#include <BackrubProtocol.hh>

Inheritance diagram for protocols::backrub::BackrubProtocol:

[legend]

Public Member Functions
	BackrubProtocol ()

	BackrubProtocol (BackrubProtocol const &bp)

	~BackrubProtocol () override

void	apply (core::pose::Pose &pose) override
	Main Method. More...

void	set_pivot_residues (utility::vector1< core::Size > pivot_residues)
	Set the pivot residues for backrub. Will use contiguous residues as segments. Within these segments, backrub will occur. More...

void	set_pivot_atoms (utility::vector1< std::string > pivot_atoms)
	Set the type of atoms to use for backrub. These are atom names. Default is to only use CA as pivots. More...

void	set_movemap (core::kinematics::MoveMapCOP movemap)
	Set the movemap for the whole protocol. Uses contiguous backbone regions for backrub to set pivot residues Within these segments, backrub will occur. More...

void	set_movemap_smallmover (core::kinematics::MoveMapCOP movemap)
	Set the MoveMap that will only be used for the SmallMover. More...

void	set_taskfactory (core::pack::task::TaskFactoryCOP tf)
	Set the taskfactory used for sidechain moves. NOTE: Clones the TF. Sets C-Beta off as they are not compatable with branch angle optimization. More...

void	set_scorefunction (core::scoring::ScoreFunctionCOP scorefxn)
	Set the Scorefunction. NOTE: Clones the scorefxn. More...

void	set_backrub_mover (protocols::backrub::BackrubMoverOP backrub_mover)
	Set a pre-configured Backrub Mover. More...

void	write_database ()

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

utility::vector1< core::Size >	get_pivot_residues () const

void	set_pivots_from_residue_subset (core::select::residue_selector::ResidueSubset residue_subset)

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...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()

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

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...

Private Member Functions
void	read_cmd_line_options ()

void	set_options (utility::vector1< core::Size > pivot_residues, utility::vector1< std::string > pivot_atoms, core::kinematics::MoveMapCOP minimize_movemap, core::kinematics::MoveMapCOP movemap_smallmover, core::pack::task::operation::TaskOperationCOP packing_operation, core::Size min_atoms, core::Size max_atoms, bool initial_pack, core::Real mm_bend_weight, core::Real sm_prob, core::Real sc_prob, core::Real sc_prob_uniform, core::Real sc_prob_withinrot, core::Real mc_kt, core::Size ntrials, bool trajectory, bool trajectory_gz, core::Size trajectory_stride)
	Sets all member variables that are options that control behavior. These options can be set via parse_my_tag or command line options. More...

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

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_

core::pack::task::TaskFactoryOP	main_task_factory_

protocols::backrub::BackrubMoverOP	backrubmover_

protocols::simple_moves::SmallMoverOP	smallmover_

protocols::simple_moves::sidechain_moves::SidechainMoverOP	sidechainmover_

protocols::minimization_packing::PackRotamersMoverOP	packrotamersmover_

core::Size	ntrials_

core::kinematics::MoveMapCOP	movemap_smallmover_

core::kinematics::MoveMapCOP	minimize_movemap_

core::pack::task::operation::TaskOperationCOP	packing_operation_

utility::vector1< core::Size >	pivot_residues_

utility::vector1< std::string >	pivot_atoms_

core::Size	min_atoms_

core::Size	max_atoms_

core::Real	mm_bend_weight_

core::Real	sm_prob_

core::Real	sc_prob_

core::Real	sc_prob_uniform_

core::Real	sc_prob_withinrot_

core::Real	mc_kt_

bool	initial_pack_

bool	trajectory_

bool	trajectory_gz_

bool	recover_low_

core::Size	trajectory_stride_

protocols::moves::MoverOP	trajectory_apply_mover_

core::select::residue_selector::ResidueSelectorCOP	pivots_residue_selector_
	Residue selector to select pivot residues. More...

Additional Inherited Members
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

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...

Constructor & Destructor Documentation

◆ BackrubProtocol() [1/2]

protocols::backrub::BackrubProtocol::BackrubProtocol ( )

References read_cmd_line_options().

◆ BackrubProtocol() [2/2]

protocols::backrub::BackrubProtocol::BackrubProtocol ( BackrubProtocol const & bp )

References initial_pack_, max_atoms_, mc_kt_, min_atoms_, minimize_movemap_, mm_bend_weight_, movemap_smallmover_, ntrials_, packing_operation_, pivot_atoms_, pivot_residues_, sc_prob_, sc_prob_uniform_, sc_prob_withinrot_, set_options(), sm_prob_, trajectory_, trajectory_gz_, and trajectory_stride_.

◆ ~BackrubProtocol()

protocols::backrub::BackrubProtocol::~BackrubProtocol ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::backrub::BackrubProtocol::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::viewer::add_monte_carlo_viewer(), protocols::backrub::append_fold_tree_to_file(), protocols::minimization_packing::MinMover::apply(), backrubmover_, core::id::BB, protocols::moves::MonteCarlo::boltzmann(), core::id::CHI, protocols::jd2::current_input_tag(), protocols::jd2::current_output_name(), core::pose::Pose::dump_pdb(), protocols::canonical_sampling::TrajectoryRecorder::file_name(), finalize_setup(), core::pose::Pose::fold_tree(), initial_pack_, core::pose::Pose::is_centroid(), core::id::JUMP, protocols::moves::MonteCarlo::last_accepted_pose(), protocols::moves::MonteCarlo::lowest_score_pose(), main_task_factory_, mc_kt_, protocols::minimization_packing::MinMover::min_type(), minimize_movemap_, protocols::minimization_packing::MinMover::movemap(), ntrials_, packrotamersmover_, protocols::backrub::positions_incompatible_with_task(), protocols::backrub::read_fold_tree_from_file(), recover_low_, protocols::moves::MonteCarlo::reset(), protocols::canonical_sampling::PDBTrajectoryRecorder::reset(), core::scoring::rg, sc_prob_, protocols::minimization_packing::MinMover::score_function(), scorefxn_, protocols::moves::MonteCarlo::show_counters(), sidechainmover_, sm_prob_, smallmover_, protocols::canonical_sampling::TrajectoryRecorder::stride(), protocols::TR(), trajectory_, trajectory_apply_mover_, trajectory_gz_, trajectory_stride_, and protocols::canonical_sampling::TrajectoryRecorder::update_after_boltzmann().

◆ clone()

protocols::moves::MoverOP protocols::backrub::BackrubProtocol::clone ( ) const

overridevirtual

Return a clone of the Mover object.

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.

◆ finalize_setup()

void protocols::backrub::BackrubProtocol::finalize_setup ( core::pose::Pose & pose )

private

References core::scoring::constraints::add_constraints_from_cmdline_to_scorefxn(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_scorefxn(), backrubmover_, core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score(), core::scoring::methods::EnergyMethodOptions::bond_angle_residue_type_param_set(), core::scoring::hbonds::HBondOptions::decompose_bb_hb_into_pair_energies(), core::scoring::get_score_function(), core::scoring::methods::EnergyMethodOptions::hbond_options(), core::pose::Pose::is_centroid(), main_task_factory_, max_atoms_, min_atoms_, core::scoring::mm_bend, mm_bend_weight_, movemap_smallmover_, packing_operation_, packrotamersmover_, pivot_atoms_, pivot_residues_, pivots_residue_selector_, sc_prob_uniform_, sc_prob_withinrot_, scorefxn_, set_pivots_from_residue_subset(), sidechainmover_, sm_prob_, and smallmover_.

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::backrub::BackrubProtocol::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::backrub::BackrubProtocol::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_pivot_residues()

utility::vector1< core::Size > protocols::backrub::BackrubProtocol::get_pivot_residues ( ) const

References pivot_residues_.

◆ mover_name()

std::string protocols::backrub::BackrubProtocol::mover_name ( )

static

Referenced by get_name(), protocols::backrub::BackrubProtocolCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::backrub::BackrubProtocol::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::select::residue_selector::get_residue_selector(), core::pose::get_resnum_selector(), main_task_factory_, protocols::rosetta_scripts::parse_mover(), core::pack::task::parse_task_operations(), pivots_residue_selector_, recover_low_, set_options(), and trajectory_apply_mover_.

◆ provide_xml_schema()

void protocols::backrub::BackrubProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::backrub::BackrubProtocolCreator::provide_xml_schema().

◆ read_cmd_line_options()

void protocols::backrub::BackrubProtocol::read_cmd_line_options ( )

private

References movemap_smallmover_, and set_options().

Referenced by BackrubProtocol().

◆ set_backrub_mover()

void protocols::backrub::BackrubProtocol::set_backrub_mover ( protocols::backrub::BackrubMoverOP backrub_mover )

Set a pre-configured Backrub Mover.

References backrubmover_.

◆ set_movemap()

void protocols::backrub::BackrubProtocol::set_movemap ( core::kinematics::MoveMapCOP movemap )

Set the movemap for the whole protocol. Uses contiguous backbone regions for backrub to set pivot residues Within these segments, backrub will occur.

References protocols::backrub::get_pivot_residues_from_movemap(), set_movemap_smallmover(), and set_pivot_residues().

◆ set_movemap_smallmover()

void protocols::backrub::BackrubProtocol::set_movemap_smallmover ( core::kinematics::MoveMapCOP movemap )

Set the MoveMap that will only be used for the SmallMover.

References movemap_smallmover_.

Referenced by set_movemap(), and set_options().

◆ set_options()

void protocols::backrub::BackrubProtocol::set_options	(	utility::vector1< core::Size >	pivot_residues,
		utility::vector1< std::string >	pivot_atoms,
		core::kinematics::MoveMapCOP	minimize_movemap,
		core::kinematics::MoveMapCOP	movemap_smallmover,
		core::pack::task::operation::TaskOperationCOP	packing_operation,
		core::Size	min_atoms,
		core::Size	max_atoms,
		bool	initial_pack,
		core::Real	mm_bend_weight,
		core::Real	sm_prob,
		core::Real	sc_prob,
		core::Real	sc_prob_uniform,
		core::Real	sc_prob_withinrot,
		core::Real	mc_kt,
		core::Size	ntrials,
		bool	trajectory,
		bool	trajectory_gz,
		core::Size	trajectory_stride
	)