The loop-rebuild protocol. More...

#include <looprelax_protocols.hh>

Inheritance diagram for protocols::LoopRebuild:

[legend]

Public Member Functions
	LoopRebuild (core::scoring::ScoreFunctionOP scorefxn, protocols::loops::Loops Loops_in)
	Construct te protocol object given a score function, list of loop segments to rebuild, and the fragment library to use. The skip rate of each loop is ignored (the decision of which loops to rebuild should be made outside the protocol). More...

	~LoopRebuild () override

protocols::moves::MoverOP	clone () const override
	Clone this object. More...

void	set_default_settings ()
	sets all the standard settings for LoopBuild More...

protocols::moves::MonteCarloOP	get_mc (core::pose::Pose &pose)
	Get the protocol's Monte Carlo object. More...

void	set_default_mc (core::pose::Pose &pose)
	setting the mc object More...

void	apply (core::pose::Pose &pose) override
	Apply the loop-rebuild protocol to the input pose. More...

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

bool	extended_loop ()
	Are we extending the loops before running loop-rebuild? More...

void	set_extended_loop (bool val)
	Specify whether the protocol should extend the loops before running loop-rebuild. More...

bool	get_success ()
	Were loops successfully built? More...

bool	get_random_loop_flag ()

void	set_random_loop_flag (bool setting=true)

int	get_allowed_failure_before_extend ()

void	set_allowed_failure_before_extend (int setting)

int	get_allowed_failure_before_stop ()

void	set_allowed_failure_before_stop (int setting)

bool	get_abort_on_failed_loop ()

void	set_abort_on_failed_loop (bool setting=true)

bool	loop_model ()

bool	get_ccd_closure_exist ()

bool	get_desired_loops_exist ()

core::Size	desired_loops ()

core::Real	get_loop_combine_rate ()

bool	get_combine_if_fail_exist ()

core::Real	get_rmsd_tolerance ()
	Gets the RMSd tolerence, the most a loop may move during reconstruction. More...

core::Real	get_chain_break_tolerance ()
	Gets the chainbreak tolerence, the largest the chainbreak score may be to accept a loop conformation. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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

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

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...

Public Attributes
int	allowed_failure_before_stop

Private Member Functions
bool	build_random_loops (core::pose::Pose &pose)
	Rebuild all loops in the pose, chosen in a random order. More...

void	set_looprlx_allow_move_map (int const &loop_begin, int const &loop_end, core::kinematics::MoveMap &mm)

core::Real	get_score_filter_cutoff ()
	Get the cutoff for score filtering loop conformations. CURRENTLY UNUSED IN THE PROTOCOL. More...

bool	select_one_loop (int nres, int &selected_loop, std::vector< int > &folded_loops, std::vector< int > &inter_res, int &loop_begin, int &loop_end, int &cutpoint, bool &extend_this_loop, bool &are_loops_combined, int &combine_interval, int &loop_counter)
	Select a loop at random from the input list. More...

void	barcode_extend_stems (core::pose::Pose &pose, int &barcst_extend_begin, int &barcst_extend_end, int &loop_begin, int &loop_end, int const &old_loop_begin, int const &old_loop_end, int const &nres, int const &selected_loop, int const &total_combine, int const &backward_combine)
	Extend the loop stems. More...

void	extend_barcode_regions_if_chain_break (core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int &n_chain_break_fail, bool &is_chain_break, int &barcst_extend_begin, int &barcst_extend_end)
	If chainbreak score is greater than the tolerance, extend the loop. More...

bool	shorten_long_terminal_loop ()

bool	acceptable_rmsd_change (core::pose::Pose &pose1, core::pose::Pose &pose2)
	Is the RMS change between these two poses below the acceptible threshold? More...

core::Real	get_looprlx_cycle_ratio ()

void	build_loop_with_ccd_closure (core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int &cutpoint, bool const &extend_this_loop)
	frag insertion + ccd close + minimize More...

void	fast_ccd_close_loops (core::pose::Pose &pose, int const &loop_begin, int const &loop_end, int const &cutpoint, core::kinematics::MoveMap &mm)
	Apply ccd moves to close the specified loop. More...

Private Attributes
core::pose::PoseOP	pose_

core::scoring::ScoreFunctionOP	scorefxn_

core::kinematics::MoveMapOP	movemap_

protocols::moves::MonteCarloOP	mc_

protocols::loops::Loops	Loops_in_

std::vector< core::fragment::FragSetOP >	frag_libs_

bool	extend_loops

bool	use_default_extend_loops

bool	random_loop_flag_

int	allowed_failure_before_extend_

int	allowed_failure_before_stop_

bool	abort_on_failed_loop_

core::Real	m_Temperature_

bool	mc_created

bool	success

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

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 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...

Detailed Description

The loop-rebuild protocol.

Constructor & Destructor Documentation

◆ LoopRebuild()

protocols::LoopRebuild::LoopRebuild	(	core::scoring::ScoreFunctionOP	scorefxn,
		protocols::loops::Loops	Loops_in
	)

Construct te protocol object given a score function, list of loop segments to rebuild, and the fragment library to use. The skip rate of each loop is ignored (the decision of which loops to rebuild should be made outside the protocol).

References frag_libs_, protocols::loops::read_loop_fragments(), and set_default_settings().

◆ ~LoopRebuild()

protocols::LoopRebuild::~LoopRebuild ( )

overridedefault

Member Function Documentation

◆ acceptable_rmsd_change()

bool protocols::LoopRebuild::acceptable_rmsd_change	(	core::pose::Pose &	pose1,
		core::pose::Pose &	pose2
	)

private

Is the RMS change between these two poses below the acceptible threshold?

References get_rmsd_tolerance(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by build_random_loops().

◆ apply()

void protocols::LoopRebuild::apply ( core::pose::Pose & pose )

overridevirtual

Apply the loop-rebuild protocol to the input pose.

Apply the loop rebuilding protocol to a pose. The loops to be rebuilt and fragments are defined upon object construction.

Implements protocols::moves::Mover.

References build_random_loops(), Loops_in_, mc_created, set_default_mc(), protocols::loops::set_secstruct_from_psipred_ss2(), protocols::loops::Loops::size(), success, protocols::TR(), and protocols::loops::Loops::verify_against().

Referenced by protocols::relax::loop::LoopRelaxMover::apply().

◆ barcode_extend_stems()

void protocols::LoopRebuild::barcode_extend_stems	(	core::pose::Pose &	pose,
		int &	barcst_extend_begin,
		int &	barcst_extend_end,
		int &	loop_begin,
		int &	loop_end,
		int const &	old_loop_begin,
		int const &	old_loop_end,
		int const &	nres,
		int const &	selected_loop,
		int const &	total_combine,
		int const &	backward_combine
	)

private

Extend the loop stems.

References loop_model(), Loops_in_, protocols::mean_field::min(), core::conformation::Residue::name3(), core::pose::Pose::residue(), shorten_long_terminal_loop(), protocols::loops::Loops::size(), protocols::loops::start, protocols::loops::stop, and protocols::TR().

Referenced by build_random_loops().

◆ build_loop_with_ccd_closure()

void protocols::LoopRebuild::build_loop_with_ccd_closure	(	core::pose::Pose &	pose,
		int const &	loop_begin,
		int const &	loop_end,
		int &	cutpoint,
		bool const &	extend_this_loop
	)

private

frag insertion + ccd close + minimize

Rebuild a loop via fragment insertion + ccd closure + minimization

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::chemical::aa_vrt, core::pose::add_variant_type_to_pose_residue(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), core::chemical::ResidueType::atom_index(), core::conformation::Residue::atom_name(), core::scoring::atom_pair_constraint, core::scoring::chainbreak, protocols::loops::Loop::choose_cutpoint(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Conformation::declare_chemical_bond(), extended_loop(), fast_ccd_close_loops(), frag_libs_, get_ccd_closure_exist(), get_looprlx_cycle_ratio(), protocols::loops::idealize_loop(), core::scoring::linear_chainbreak, loop_model(), core::conformation::Residue::lower_connect_atom(), protocols::mean_field::max(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_cycles(), mc_, protocols::mean_field::min(), protocols::rigid::random, core::pose::Pose::residue(), core::pose::Pose::residue_type(), scorefxn_, protocols::loops::set_extended_torsions(), set_looprlx_allow_move_map(), protocols::forge::methods::set_single_loop_fold_tree(), core::pose::Pose::size(), protocols::TR(), and core::conformation::Residue::upper_connect_atom().

Referenced by build_random_loops().

◆ build_random_loops()

bool protocols::LoopRebuild::build_random_loops ( core::pose::Pose & pose )

private

Rebuild all loops in the pose, chosen in a random order.

Rebuild all the loops in the pose, one at a time, choosing each in random order.

References acceptable_rmsd_change(), barcode_extend_stems(), build_loop_with_ccd_closure(), core::pose::Pose::clear(), desired_loops(), extend_barcode_regions_if_chain_break(), core::chemical::element::F, core::pose::Pose::fold_tree(), core::scoring::free_res, get_abort_on_failed_loop(), get_allowed_failure_before_extend(), get_allowed_failure_before_stop(), get_combine_if_fail_exist(), get_desired_loops_exist(), get_random_loop_flag(), core::chemical::element::I, loop_model(), Loops_in_, protocols::mean_field::min(), protocols::loops::Loops::push_back(), core::util::remove_cutpoint_variants(), select_one_loop(), core::pose::Pose::size(), protocols::loops::Loops::size(), and protocols::TR().

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::LoopRebuild::clone ( ) const

overridevirtual

Clone this object.

Reimplemented from protocols::moves::Mover.

◆ desired_loops()

core::Size protocols::LoopRebuild::desired_loops ( )

References core::init::init().

Referenced by build_random_loops().

◆ extend_barcode_regions_if_chain_break()

void protocols::LoopRebuild::extend_barcode_regions_if_chain_break	(	core::pose::Pose &	pose,
		int const &	loop_begin,
		int const &	loop_end,
		int &	n_chain_break_fail,
		bool &	is_chain_break,
		int &	barcst_extend_begin,
		int &	barcst_extend_end
	)

private

If chainbreak score is greater than the tolerance, extend the loop.

References core::scoring::chainbreak, core::pose::Pose::energies(), core::pose::Pose::fold_tree(), get_chain_break_tolerance(), get_random_loop_flag(), core::scoring::linear_chainbreak, protocols::mean_field::max(), scorefxn_, core::pose::Pose::size(), core::scoring::Energies::total_energies(), and protocols::TR().

Referenced by build_random_loops().

◆ extended_loop()

bool protocols::LoopRebuild::extended_loop ( )

Are we extending the loops before running loop-rebuild?

References extend_loops, and use_default_extend_loops.

Referenced by build_loop_with_ccd_closure(), and select_one_loop().

◆ fast_ccd_close_loops()

void protocols::LoopRebuild::fast_ccd_close_loops	(	core::pose::Pose &	pose,
		int const &	loop_begin,
		int const &	loop_end,
		int const &	cutpoint,
		core::kinematics::MoveMap &	mm
	)

private

Apply ccd moves to close the specified loop.

CCD close the loop [loop_begin,loop_end]. Wraps protocols::loops::loop_closure::ccd::CCDLoopClosureMover.apply() using most of its default options. rama scores are not checked, however, and the secondary structure is "fixed" afterward.

Remarks: This is a misnomer; it actually closes a single loop only. ~Labonte

References protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::check_rama_scores(), core::pose::Pose::conformation(), core::conformation::Conformation::secstruct(), and core::pose::Pose::set_secstruct().

Referenced by build_loop_with_ccd_closure().

◆ get_abort_on_failed_loop()

bool protocols::LoopRebuild::get_abort_on_failed_loop ( )

inline

References abort_on_failed_loop_.

Referenced by build_random_loops().

◆ get_allowed_failure_before_extend()

int protocols::LoopRebuild::get_allowed_failure_before_extend ( )

inline

References allowed_failure_before_extend_.

Referenced by build_random_loops().

◆ get_allowed_failure_before_stop()

int protocols::LoopRebuild::get_allowed_failure_before_stop ( )

inline

References allowed_failure_before_stop_.

Referenced by build_random_loops().

◆ get_ccd_closure_exist()

bool protocols::LoopRebuild::get_ccd_closure_exist ( )

References core::init::init().

Referenced by build_loop_with_ccd_closure().

◆ get_chain_break_tolerance()

core::Real protocols::LoopRebuild::get_chain_break_tolerance ( )

Gets the chainbreak tolerence, the largest the chainbreak score may be to accept a loop conformation.

References core::init::init().

Referenced by extend_barcode_regions_if_chain_break().

◆ get_combine_if_fail_exist()

bool protocols::LoopRebuild::get_combine_if_fail_exist ( )

References core::init::init().

Referenced by build_random_loops().

◆ get_desired_loops_exist()

bool protocols::LoopRebuild::get_desired_loops_exist ( )

References core::init::init().

Referenced by build_random_loops().

◆ get_loop_combine_rate()

core::Real protocols::LoopRebuild::get_loop_combine_rate ( )

References core::init::init().

Referenced by select_one_loop().

◆ get_looprlx_cycle_ratio()

core::Real protocols::LoopRebuild::get_looprlx_cycle_ratio ( )

private

References core::init::init().

Referenced by build_loop_with_ccd_closure().

◆ get_mc()

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

Get the protocol's Monte Carlo object.

returns mc object

References mc_, mc_created, and set_default_mc().

◆ get_name()

std::string protocols::LoopRebuild::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ get_random_loop_flag()

bool protocols::LoopRebuild::get_random_loop_flag ( )

inline

References random_loop_flag_.

Referenced by build_random_loops(), extend_barcode_regions_if_chain_break(), and select_one_loop().

◆ get_rmsd_tolerance()

core::Real protocols::LoopRebuild::get_rmsd_tolerance ( )

Gets the RMSd tolerence, the most a loop may move during reconstruction.

References core::init::init().

Referenced by acceptable_rmsd_change().

◆ get_score_filter_cutoff()

core::Real protocols::LoopRebuild::get_score_filter_cutoff ( )

private

Get the cutoff for score filtering loop conformations. CURRENTLY UNUSED IN THE PROTOCOL.

References core::init::init().

◆ get_success()

bool protocols::LoopRebuild::get_success ( )

inline

Were loops successfully built?

References success.

◆ loop_model()

bool protocols::LoopRebuild::loop_model ( )

References core::init::init().

Referenced by barcode_extend_stems(), build_loop_with_ccd_closure(), build_random_loops(), and select_one_loop().

◆ select_one_loop()

bool protocols::LoopRebuild::select_one_loop	(	int	nres,
		int &	selected_loop,
		std::vector< int > &	folded_loops,
		std::vector< int > &	inter_res,
		int &	loop_begin,
		int &	loop_end,
		int &	cutpoint,
		bool &	extend_this_loop,
		bool &	are_loops_combined,
		int &	combine_interval,
		int &	loop_counter
	)