,
		core::pose::Pose const &	start_pose,
		std::vector< core::Real > &	best_score_log,
		std::vector< core::Real > &	curr_score_log,
		int const
	)

private

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().

Referenced by apply().

◆ inner_loop_dumpall_command()

void protocols::relax::FastRelax::inner_loop_dumpall_command ( RelaxScriptCommand const & cmd )

private

References protocols::relax::RelaxScriptCommand::command, and dumpall_.

Referenced by apply().

◆ inner_loop_md_command()

void protocols::relax::FastRelax::inner_loop_md_command	(	RelaxScriptCommand const &	cmd,
		core::Size &	chk_counter,
		core::pose::Pose &	pose,
		core::kinematics::MoveMapOP const &	local_movemap,
		core::scoring::ScoreFunctionOP const &	local_scorefxn
	)

private

References protocols::checkpoint::CheckPointer::checkpoint(), checkpoints_, protocols::relax::RelaxScriptCommand::command, do_md(), protocols::moves::Mover::get_current_tag(), protocols::relax::RelaxScriptCommand::nparams, protocols::relax::RelaxScriptCommand::param1, protocols::relax::RelaxScriptCommand::param2, and protocols::checkpoint::CheckPointer::recover_checkpoint().

Referenced by apply().

◆ inner_loop_min_command()

void protocols::relax::FastRelax::inner_loop_min_command	(	RelaxScriptCommand const &	cmd,
		core::pose::Pose &	pose,
		core::kinematics::MoveMapOP const &	local_movemap,
		core::scoring::ScoreFunctionOP const &	local_scorefxn,
		core::Size &	chk_counter,
		int &	dump_counter
	)

private

References protocols::checkpoint::CheckPointer::checkpoint(), checkpoints_, protocols::relax::RelaxScriptCommand::command, do_minimize(), core::pose::Pose::dump_pdb(), dumpall_, protocols::moves::Mover::get_current_tag(), protocols::relax::RelaxScriptCommand::nparams, protocols::relax::RelaxScriptCommand::param1, and protocols::checkpoint::CheckPointer::recover_checkpoint().

Referenced by apply().

◆ inner_loop_ramp_repack_min_command()

void protocols::relax::FastRelax::inner_loop_ramp_repack_min_command	(	RelaxScriptCommand const &	cmd,
		int const	total_repeat_count,
		bool const	do_rama_repair,
		core::scoring::EnergyMap &	full_weights,
		core::pose::Pose &	pose,
		minimization_packing::PackRotamersMoverOP const &	pack_full_repack,
		int const	repeat_count,
		int const	total_count,
		core::kinematics::MoveMapOP const &	local_movemap,
		core::scoring::ScoreFunctionOP const &	local_scorefxn,
		core::Size &	chk_counter,
		int &	dump_counter
	)

private

Referenced by apply().

◆ inner_loop_reference_command()

void protocols::relax::FastRelax::inner_loop_reference_command	(	RelaxScriptCommand const &	cmd,
		core::scoring::ScoreFunctionOP const &	local_scorefxn
	)		const

private

References protocols::relax::RelaxScriptCommand::command, protocols::relax::RelaxScriptCommand::nparams, protocols::relax::RelaxScriptCommand::params_vec, core::scoring::score_type_from_name(), and core::scoring::methods::EnergyMethodOptions::set_method_weights().

Referenced by apply().

◆ inner_loop_repack_command()

void protocols::relax::FastRelax::inner_loop_repack_command	(	core::Size const	chk_counter,
		core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP const &	local_scorefxn,
		minimization_packing::PackRotamersMoverOP const &	pack_full_repack,
		int &	dump_counter
	)

private

References protocols::checkpoint::CheckPointer::checkpoint(), checkpoints_, core::pose::Pose::dump_pdb(), dumpall_, protocols::moves::Mover::get_current_tag(), and protocols::checkpoint::CheckPointer::recover_checkpoint().

Referenced by apply().

◆ inner_loop_reset_reference_command()

void protocols::relax::FastRelax::inner_loop_reset_reference_command ( core::scoring::ScoreFunctionOP const & local_scorefxn ) const

private

References protocols::relax::RelaxProtocolBase::get_scorefxn(), core::scoring::methods::EnergyMethodOptions::method_weights(), core::scoring::ref, core::scoring::methods::EnergyMethodOptions::set_method_weights(), and protocols::relax::TR().

Referenced by apply().

◆ movemap_disables_packing_of_fixed_chi_positions()

bool protocols::relax::FastRelax::movemap_disables_packing_of_fixed_chi_positions ( ) const

inline

Get whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false.

References movemap_disables_packing_of_fixed_chi_positions_.

◆ mover_name()

std::string protocols::relax::FastRelax::mover_name ( )

static

Return the name of this mover.

Referenced by get_name(), protocols::relax::FastRelaxCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::relax::FastRelax::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Parses the FastRelaxTags.

Reimplemented from protocols::moves::Mover.

◆ provide_citation_info()

void protocols::relax::FastRelax::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name(), and protocols::relax::RelaxProtocolBase::provide_citation_info().

Referenced by protocols::trRosetta_protocols::movers::trRosettaProtocolMover::provide_citation_info().

◆ provide_xml_schema()

void protocols::relax::FastRelax::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References complex_type_generator_for_fast_relax(), and mover_name().

Referenced by protocols::relax::FastRelaxCreator::provide_xml_schema().

◆ read_script_file()

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

private

References determine_default_relax_script(), dualspace_, protocols::relax::RelaxScriptFileContents::get_file_lines(), protocols::relax::RelaxProtocolBase::get_scorefxn(), script_, set_script_from_lines(), protocols::relax::VariableSubstitutionPair::string_being_added, protocols::relax::VariableSubstitutionPair::string_being_replaced, and protocols::relax::TR().

Referenced by FastRelax(), and parse_my_tag().

◆ set_constraint_weight()

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()

Reimplemented in protocols::denovo_design::movers::FastDesign.

References core::scoring::coordinate_constraint.

Referenced by apply(), and inner_loop_ramp_repack_min_command().

◆ set_enable_design()

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 protocols::denovo_design::movers::FastDesign::FastDesign(), and parse_my_tag().

◆ set_force_nonideal()

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().

◆ set_movemap_disables_packing_of_fixed_chi_positions()

void protocols::relax::FastRelax::set_movemap_disables_packing_of_fixed_chi_positions ( bool const setting )

Set whether the MoveMap can automatically disable packing of positions where sidechain minimization is prohibited. Default false.

References movemap_disables_packing_of_fixed_chi_positions_.

Referenced by protocols::cyclic_peptide::CrosslinkerMover::pack_and_minimize_linker_and_sidechains(), and parse_my_tag().

◆ set_script_from_lines()

void protocols::relax::FastRelax::set_script_from_lines ( std::vector< std::string > const & filelines )

replace schedule by providing lines of commands explicitly

References protocols::relax::RelaxScriptCommand::command, protocols::relax::RelaxScriptCommand::nparams, protocols::relax::RelaxScriptCommand::param1, protocols::relax::RelaxScriptCommand::param2, protocols::relax::RelaxScriptCommand::param3, protocols::relax::RelaxScriptCommand::param4, protocols::relax::RelaxScriptCommand::params_vec, script_, protocols::sparta::split(), and protocols::relax::TR().

Referenced by read_script_file(), and set_script_to_batchrelax_default().

◆ set_script_to_batchrelax_default()

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

Override the stored script with the default script for batchrelax Ignores '-default_repeat' value.

References default_repeats_, script_, and set_script_from_lines().

Referenced by protocols::hybridization::HybridizeProtocol::apply(), and parse_my_tag().

◆ set_to_default()

void protocols::relax::FastRelax::set_to_default ( )

Initializes class using option system. This is called by the constructors.

References default_repeats_, delete_virtual_residues_after_FastRelax_, dna_move_, protocols::antibody::design::dualspace, dualspace_, dumpall_, enable_design_, force_nonideal_, movemap_disables_packing_of_fixed_chi_positions_, ramady_, ramady_cutoff_, ramady_force_, ramady_num_rebuild_, ramady_rms_limit_, repack_, script_max_accept_, symmetric_rmsd_, and test_cycles_.

Referenced by FastRelax().

◆ setup_local_tf()

core::pack::task::TaskFactoryOP protocols::relax::FastRelax::setup_local_tf	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP const &	local_movemap
	)

protected

helper function for apply(). Helps setup the task factory

References protocols::relax::RelaxProtocolBase::get_task_factory(), protocols::relax::RelaxProtocolBase::limit_aroma_chi2(), movemap_disables_packing_of_fixed_chi_positions_, core::pose::Pose::size(), and protocols::relax::TR().

Referenced by apply().

Friends And Related Function Documentation

◆ ::FastRelaxTests

friend class ::FastRelaxTests

friend

Member Data Documentation

◆ checkpoints_

protocols::checkpoint::CheckPointer protocols::relax::FastRelax::checkpoints_

private

Referenced by apply(), inner_loop_md_command(), inner_loop_min_command(), inner_loop_ramp_repack_min_command(), and inner_loop_repack_command().

◆ default_repeats_

core::Size protocols::relax::FastRelax::default_repeats_

private

Number of repeats if using default script.

Referenced by default_repeats(), FastRelax(), parse_my_tag(), set_script_to_batchrelax_default(), and set_to_default().

◆ delete_virtual_residues_after_FastRelax_

bool protocols::relax::FastRelax::delete_virtual_residues_after_FastRelax_

private

If true, delete virtual residues at the end of FastRelax for smooth rmsd calculation later.

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

◆ dna_move_

bool protocols::relax::FastRelax::dna_move_

private

Allow DNA to move? default is False. If True will setup DNA-specific relax settings.

Referenced by apply(), and set_to_default().

◆ dualspace_

bool protocols::relax::FastRelax::dualspace_

private

Use dualspace (Dihedral + Cartesian) Relax?

Referenced by dualspace(), get_possible_relax_script_names(), read_script_file(), and set_to_default().

◆ dumpall_

bool protocols::relax::FastRelax::dumpall_

private

Dump pdb after repack, min, or ramp_repack_min?

Referenced by inner_loop_dumpall_command(), inner_loop_min_command(), inner_loop_ramp_repack_min_command(), inner_loop_repack_command(), and set_to_default().

◆ enable_design_

bool protocols::relax::FastRelax::enable_design_

private

Enable design – if false, a RestrictToRepacking task will be added to the TaskFactory.

Referenced by determine_default_relax_script(), parse_my_tag(), set_enable_design(), and set_to_default().

◆ force_nonideal_

bool protocols::relax::FastRelax::force_nonideal_

private

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

Referenced by batch_apply(), set_force_nonideal(), and set_to_default().

◆ movemap_disables_packing_of_fixed_chi_positions_

bool protocols::relax::FastRelax::movemap_disables_packing_of_fixed_chi_positions_ = false

private

Option to have the MoveMap disable packing at positions where sidechain minimization is disabled.

Defaults to false.

Author: Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Referenced by movemap_disables_packing_of_fixed_chi_positions(), parse_my_tag(), set_movemap_disables_packing_of_fixed_chi_positions(), set_to_default(), and setup_local_tf().

◆ ramady_

bool protocols::relax::FastRelax::ramady_

private

Apply Ramady(tm) fix to residues with bad rama scores ?

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

◆ ramady_cutoff_

core::Real protocols::relax::FastRelax::ramady_cutoff_

private

Cutoff for calling a rama 'bad'.

Referenced by batch_apply(), inner_loop_ramp_repack_min_command(), and set_to_default().

◆ ramady_force_

bool protocols::relax::FastRelax::ramady_force_

private

Force ramady to be run (normally skip rate of 10%)

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

◆ ramady_num_rebuild_

core::Size protocols::relax::FastRelax::ramady_num_rebuild_

private

Number of bad ramas to fix per call to 'fix_worst_bad_ramas'.

Referenced by batch_apply(), inner_loop_ramp_repack_min_command(), and set_to_default().

◆ ramady_rms_limit_

core::Real protocols::relax::FastRelax::ramady_rms_limit_

private

Reject ramady changes perturbing structure more than this amount.

Referenced by batch_apply(), inner_loop_ramp_repack_min_command(), and set_to_default().

◆ repack_

bool protocols::relax::FastRelax::repack_

private

Allow Chi angles to move ?

Referenced by set_to_default().

◆ script_

std::vector< RelaxScriptCommand > protocols::relax::FastRelax::script_

private

Referenced by apply(), batch_apply(), read_script_file(), set_script_from_lines(), and set_script_to_batchrelax_default().

◆ script_max_accept_

core::Size protocols::relax::FastRelax::script_max_accept_

private

Quit after this many accepts ?// limits themaximum number of accepts, default is 1000000.

Referenced by apply(), and set_to_default().

◆ symmetric_rmsd_

bool protocols::relax::FastRelax::symmetric_rmsd_

private

Do a symmetric RMSD calculation rather then a monomeric one.

Referenced by apply(), cmd_accept_to_best(), inner_loop_accept_to_best_command(), and set_to_default().

◆ test_cycles_

bool protocols::relax::FastRelax::test_cycles_

private

Do only a few test_cycles ?

Referenced by apply(), and set_to_default().

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

src/protocols/relax/FastRelax.hh
src/protocols/relax/FastRelax.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

◆ FastRelax() [1/4]

FastRelax main code:

◆ FastRelax() [2/4]

◆ FastRelax() [3/4]

◆ FastRelax() [4/4]

◆ ~FastRelax()

Member Function Documentation

◆ apply()

◆ batch_apply()

◆ check_nonideal_mintype()

◆ clone()

◆ cmd_accept_to_best()

◆ complex_type_generator_for_fast_relax()

◆ default_repeats()

◆ determine_default_relax_script()

◆ do_md()

◆ do_minimize()

◆ dualspace() [1/2]

◆ dualspace() [2/2]

◆ get_name()

◆ get_possible_relax_script_names()

◆ inner_loop_accept_to_best_command()

◆ inner_loop_dumpall_command()

◆ inner_loop_md_command()

◆ inner_loop_min_command()

◆ inner_loop_ramp_repack_min_command()

◆ inner_loop_reference_command()

◆ inner_loop_repack_command()

◆ inner_loop_reset_reference_command()

◆ movemap_disables_packing_of_fixed_chi_positions()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ read_script_file()

◆ set_constraint_weight()

◆ set_enable_design()

◆ set_force_nonideal()

◆ set_movemap_disables_packing_of_fixed_chi_positions()

◆ set_script_from_lines()

◆ set_script_to_batchrelax_default()

◆ set_to_default()

◆ setup_local_tf()

Friends And Related Function Documentation

◆ ::FastRelaxTests

Member Data Documentation

◆ checkpoints_

◆ default_repeats_

◆ delete_virtual_residues_after_FastRelax_

◆ dna_move_

◆ dualspace_

◆ dumpall_

◆ enable_design_

◆ force_nonideal_

◆ movemap_disables_packing_of_fixed_chi_positions_

◆ ramady_

◆ ramady_cutoff_

◆ ramady_force_

◆ ramady_num_rebuild_

◆ ramady_rms_limit_

◆ repack_

◆ script_

◆ script_max_accept_

◆ symmetric_rmsd_

◆ test_cycles_