Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++. More...

#include <RemodelLoopMover.hh>

Inheritance diagram for protocols::forge::remodel::RemodelLoopMover:

Collaboration diagram for protocols::forge::remodel::RemodelLoopMover:

Public Types
typedef core::Real	Real

typedef core::Size	Size

typedef std::string	String

typedef core::kinematics::MoveMap	MoveMap

typedef core::fragment::FragSetCOP	FragSetCOP

typedef core::fragment::FragSetOP	FragSetOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseOP	PoseOP

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::simple_moves::ClassicFragmentMoverOP	ClassicFragmentMoverOP

typedef protocols::simple_moves::FragmentMoverOP	FragmentMoverOP

typedef protocols::loops::Loop	Loop

typedef protocols::loops::Loops	Loops

typedef protocols::moves::MonteCarlo	MonteCarlo

typedef protocols::moves::MoverOP	MoverOP

typedef utility::vector1 < FragSetOP >	FragSetOPs

typedef utility::vector1 < FragmentMoverOP >	FragmentMoverOPs

typedef utility::tag::TagPtr	TagPtr

typedef protocols::filters::Filters_map	Filters_map

typedef protocols::moves::DataMap	DataMap

typedef protocols::moves::Movers_map	Movers_map

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Public Member Functions
	RemodelLoopMover ()
	default constructor More...

	RemodelLoopMover (loops::LoopsOP const loops)
	loops constructor More...

	RemodelLoopMover (RemodelLoopMover const &rval)
	copy constructor More...

virtual	~RemodelLoopMover ()
	default destructor More...

void	set_param_from_options ()
	set parameters from options More...

virtual MoverOP	clone () const
	clone this object More...

virtual MoverOP	fresh_instance () const
	create this type of object More...

ScoreFunction const &	scorefunction () const
	the ScoreFunction to use during modeling; More...

MoveMap const &	false_movemap () const
	get the false movemap More...

Real	max_linear_chainbreak () const
	if linear chainbreak is <= this value, loop is considered closed (default 0.07) More...

bool	randomize_loops () const
	randomize loops prior to running main protocol? (default true) More...

Size	allowed_closure_attempts () const
	the allowed number of overall closure attempts before apply() exits (default 3) More...

Size	loophash_cycles () const
	the number of loophash closure cycles to perform (default 8) More...

Size	simultaneous_cycles () const
	the number of simultaneous closure cycles to perform (default 2) More...

Size	independent_cycles () const
	the number of independent closure cycles to perform (default 8) More...

Size	boost_closure_cycles () const
	the maximum number of possible lockdown closure cycles to perform (default 30) More...

Size	total_standard_cycles () const
	the total number of "standard" (equal to simul + independent) to perform More...

Real	temperature () const
	temperature for mc ( default 2.0 ) More...

void	repeat_generation_with_additional_residue (Pose &pose, Pose &repeat_pose)

void	repeat_generation (Pose &pose, Pose &repeat_pose)

void	repeat_sync (core::pose::Pose &repeat_pose, core::Size repeat_number)

void	repeat_propagation (Pose &pose, Pose &repeat_pose, Size repeat_number)

void	scorefunction (ScoreFunction const &sfx)
	the ScoreFunction to use during modeling More...

void	false_movemap (MoveMap const &movemap)
	set the false movemap to use More...

void	max_linear_chainbreak (Real const val)
	if linear chainbreak is <= this value, loop is considered closed More...

void	randomize_loops (bool const flag)
	randomize loops prior to running main protocol? More...

void	allowed_closure_attempts (Size const attempts)
	the allowed number of overall closure attempts before apply() exits More...

void	loophash_cycles (Size const cycles)
	the number of loophash closure cycles to perform More...

void	simultaneous_cycles (Size const cycles)
	the number of simultaneous closure cycles to perform More...

void	independent_cycles (Size const cycles)
	the number of independent closure cycles to perform More...

void	set_user_provided_movers (utility::vector1< moves::MoverOP > const &movers)

void	user_provided_movers_apply_cycle (Size const cycle)

void	boost_closure_cycles (Size const cycles)
	the maximum number of possible lockdown closure cycles to perform More...

void	temperature (Real const temp)
	temperature for mc More...

void	set_repeat_tail_length (Size const length)

void	set_keep_input_foldtree (bool const setting)

loops::LoopsOP const	loops () const
	the loops to model More...

void	loops (loops::LoopsOP const loops)
	set the loops to model More...

void	add_loop (Loop const loop)
	add a loop to model More...

void	add_fragments (FragSetCOP fragset)
	add a fragment set More...

void	clear_fragments ()
	clear all fragment sets More...

virtual void	apply (Pose &pose)
	apply defined moves to given Pose More...

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

void	randomize_stage (Pose &pose)
	randomize loops More...

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

virtual	~Mover ()

virtual MoverSP	create ()

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

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)

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
	this function informs 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
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

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

jobdist::BasicJobCOP	get_current_job () const

Static Public Member Functions
static void	register_options ()
	options More...

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions
void	insert_random_smallestmer_per_loop (Pose &pose, bool const only_broken_loops=true)
	find the smallest fragment size and insert a single such smallmer into each loop; for breaking up trapped trajectories More...

void	loophash_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
	independent stage: single loop movement prior to MC accept/reject More...

void	simultaneous_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
	simultaneous stage: multiple loop movement prior to MC accept/reject More...

void	independent_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
	independent stage: single loop movement prior to MC accept/reject More...

void	boost_closure_stage (Pose &pose, MonteCarlo &mc, Real const cbreak_increment)
	lockdown stage: close loops within some threshold w/ smallest-mer (typically 1-mer) + ccd_move only More...

loops::LoopsOP	determine_loops_to_model (Pose &pose)
	determine which loops need modeling wrt to given Pose More...

bool	check_closure_criteria (Pose &pose, bool const show_in_tracer=false)
	check all loops for closure criteria More...

FragmentMoverOPs	create_fragment_movers (MoveMap const &movemap, Size const largest_frag_size=0)
	return fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set More...

void	create_fragment_movers (MoveMap const &movemap, FragmentMoverOPs &frag_movers, Size const largest_frag_size=0)
	append fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set More...

FragmentMoverOPs	create_per_loop_fragment_movers (loops::LoopsOP const loops, Size const largest_frag_size=0)
	create per-loop fragment movers: 1 fragment mover for each loop (uses movemaps to lock down non-loop residues) More...

void	enforce_false_movemap (MoveMap &movemap)
	enforce settings in the false movemap More...

void	mark_loops_moveable (loops::LoopsOP const loops, MoveMap &movemap, bool const allow_omega)
	mark bb/chi torsions of multiple loops moveable in a movemap More...

void	mark_loop_moveable (Loop const &loop, MoveMap &movemap, bool const allow_omega)
	mark bb/chi torsion of a single loop moveable in movemap More...

Size	count_moveable_residues (MoveMap const &movemap, Size const left, Size const right)
	count number of residues with moveable backbone torsions in the given range [left, right] 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...

Private Types
typedef protocols::moves::Mover	Super

Private Member Functions
RemodelLoopMover &	operator= (RemodelLoopMover const &rval)
	copy assignment More...

void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &, Movers_map const &, Pose const &pose)
	parse xml More...

Private Attributes
ScoreFunctionOP	sfx_
	the score function to use More...

MoveMap	false_movemap_
	the false movemap to use More...

loops::LoopsOP	loops_
	list of loops to model More...

Real	max_linear_chainbreak_
	if linear chainbreak is <= this value, loop is considered closed (default 0.07) More...

bool	randomize_loops_
	randomize loops prior to running main protocol? (default true) More...

Size	repeat_tail_length_

Size	allowed_closure_attempts_
	the allowed number of overall closure attempts before apply() exits (default 3) More...

Size	loophash_cycles_
	the number of loophash closure cycles to perform (default 8) More...

Size	simultaneous_cycles_
	the number of simultaneous closure cycles to perform (default 2) More...

Size	independent_cycles_
	the number of independent closure cycles to perform (default 8) More...

utility::vector1< moves::MoverOP >	user_provided_movers_
	collection of movers that mess with the pose every n fragment/ccd steps during inneriterations of simultaneous, and independent stage, where n is determined by the variable below gives the user a chance to add their own flavor to the fragment sampling done by this protocol More...

Size	user_provided_movers_apply_cycle_
	determines how often the above movers get called during fragment insertion/ccd steps (default 3 ) More...

Size	boost_closure_cycles_
	the maximum number of possible boost closure cycles to perform (default 30) More...

Real	temperature_
	temperature for mc More...

FragSetOPs	fragsets_
	fragment sets to use More...

Pose	repeat_pose_
	local copy of repeat pose More...

bool	keep_input_foldtree_
	whether to keep the FoldTree untouched, i.e. trust the user to supply a decent FoldTree More...

Detailed Description

Loop modeling protocol based on routines from Remodel and EpiGraft packages in Rosetta++.

Definition at line 49 of file RemodelLoopMover.hh.

Member Typedef Documentation

typedef protocols::simple_moves::ClassicFragmentMoverOP protocols::forge::remodel::RemodelLoopMover::ClassicFragmentMoverOP

Definition at line 73 of file RemodelLoopMover.hh.

typedef protocols::moves::DataMap protocols::forge::remodel::RemodelLoopMover::DataMap

Definition at line 85 of file RemodelLoopMover.hh.

typedef protocols::filters::Filters_map protocols::forge::remodel::RemodelLoopMover::Filters_map

Definition at line 84 of file RemodelLoopMover.hh.

typedef protocols::simple_moves::FragmentMoverOP protocols::forge::remodel::RemodelLoopMover::FragmentMoverOP

Definition at line 74 of file RemodelLoopMover.hh.

typedef utility::vector1< FragmentMoverOP > protocols::forge::remodel::RemodelLoopMover::FragmentMoverOPs

Definition at line 81 of file RemodelLoopMover.hh.

typedef core::fragment::FragSetCOP protocols::forge::remodel::RemodelLoopMover::FragSetCOP

Definition at line 66 of file RemodelLoopMover.hh.

typedef core::fragment::FragSetOP protocols::forge::remodel::RemodelLoopMover::FragSetOP

Definition at line 67 of file RemodelLoopMover.hh.

typedef utility::vector1< FragSetOP > protocols::forge::remodel::RemodelLoopMover::FragSetOPs

Definition at line 80 of file RemodelLoopMover.hh.

typedef protocols::loops::Loop protocols::forge::remodel::RemodelLoopMover::Loop

Definition at line 75 of file RemodelLoopMover.hh.

typedef protocols::loops::Loops protocols::forge::remodel::RemodelLoopMover::Loops

Definition at line 76 of file RemodelLoopMover.hh.

typedef protocols::moves::MonteCarlo protocols::forge::remodel::RemodelLoopMover::MonteCarlo

Definition at line 77 of file RemodelLoopMover.hh.

typedef core::kinematics::MoveMap protocols::forge::remodel::RemodelLoopMover::MoveMap

Definition at line 65 of file RemodelLoopMover.hh.

typedef protocols::moves::MoverOP protocols::forge::remodel::RemodelLoopMover::MoverOP

Definition at line 78 of file RemodelLoopMover.hh.

typedef protocols::moves::Movers_map protocols::forge::remodel::RemodelLoopMover::Movers_map

Definition at line 86 of file RemodelLoopMover.hh.

typedef core::pose::Pose protocols::forge::remodel::RemodelLoopMover::Pose

Definition at line 68 of file RemodelLoopMover.hh.

typedef core::pose::PoseOP protocols::forge::remodel::RemodelLoopMover::PoseOP

Definition at line 69 of file RemodelLoopMover.hh.

typedef core::Real protocols::forge::remodel::RemodelLoopMover::Real

Definition at line 61 of file RemodelLoopMover.hh.

typedef core::scoring::ScoreFunction protocols::forge::remodel::RemodelLoopMover::ScoreFunction

Definition at line 70 of file RemodelLoopMover.hh.

typedef core::scoring::ScoreFunctionOP protocols::forge::remodel::RemodelLoopMover::ScoreFunctionOP

Definition at line 71 of file RemodelLoopMover.hh.

typedef core::Size protocols::forge::remodel::RemodelLoopMover::Size

Definition at line 62 of file RemodelLoopMover.hh.

typedef std::string protocols::forge::remodel::RemodelLoopMover::String

Definition at line 63 of file RemodelLoopMover.hh.

typedef protocols::moves::Mover protocols::forge::remodel::RemodelLoopMover::Super

private

Definition at line 55 of file RemodelLoopMover.hh.

typedef utility::tag::TagPtr protocols::forge::remodel::RemodelLoopMover::TagPtr

Definition at line 83 of file RemodelLoopMover.hh.

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover ( )

default constructor

Definition at line 123 of file RemodelLoopMover.cc.

References set_param_from_options().

Referenced by clone(), and fresh_instance().

protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover ( loops::LoopsOP const loops)

loops constructor

Definition at line 142 of file RemodelLoopMover.cc.

References set_param_from_options().

protocols::forge::remodel::RemodelLoopMover::RemodelLoopMover ( RemodelLoopMover const & rval)

copy constructor

Definition at line 162 of file RemodelLoopMover.cc.

protocols::forge::remodel::RemodelLoopMover::~RemodelLoopMover ( )

virtual

default destructor

Definition at line 184 of file RemodelLoopMover.cc.

Member Function Documentation

void protocols::forge::remodel::RemodelLoopMover::add_fragments ( FragSetCOP fragset)

add a fragment set

Definition at line 252 of file RemodelLoopMover.cc.

References fragsets_.

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply(), and parse_my_tag().

void protocols::forge::remodel::RemodelLoopMover::add_loop ( Loop const loop)

inline

add a loop to model

Definition at line 341 of file RemodelLoopMover.hh.

References loops_.

Size protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts ( ) const

inline

the allowed number of overall closure attempts before apply() exits (default 3)

Definition at line 172 of file RemodelLoopMover.hh.

References allowed_closure_attempts_.

void protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts ( Size const attempts)

inline

the allowed number of overall closure attempts before apply() exits

Definition at line 268 of file RemodelLoopMover.hh.

References allowed_closure_attempts_.

void protocols::forge::remodel::RemodelLoopMover::apply ( Pose & pose)

virtual

apply defined moves to given Pose

Remarks: Sets protocols::moves::MS_SUCCESS upon successful closure of all loops, otherwise sets protocols::moves::FAIL_RETRY.

Implements protocols::moves::Mover.

Definition at line 940 of file RemodelLoopMover.cc.

References allowed_closure_attempts_, core::scoring::atom_pair_constraint, boost_closure_cycles(), boost_closure_stage(), check_closure_criteria(), core::pose::Pose::energies(), protocols::moves::FAIL_RETRY, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_pose(), independent_stage(), insert_random_smallestmer_per_loop(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, loophash_stage(), protocols::moves::MS_SUCCESS, core::pose::Pose::phi(), randomize_loops_, randomize_stage(), repeat_generation_with_additional_residue(), repeat_pose_, repeat_propagation(), protocols::moves::MonteCarlo::reset(), core::kinematics::FoldTree::root(), protocols::moves::MonteCarlo::score_function(), core::pose::symmetry::sealed_symmetric_fold_tree(), protocols::moves::Mover::set_last_move_status(), sfx_, simultaneous_stage(), temperature_, core::scoring::Energies::total_energy(), total_standard_cycles(), and protocols::forge::remodel::TR().

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply().

Size protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles ( ) const

inline

the maximum number of possible lockdown closure cycles to perform (default 30)

Definition at line 199 of file RemodelLoopMover.hh.

References boost_closure_cycles_.

Referenced by apply(), and boost_closure_stage().

void protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles ( Size const cycles)

inline

the maximum number of possible lockdown closure cycles to perform

Definition at line 301 of file RemodelLoopMover.hh.

References boost_closure_cycles_.

void protocols::forge::remodel::RemodelLoopMover::boost_closure_stage	(	Pose &	pose,
		MonteCarlo &	mc,
		Real const	cbreak_increment
	)

protected

lockdown stage: close loops within some threshold w/ smallest-mer (typically 1-mer) + ccd_move only

lock down stage: close loops within some threshold w/ smallest-mer (typically 1-mer) + ccd_move only

This stage differs from simultaneous_stage() and independent_stage() in that once a loop is closed, it breaks out of the closure cycle and goes to the next one. The rationale is that once we hit the boost_closure_stage() we are desperate to close the loop, so we sacrifice diversity and instead just seek a closed solution.

Definition at line 2306 of file RemodelLoopMover.cc.

References core::util::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), boost_closure_cycles(), protocols::loops::loop_closure::ccd::ccd_moves(), check_closure_criteria(), count_moveable_residues(), create_fragment_movers(), protocols::loops::Loop::cut(), determine_loops_to_model(), enforce_false_movemap(), core::pose::Pose::fold_tree(), fragsets_, core::pose::symmetry::is_symmetric(), keep_input_foldtree_, protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), max_linear_chainbreak_, core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), repeat_pose_, repeat_propagation(), repeat_sync(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), protocols::forge::remodel::RG(), protocols::moves::MonteCarlo::score_function(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and protocols::forge::remodel::TR().

Referenced by apply().

bool protocols::forge::remodel::RemodelLoopMover::check_closure_criteria	(	Pose &	pose,
		bool const	show_in_tracer = `false`
	)

protected

check all loops for closure criteria

Parameters

[in]	pose	The pose being checked.
[in]	show_in_tracer	Output state of each loop to tracer?

Returns: true if all criteria pass, false otherwise

Definition at line 2574 of file RemodelLoopMover.cc.

References protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loops_, max_linear_chainbreak_, and protocols::forge::remodel::TR().

Referenced by apply(), boost_closure_stage(), independent_stage(), loophash_stage(), randomize_stage(), and simultaneous_stage().

void protocols::forge::remodel::RemodelLoopMover::clear_fragments ( )

clear all fragment sets

Definition at line 260 of file RemodelLoopMover.cc.

References fragsets_.

RemodelLoopMover::MoverOP protocols::forge::remodel::RemodelLoopMover::clone ( ) const

virtual

clone this object

Reimplemented from protocols::moves::Mover.

Definition at line 188 of file RemodelLoopMover.cc.

References RemodelLoopMover().

RemodelLoopMover::Size protocols::forge::remodel::RemodelLoopMover::count_moveable_residues	(	MoveMap const &	movemap,
		Size const	left,
		Size const	right
	)

protected

count number of residues with moveable backbone torsions in the given range [left, right]

Definition at line 2767 of file RemodelLoopMover.cc.

References core::kinematics::MoveMap::get_bb().

Referenced by boost_closure_stage(), independent_stage(), randomize_stage(), and simultaneous_stage().

RemodelLoopMover::FragmentMoverOPs protocols::forge::remodel::RemodelLoopMover::create_fragment_movers	(	MoveMap const &	movemap,
		Size const	largest_frag_size = `0`
	)

protected

return fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set

return fragment movers for the list of internally kept fragment sets

Parameters

[in]	movemap	Use this movemap when initializing fragment movers.
[in]	largest_frag_size	Only use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.

Definition at line 2640 of file RemodelLoopMover.cc.

References core::kinematics::MoveMap::clone(), and fragsets_.

Referenced by boost_closure_stage(), create_per_loop_fragment_movers(), independent_stage(), loophash_stage(), and randomize_stage().

void protocols::forge::remodel::RemodelLoopMover::create_fragment_movers	(	MoveMap const &	movemap,
		FragmentMoverOPs &	frag_movers,
		Size const	largest_frag_size = `0`
	)

protected

append fragment movers for the list of internally kept fragment sets, 1 fragment mover for each fragment set

append fragment movers for the list of internally kept fragment sets

Parameters

[in]	movemap	Use this movemap when initializing fragment movers.
[out]	frag_movers	Append fragment movers to this list.
[in]	largest_frag_size	Only use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.

Definition at line 2668 of file RemodelLoopMover.cc.

References core::kinematics::MoveMap::clone(), and fragsets_.

RemodelLoopMover::FragmentMoverOPs protocols::forge::remodel::RemodelLoopMover::create_per_loop_fragment_movers	(	loops::LoopsOP const	loops,
		Size const	largest_frag_size = `0`
	)

protected

create per-loop fragment movers: 1 fragment mover for each loop (uses movemaps to lock down non-loop residues)

Parameters

[in]	loops	The loops to use.
[in]	largest_frag_size	Only use fragment sets whose largest fragment size is this number. If zero, uses all fragment sets.

Definition at line 2693 of file RemodelLoopMover.cc.

References create_fragment_movers(), enforce_false_movemap(), and mark_loop_moveable().

Referenced by insert_random_smallestmer_per_loop(), and simultaneous_stage().

loops::LoopsOP protocols::forge::remodel::RemodelLoopMover::determine_loops_to_model ( Pose & pose)

protected

determine which loops need modeling wrt to given Pose

Remarks: Skips closed loops and shuffles the order of the remaining loops.

Definition at line 2542 of file RemodelLoopMover.cc.

References protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loops_, max_linear_chainbreak_, and protocols::forge::remodel::RG().

Referenced by boost_closure_stage(), independent_stage(), and insert_random_smallestmer_per_loop().

void protocols::forge::remodel::RemodelLoopMover::enforce_false_movemap ( MoveMap & movemap)

protected

enforce settings in the false movemap

Definition at line 2714 of file RemodelLoopMover.cc.

References false_movemap_, and core::kinematics::MoveMap::import_false().

Referenced by boost_closure_stage(), create_per_loop_fragment_movers(), independent_stage(), loophash_stage(), randomize_stage(), and simultaneous_stage().

MoveMap const& protocols::forge::remodel::RemodelLoopMover::false_movemap ( ) const

inline

get the false movemap

Remarks: All movemaps are generated with respect to this movemap. Any explicit False settings within this movemap will be retained in all descendant movemaps.

Definition at line 149 of file RemodelLoopMover.hh.

References false_movemap_.

void protocols::forge::remodel::RemodelLoopMover::false_movemap ( MoveMap const & movemap)

inline

set the false movemap to use

Remarks: All movemaps are generated with respect to this movemap. Any explicit False settings within this movemap will be retained in all descendant movemaps.

Definition at line 247 of file RemodelLoopMover.hh.

References false_movemap_.

RemodelLoopMover::MoverOP protocols::forge::remodel::RemodelLoopMover::fresh_instance ( ) const

virtual

create this type of object

Reimplemented from protocols::moves::Mover.

Definition at line 194 of file RemodelLoopMover.cc.

References RemodelLoopMover().

std::string protocols::forge::remodel::RemodelLoopMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 1193 of file RemodelLoopMover.cc.

Size protocols::forge::remodel::RemodelLoopMover::independent_cycles ( ) const

inline

the number of independent closure cycles to perform (default 8)

Definition at line 191 of file RemodelLoopMover.hh.

References independent_cycles_.

Referenced by independent_stage().

void protocols::forge::remodel::RemodelLoopMover::independent_cycles ( Size const cycles)

inline

the number of independent closure cycles to perform

Definition at line 287 of file RemodelLoopMover.hh.

References independent_cycles_.

void protocols::forge::remodel::RemodelLoopMover::independent_stage	(	Pose &	pose,
		MonteCarlo &	mc,
		Real const	cbreak_increment
	)

protected

independent stage: single loop movement prior to MC accept/reject

Definition at line 2042 of file RemodelLoopMover.cc.

References core::util::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), protocols::loops::loop_closure::ccd::ccd_moves(), check_closure_criteria(), count_moveable_residues(), create_fragment_movers(), protocols::loops::Loop::cut(), determine_loops_to_model(), enforce_false_movemap(), core::pose::Pose::fold_tree(), independent_cycles(), core::pose::symmetry::is_symmetric(), protocols::loops::Loop::is_terminal(), keep_input_foldtree_, protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loops_, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), core::kinematics::FoldTree::num_cutpoint(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), repeat_pose_, repeat_propagation(), repeat_sync(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), protocols::forge::remodel::RG(), protocols::moves::MonteCarlo::score_function(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), simultaneous_cycles(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), total_standard_cycles(), protocols::forge::remodel::TR(), user_provided_movers_, and user_provided_movers_apply_cycle_.

Referenced by apply().

void protocols::forge::remodel::RemodelLoopMover::insert_random_smallestmer_per_loop	(	Pose &	pose,
		bool const	only_broken_loops = `true`
	)

protected

find the smallest fragment size and insert a single such smallmer into each loop; for breaking up trapped trajectories

Parameters

[in,out]	pose	The pose to modify.
[in]	only_broken_loop	If true, only insert into broken loops, otherwise insert into all. (default true)

Definition at line 1249 of file RemodelLoopMover.cc.

References create_per_loop_fragment_movers(), determine_loops_to_model(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), fragsets_, core::pose::symmetry::is_symmetric(), keep_input_foldtree_, loops_, repeat_pose_, and repeat_propagation().

Referenced by apply().

Size protocols::forge::remodel::RemodelLoopMover::loophash_cycles ( ) const

inline

the number of loophash closure cycles to perform (default 8)

Definition at line 178 of file RemodelLoopMover.hh.

References loophash_cycles_.

Referenced by loophash_stage().

void protocols::forge::remodel::RemodelLoopMover::loophash_cycles ( Size const cycles)

inline

the number of loophash closure cycles to perform

Definition at line 274 of file RemodelLoopMover.hh.

References loophash_cycles_.

void protocols::forge::remodel::RemodelLoopMover::loophash_stage	(	Pose &	pose,
		MonteCarlo &	mc,
		Real const	cbreak_increment
	)

protected

independent stage: single loop movement prior to MC accept/reject

Definition at line 1339 of file RemodelLoopMover.cc.

References core::util::add_cutpoint_variants(), protocols::loops::add_cutpoint_variants(), core::scoring::atom_pair_constraint, protocols::moves::MonteCarlo::boltzmann(), protocols::loops::loop_closure::ccd::ccd_moves(), core::chemical::CENTROID, check_closure_criteria(), create_fragment_movers(), protocols::loops::Loop::cut(), enforce_false_movemap(), core::pose::Pose::fold_tree(), protocols::loophash::BackboneDB::get_backbone_segment(), core::chemical::ChemicalManager::get_instance(), protocols::loophash::get_rt_over_leap_fast(), protocols::loophash::LeapIndex::index, core::util::ABEGOManager::index2symbol(), core::chemical::ResidueType::is_ligand(), core::pose::symmetry::is_symmetric(), keep_input_foldtree_, protocols::forge::methods::linear_chainbreak(), core::scoring::linear_chainbreak, loophash_cycles(), loops_, protocols::moves::MonteCarlo::lowest_score_pose(), mark_loop_moveable(), protocols::loophash::LeapIndex::offset, core::scoring::omega, core::pose::Pose::omega(), protocols::swa::phi(), core::pose::Pose::phi(), core::io::pdb::pose_from_pose(), protocols::swa::psi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), repeat_pose_, repeat_propagation(), repeat_sync(), protocols::moves::MonteCarlo::reset(), protocols::moves::MonteCarlo::reset_counters(), core::pose::Pose::residue_type(), protocols::moves::MonteCarlo::score_function(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::forge::methods::set_single_loop_fold_tree(), protocols::loops::set_single_loop_fold_tree(), protocols::moves::MonteCarlo::show_state(), core::kinematics::FoldTree::simple_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::util::ABEGOManager::torsion2index(), core::pose::Pose::total_residue(), and protocols::forge::remodel::TR().

Referenced by apply().

loops::LoopsOP const protocols::forge::remodel::RemodelLoopMover::loops ( ) const

inline

the loops to model

Definition at line 327 of file RemodelLoopMover.hh.

References loops_.

Referenced by loops(), and parse_my_tag().

void protocols::forge::remodel::RemodelLoopMover::loops ( loops::LoopsOP const loops)

inline

set the loops to model

Definition at line 334 of file RemodelLoopMover.hh.

References loops(), and loops_.

void protocols::forge::remodel::RemodelLoopMover::mark_loop_moveable	(	Loop const &	loop,
		MoveMap &	movemap,
		bool const	allow_omega
	)

protected

mark bb/chi torsion of a single loop moveable in movemap

Parameters

[in]	loops	The loop to use.
[out]	movemap	The movemap to modify.
[in]	allow_omega	Allow bb omega to move? (should be yes when doing either fragment insertion or scoring function has omega tether, otherwise should probably be no)

Definition at line 2744 of file RemodelLoopMover.cc.

References core::id::BB, core::id::omega_torsion(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by boost_closure_stage(), create_per_loop_fragment_movers(), independent_stage(), loophash_stage(), and mark_loops_moveable().

void protocols::forge::remodel::RemodelLoopMover::mark_loops_moveable	(	loops::LoopsOP const	loops,
		MoveMap &	movemap,
		bool const	allow_omega
	)

protected

mark bb/chi torsions of multiple loops moveable in a movemap

Parameters

[in]	loops	The loops to use.
[out]	movemap	The movemap to modify.
[in]	allow_omega	Allow bb omega to move? (should be yes when doing either fragment insertion or scoring function has omega tether, otherwise should probably be no)

Definition at line 2726 of file RemodelLoopMover.cc.

References mark_loop_moveable().

Referenced by randomize_stage(), and simultaneous_stage().

Real protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak ( ) const

inline

if linear chainbreak is <= this value, loop is considered closed (default 0.07)

Definition at line 157 of file RemodelLoopMover.hh.

References max_linear_chainbreak_.

void protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak ( Real const val)

inline

if linear chainbreak is <= this value, loop is considered closed

Definition at line 254 of file RemodelLoopMover.hh.

References max_linear_chainbreak_.

RemodelLoopMover& protocols::forge::remodel::RemodelLoopMover::operator= ( RemodelLoopMover const & rval)

private

copy assignment

Remarks: Mover base class prevents this from working properly...

void protocols::forge::remodel::RemodelLoopMover::parse_my_tag	(	TagPtr const	tag,
		DataMap &	data,
		Filters_map const &	,
		Movers_map const &	,
		Pose const &	pose
	)

privatevirtual

bool protocols::forge::remodel::RemodelLoopMover::randomize_loops ( ) const

inline

randomize loops prior to running main protocol? (default true)

Definition at line 164 of file RemodelLoopMover.hh.

References randomize_loops_.

void protocols::forge::remodel::RemodelLoopMover::randomize_loops ( bool const flag)

inline

randomize loops prior to running main protocol?

Definition at line 261 of file RemodelLoopMover.hh.

References randomize_loops_.

void protocols::forge::remodel::RemodelLoopMover::randomize_stage ( Pose & pose)

randomize loops

Definition at line 1198 of file RemodelLoopMover.cc.

References check_closure_criteria(), count_moveable_residues(), create_fragment_movers(), enforce_false_movemap(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), protocols::loops::fold_tree_from_loops(), core::pose::symmetry::is_symmetric(), keep_input_foldtree_, loops_, mark_loops_moveable(), core::pose::Pose::n_residue(), and protocols::forge::remodel::TR().

Referenced by apply().

void protocols::forge::remodel::RemodelLoopMover::register_options ( )

static

options

Definition at line 218 of file RemodelLoopMover.cc.

void protocols::forge::remodel::RemodelLoopMover::repeat_generation	(	Pose &	pose,
		Pose &	repeat_pose
	)

Definition at line 503 of file RemodelLoopMover.cc.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::loops::Loop::cut(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::is_terminus(), core::pose::Pose::jump(), loops_, core::pose::Pose::n_residue(), core::conformation::Conformation::num_chains(), core::pose::Pose::num_jump(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::conformation::Conformation::set_jump(), core::pose::Pose::set_omega(), core::kinematics::Jump::set_rotation(), core::kinematics::Jump::set_translation(), core::kinematics::FoldTree::simple_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and core::pose::Pose::total_residue().

void protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue	(	Pose &	pose,
		Pose &	repeat_pose
	)

Definition at line 264 of file RemodelLoopMover.cc.

References core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::loops::Loop::cut(), core::conformation::Conformation::delete_residue_slow(), core::kinematics::Edge::downstream_atom(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), core::kinematics::Jump::get_rotation(), core::kinematics::Jump::get_translation(), core::conformation::Conformation::insert_ideal_geometry_at_polymer_bond(), core::conformation::Residue::is_terminus(), core::pose::Pose::jump(), core::kinematics::FoldTree::jump_edge(), loops_, core::pose::Pose::n_residue(), core::conformation::Conformation::num_chains(), core::pose::Pose::num_jump(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::util::remove_cutpoint_variants(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::kinematics::FoldTree::renumber_jumps(), core::kinematics::FoldTree::reorder(), repeat_tail_length_, core::pose::Pose::residue(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::kinematics::FoldTree::set_jump_atoms(), core::conformation::Conformation::set_jump_now(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::kinematics::Jump::set_rotation(), core::kinematics::Jump::set_translation(), core::kinematics::FoldTree::simple_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), protocols::forge::remodel::TR(), and core::kinematics::Edge::upstream_atom().

Referenced by apply(), protocols::forge::components::VarLengthBuild::apply(), and protocols::forge::remodel::RemodelMover::centroid_build().

void protocols::forge::remodel::RemodelLoopMover::repeat_propagation	(	Pose &	pose,
		Pose &	repeat_pose,
		core::Size	repeat_number
	)

Definition at line 762 of file RemodelLoopMover.cc.

Referenced by apply(), boost_closure_stage(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), and simultaneous_stage().

void protocols::forge::remodel::RemodelLoopMover::repeat_sync	(	core::pose::Pose &	repeat_pose,
		core::Size	repeat_number
	)

Definition at line 675 of file RemodelLoopMover.cc.

References loops_, core::pose::Pose::n_residue(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::pose::Pose::total_residue(), and protocols::forge::remodel::TR().

Referenced by boost_closure_stage(), independent_stage(), loophash_stage(), and simultaneous_stage().

RemodelLoopMover::ScoreFunction const & protocols::forge::remodel::RemodelLoopMover::scorefunction ( ) const

the ScoreFunction to use during modeling;

Definition at line 232 of file RemodelLoopMover.cc.

References sfx_.

Referenced by protocols::protein_interface_design::movers::LoopRemodel::apply().

void protocols::forge::remodel::RemodelLoopMover::scorefunction ( ScoreFunction const & sfx)

the ScoreFunction to use during modeling

Definition at line 238 of file RemodelLoopMover.cc.

References core::scoring::ScoreFunction::clone(), and sfx_.

void protocols::forge::remodel::RemodelLoopMover::set_keep_input_foldtree ( bool const setting)

inline

Definition at line 319 of file RemodelLoopMover.hh.

References keep_input_foldtree_.

void protocols::forge::remodel::RemodelLoopMover::set_param_from_options ( )

set parameters from options

Definition at line 200 of file RemodelLoopMover.cc.

References allowed_closure_attempts_, boost_closure_cycles_, independent_cycles_, keep_input_foldtree_, loophash_cycles_, max_linear_chainbreak_, randomize_loops_, simultaneous_cycles_, and temperature_.

Referenced by RemodelLoopMover().

void protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length ( Size const length)

inline

Definition at line 313 of file RemodelLoopMover.hh.

References repeat_tail_length_.

Referenced by protocols::forge::components::VarLengthBuild::apply(), and protocols::forge::remodel::RemodelMover::centroid_build().

void protocols::forge::remodel::RemodelLoopMover::set_user_provided_movers ( utility::vector1< moves::MoverOP > const & movers)

Definition at line 244 of file RemodelLoopMover.cc.

References user_provided_movers_.

Size protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles ( ) const

inline

the number of simultaneous closure cycles to perform (default 2)

Definition at line 184 of file RemodelLoopMover.hh.

References simultaneous_cycles_.

Referenced by independent_stage(), and simultaneous_stage().

void protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles ( Size const cycles)

inline

the number of simultaneous closure cycles to perform

Definition at line 280 of file RemodelLoopMover.hh.

References simultaneous_cycles_.

void protocols::forge::remodel::RemodelLoopMover::simultaneous_stage	(	Pose &	pose,
		MonteCarlo &	mc,
		Real const	cbreak_increment
	)

protected

simultaneous stage: multiple loop movement prior to MC accept/reject

Definition at line 1805 of file RemodelLoopMover.cc.

Referenced by apply().

Real protocols::forge::remodel::RemodelLoopMover::temperature ( ) const

inline

temperature for mc ( default 2.0 )

Definition at line 213 of file RemodelLoopMover.hh.

References temperature_.

void protocols::forge::remodel::RemodelLoopMover::temperature ( Real const temp)

inline

temperature for mc

Definition at line 307 of file RemodelLoopMover.hh.

References temperature_.

Size protocols::forge::remodel::RemodelLoopMover::total_standard_cycles ( ) const

inline

the total number of "standard" (equal to simul + independent) to perform

Definition at line 207 of file RemodelLoopMover.hh.

References independent_cycles_, loophash_cycles_, and simultaneous_cycles_.

Referenced by apply(), independent_stage(), and simultaneous_stage().

void protocols::forge::remodel::RemodelLoopMover::user_provided_movers_apply_cycle ( Size const cycle)

inline

Definition at line 295 of file RemodelLoopMover.hh.

References user_provided_movers_apply_cycle_.

Member Data Documentation

Size protocols::forge::remodel::RemodelLoopMover::allowed_closure_attempts_

private

the allowed number of overall closure attempts before apply() exits (default 3)

Definition at line 558 of file RemodelLoopMover.hh.

Referenced by allowed_closure_attempts(), apply(), parse_my_tag(), and set_param_from_options().

Size protocols::forge::remodel::RemodelLoopMover::boost_closure_cycles_

private

the maximum number of possible boost closure cycles to perform (default 30)

Definition at line 583 of file RemodelLoopMover.hh.

Referenced by boost_closure_cycles(), parse_my_tag(), and set_param_from_options().

MoveMap protocols::forge::remodel::RemodelLoopMover::false_movemap_

private

the false movemap to use

Remarks: All movemaps are generated with respect to this movemap. Any False explicit settings within this movemap will be retained in all descendant movemaps.

Definition at line 538 of file RemodelLoopMover.hh.

Referenced by enforce_false_movemap(), and false_movemap().

FragSetOPs protocols::forge::remodel::RemodelLoopMover::fragsets_

private

fragment sets to use

Definition at line 590 of file RemodelLoopMover.hh.

Referenced by add_fragments(), boost_closure_stage(), clear_fragments(), create_fragment_movers(), and insert_random_smallestmer_per_loop().

Size protocols::forge::remodel::RemodelLoopMover::independent_cycles_

private

the number of independent closure cycles to perform (default 8)

Definition at line 568 of file RemodelLoopMover.hh.

Referenced by independent_cycles(), parse_my_tag(), set_param_from_options(), and total_standard_cycles().

bool protocols::forge::remodel::RemodelLoopMover::keep_input_foldtree_

private

whether to keep the FoldTree untouched, i.e. trust the user to supply a decent FoldTree

Definition at line 597 of file RemodelLoopMover.hh.

Referenced by boost_closure_stage(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), randomize_stage(), set_keep_input_foldtree(), set_param_from_options(), and simultaneous_stage().

Size protocols::forge::remodel::RemodelLoopMover::loophash_cycles_

private

the number of loophash closure cycles to perform (default 8)

Definition at line 561 of file RemodelLoopMover.hh.

Referenced by loophash_cycles(), parse_my_tag(), set_param_from_options(), and total_standard_cycles().

loops::LoopsOP protocols::forge::remodel::RemodelLoopMover::loops_

private

list of loops to model

Definition at line 542 of file RemodelLoopMover.hh.

Referenced by add_loop(), check_closure_criteria(), determine_loops_to_model(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), loops(), parse_my_tag(), randomize_stage(), repeat_generation(), repeat_generation_with_additional_residue(), repeat_propagation(), repeat_sync(), and simultaneous_stage().

Real protocols::forge::remodel::RemodelLoopMover::max_linear_chainbreak_

private

if linear chainbreak is <= this value, loop is considered closed (default 0.07)

Definition at line 547 of file RemodelLoopMover.hh.

Referenced by boost_closure_stage(), check_closure_criteria(), determine_loops_to_model(), max_linear_chainbreak(), parse_my_tag(), and set_param_from_options().

bool protocols::forge::remodel::RemodelLoopMover::randomize_loops_

private

randomize loops prior to running main protocol? (default true)

Definition at line 551 of file RemodelLoopMover.hh.

Referenced by apply(), parse_my_tag(), randomize_loops(), and set_param_from_options().

Pose protocols::forge::remodel::RemodelLoopMover::repeat_pose_

private

local copy of repeat pose

Definition at line 593 of file RemodelLoopMover.hh.

Referenced by apply(), boost_closure_stage(), independent_stage(), insert_random_smallestmer_per_loop(), loophash_stage(), and simultaneous_stage().

Size protocols::forge::remodel::RemodelLoopMover::repeat_tail_length_

private

Definition at line 553 of file RemodelLoopMover.hh.

Referenced by repeat_generation_with_additional_residue(), set_repeat_tail_length(), and simultaneous_stage().

ScoreFunctionOP protocols::forge::remodel::RemodelLoopMover::sfx_

private

the score function to use

Definition at line 531 of file RemodelLoopMover.hh.

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

Size protocols::forge::remodel::RemodelLoopMover::simultaneous_cycles_

private

the number of simultaneous closure cycles to perform (default 2)

Definition at line 564 of file RemodelLoopMover.hh.

Referenced by parse_my_tag(), set_param_from_options(), simultaneous_cycles(), and total_standard_cycles().

Real protocols::forge::remodel::RemodelLoopMover::temperature_

private

temperature for mc

Definition at line 586 of file RemodelLoopMover.hh.

Referenced by apply(), parse_my_tag(), set_param_from_options(), and temperature().

utility::vector1< moves::MoverOP > protocols::forge::remodel::RemodelLoopMover::user_provided_movers_

private

collection of movers that mess with the pose every n fragment/ccd steps during inneriterations of simultaneous, and independent stage, where n is determined by the variable below gives the user a chance to add their own flavor to the fragment sampling done by this protocol

Definition at line 575 of file RemodelLoopMover.hh.

Referenced by independent_stage(), set_user_provided_movers(), and simultaneous_stage().

Size protocols::forge::remodel::RemodelLoopMover::user_provided_movers_apply_cycle_

private

determines how often the above movers get called during fragment insertion/ccd steps (default 3 )

Definition at line 579 of file RemodelLoopMover.hh.

Referenced by independent_stage(), simultaneous_stage(), and user_provided_movers_apply_cycle().

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

src/protocols/forge/remodel/RemodelLoopMover.hh
src/protocols/forge/remodel/RemodelLoopMover.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Types

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation