The loop-rebuild protocol. More...

#include <looprelax_protocols.hh>

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 ()

virtual protocols::moves::MoverOP	clone () const
	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)
	Apply the loop-rebuild protocol to the input pose. More...

virtual std::string	get_name () const
	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	~Mover ()

virtual MoverSP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

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

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

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)

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

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...

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

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...

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 protocols::filters::Filters_map	Filters_map

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

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().

Referenced by clone().

protocols::LoopRebuild::~LoopRebuild ( )

Member Function Documentation

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(), numeric::model_quality::rms_wrapper(), runtime_assert, core::pose::Pose::total_residue(), protocols::TR(), and core::conformation::Residue::xyz().

Referenced by build_random_loops().

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

virtual

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::comparative_modeling::LoopRelaxMover::apply().

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_, 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().

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::scoring::atom_pair_constraint, chainbreak, protocols::loops::Loop::choose_cutpoint(), core::pose::Pose::constraint_set(), protocols::loops::Loop::cut(), extended_loop(), fast_ccd_close_loops(), frag_libs_, get_ccd_closure_exist(), get_looprlx_cycle_ratio(), protocols::loops::idealize_loop(), linear_chainbreak, loop_model(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::max_cycles(), mc_, option, options, 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::total_residue(), protocols::TR(), and uniform().

Referenced by 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(), protocols::loops::Loops::begin(), build_loop_with_ccd_closure(), core::pose::Pose::clear(), desired_loops(), protocols::loops::Loops::end(), extend_barcode_regions_if_chain_break(), F, core::pose::Pose::fold_tree(), 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(), I, loop_model(), Loops_in_, option, protocols::loops::Loops::push_back(), remove_cutpoint_variants(), select_one_loop(), protocols::loops::Loops::size(), core::pose::Pose::total_residue(), protocols::TR(), numeric::random::uniform(), and user.

Referenced by apply().

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

virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

References LoopRebuild().

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

References protocols::init::init(), and option.

Referenced by build_random_loops().

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::pose::Pose::energies(), core::pose::Pose::fold_tree(), get_chain_break_tolerance(), get_random_loop_flag(), scorefxn_, core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by build_random_loops().

bool protocols::LoopRebuild::extended_loop ( )

Are we extending the loops before running loop-rebuild?

References extend_loops, basic::options::option, and use_default_extend_loops.

Referenced by build_loop_with_ccd_closure(), and select_one_loop().

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().

bool protocols::LoopRebuild::get_abort_on_failed_loop ( )

inline

References abort_on_failed_loop_.

Referenced by build_random_loops().

int protocols::LoopRebuild::get_allowed_failure_before_extend ( )

inline

References allowed_failure_before_extend_.

Referenced by build_random_loops().

int protocols::LoopRebuild::get_allowed_failure_before_stop ( )

inline

References allowed_failure_before_stop_.

Referenced by build_random_loops().

bool protocols::LoopRebuild::get_ccd_closure_exist ( )

References protocols::init::init(), and option.

Referenced by build_loop_with_ccd_closure().

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 protocols::init::init(), and option.

Referenced by extend_barcode_regions_if_chain_break().

bool protocols::LoopRebuild::get_combine_if_fail_exist ( )

References protocols::init::init(), and option.

Referenced by build_random_loops().

bool protocols::LoopRebuild::get_desired_loops_exist ( )

References protocols::init::init(), and option.

Referenced by build_random_loops().

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

References protocols::init::init(), and option.

Referenced by select_one_loop().

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

private

References protocols::init::init(), and option.

Referenced by build_loop_with_ccd_closure().

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().

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

virtual

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

Implements protocols::moves::Mover.

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().

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

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

References protocols::init::init(), and option.

Referenced by acceptable_rmsd_change().

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

private

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

References protocols::init::init(), and option.

bool protocols::LoopRebuild::get_success ( )

inline

Were loops successfully built?

References success.

bool protocols::LoopRebuild::loop_model ( )

References protocols::init::init(), and option.

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

private

Select a loop at random from the input list.

References extended_loop(), get_loop_combine_rate(), get_random_loop_flag(), loop_model(), Loops_in_, protocols::loops::Loops::size(), protocols::loops::start, protocols::loops::stop, protocols::TR(), and numeric::random::uniform().

Referenced by build_random_loops().

void protocols::LoopRebuild::set_abort_on_failed_loop ( bool setting = true )

inline

References abort_on_failed_loop_.

void protocols::LoopRebuild::set_allowed_failure_before_extend ( int setting )

inline

References allowed_failure_before_extend_.

void protocols::LoopRebuild::set_allowed_failure_before_stop ( int setting )

inline

References allowed_failure_before_stop_.

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

setting the mc object

sets mc object

References m_Temperature_, mc_, and scorefxn_.

Referenced by apply(), and get_mc().

void protocols::LoopRebuild::set_default_settings ( )

sets all the standard settings for LoopBuild

References abort_on_failed_loop_, allowed_failure_before_extend_, allowed_failure_before_stop_, mc_created, basic::options::option, random_loop_flag_, and use_default_extend_loops.

Referenced by LoopRebuild().

void protocols::LoopRebuild::set_extended_loop ( bool val )

Specify whether the protocol should extend the loops before running loop-rebuild.

References extend_loops, and use_default_extend_loops.

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

private

References BB, core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), and core::kinematics::MoveMap::set_jump().

Referenced by build_loop_with_ccd_closure().

void protocols::LoopRebuild::set_random_loop_flag ( bool setting = true )

inline

References random_loop_flag_.

bool protocols::LoopRebuild::shorten_long_terminal_loop ( )

private

References protocols::init::init(), and option.

Referenced by barcode_extend_stems().

Member Data Documentation

bool protocols::LoopRebuild::abort_on_failed_loop_

private

Referenced by get_abort_on_failed_loop(), set_abort_on_failed_loop(), and set_default_settings().

int protocols::LoopRebuild::allowed_failure_before_extend_

private

Referenced by get_allowed_failure_before_extend(), set_allowed_failure_before_extend(), and set_default_settings().

int protocols::LoopRebuild::allowed_failure_before_stop

int protocols::LoopRebuild::allowed_failure_before_stop_

private

Referenced by get_allowed_failure_before_stop(), set_allowed_failure_before_stop(), and set_default_settings().

bool protocols::LoopRebuild::extend_loops

private

Referenced by extended_loop(), and set_extended_loop().

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

private

Referenced by build_loop_with_ccd_closure(), and LoopRebuild().

protocols::loops::Loops protocols::LoopRebuild::Loops_in_

private

Referenced by apply(), protocols::LoopRefine::apply(), barcode_extend_stems(), build_random_loops(), and select_one_loop().

core::Real protocols::LoopRebuild::m_Temperature_

private

Referenced by set_default_mc().

protocols::moves::MonteCarloOP protocols::LoopRebuild::mc_

private

Referenced by build_loop_with_ccd_closure(), get_mc(), and set_default_mc().

bool protocols::LoopRebuild::mc_created

private

Referenced by apply(), get_mc(), and set_default_settings().

core::kinematics::MoveMapOP protocols::LoopRebuild::movemap_

private

bool protocols::LoopRebuild::only_remove_missing_density_flag_

private

core::pose::PoseOP protocols::LoopRebuild::pose_

private

bool protocols::LoopRebuild::random_loop_flag_

private

Referenced by get_random_loop_flag(), set_default_settings(), and set_random_loop_flag().

core::scoring::ScoreFunctionOP protocols::LoopRebuild::scorefxn_

private

Referenced by build_loop_with_ccd_closure(), extend_barcode_regions_if_chain_break(), and set_default_mc().

bool protocols::LoopRebuild::success

private

Referenced by apply(), and get_success().

bool protocols::LoopRebuild::use_default_extend_loops

private

Referenced by extended_loop(), set_default_settings(), and set_extended_loop().

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

src/protocols/loops/looprelax_protocols.hh
src/protocols/loops/looprelax_protocols.cc

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_

bool	only_remove_missing_density_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

Public Member Functions

Public Attributes

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation