#include <LoopMover_KIC.hh>

Inheritance diagram for protocols::loops::loop_mover::refine::LoopMover_Refine_KIC:

Collaboration diagram for protocols::loops::loop_mover::refine::LoopMover_Refine_KIC:

Public Member Functions
	LoopMover_Refine_KIC ()

	LoopMover_Refine_KIC (protocols::loops::LoopsOP loops_in)

	LoopMover_Refine_KIC (protocols::loops::LoopsOP const loops_in, core::scoring::ScoreFunctionCOP scorefxn)

	~LoopMover_Refine_KIC ()

void	init (core::scoring::ScoreFunctionCOP scorefxn)

void	set_default_settings ()

void	set_redesign_loop (bool value=true)

bool	get_redesign_loop ()

void	set_flank_residue_min (bool value)

void	set_task_factory (core::pack::task::TaskFactoryOP value)

bool	get_task_factory ()

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

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

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

void	update_movemap_vectors (core::pose::Pose &pose, utility::vector1< core::kinematics::MoveMap > &move_maps)
	update the vector of movemaps, one for each loop in loops_ More...

void	update_allow_sc_vectors (core::pose::Pose &pose, utility::vector1< utility::vector1< bool > > &allow_sc_vectors)
	update the vector of vectors of moveable side-chain positions, one for each loop in loops_ More...

void	set_rottrials_from_kic_segment (core::pose::Pose &pose, core::pack::task::PackerTaskOP &rottrials_packer_task, Size kic_start, Size kic_end)

void	set_movemap_from_kic_segment (core::pose::Pose &pose, core::kinematics::MoveMap &cur_mm, Size kic_start, Size kic_end)

Public Member Functions inherited from protocols::loops::loop_mover::LoopMover
	LoopMover ()

	LoopMover (protocols::loops::LoopsOP loops_in)

	LoopMover (protocols::loops::LoopsFileData const &loops_from_file)

	LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops)

	LoopMover (LoopMover const &rhs)
	copy ctor More...

LoopMover &	operator= (LoopMover const &rhs)
	assignment operator More...

virtual	~LoopMover ()

void	set_guarded_loops_not_in_charge ()
	Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More...

void	set_scorefxn (const core::scoring::ScoreFunctionOP score_in)

const core::scoring::ScoreFunctionOP &	scorefxn () const

void	loops (protocols::loops::LoopsOP lptr)
	Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More...

void	loops (LoopsFileData const &loop_file_data)
	Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More...

void	loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
	Set the guarded_loops pointer. More...

protocols::loops::LoopsCOP	loops () const
	Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...

protocols::loops::LoopsOP	loops ()
	non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...

const utility::vector1 < core::fragment::FragSetOP > &	frag_libs () const

std::string	torsion_features_string (core::pose::Pose const &pose) const
	bin torsion angles as described in http://www.ncbi.nlm.nih.gov/pubmed/19646450 generates a string with the torsion angle bins, using uppercase letters as in the publication above for omega ~ 180, and lowercase letters for omega ~ 0; to be used in loop sampling analysis More...

virtual void	set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
	Extend a loop. More...

void	add_fragments (core::fragment::FragSetOP fragset)
	add a fragment set More...

void	clear_fragments ()
	clear the list of fragment sets More...

MoveMapOP const &	false_movemap () const
	explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...

void	false_movemap (MoveMapOP const &mm)
	explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...

checkpoint::CheckPointerOP &	get_checkpoints ()

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)

virtual void	parse_my_tag (TagPtr const tag, 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
	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...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

Protected Member Functions
virtual basic::Tracer &	tr () const

Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover
Size	enforce_false_movemap (MoveMapOP &mm) const
	import the false_movemap's explicit False settings into the given MoveMap More...

void	set_loops_from_pose_observer_cache (core::pose::Pose const &pose)
	allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More...

bool	use_loops_from_observer_cache () const

void	set_use_loops_from_observer_cache (bool const loops_from_observer_cache)

void	resolve_loop_indices (core::pose::Pose const &p)
	Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. 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...

Protected Attributes
core::pack::task::TaskFactoryOP	task_factory

bool	redesign_loop_

Private Attributes
core::Real	neighbor_dist_

core::Size	max_seglen_

bool	recover_low_

bool	min_after_repack_

bool	fix_natsc_

bool	optimize_only_kic_region_sidechains_after_move_

bool	flank_residue_min_

Additional Inherited Members
Public Types inherited from protocols::loops::loop_mover::LoopMover
typedef core::kinematics::MoveMapOP	MoveMapOP

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...

Detailed Description

Definition at line 43 of file LoopMover_KIC.hh.

Constructor & Destructor Documentation

protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC ( )

Definition at line 100 of file LoopMover_KIC.cc.

References protocols::loops::get_fa_scorefxn(), and protocols::loops::loop_mover::LoopMover::init().

Referenced by clone(), and protocols::loops::loop_mover::refine::LoopMover_Refine_KICCreator::create_mover().

protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC ( protocols::loops::LoopsOP loops_in)

Definition at line 104 of file LoopMover_KIC.cc.

References protocols::loops::get_fa_scorefxn(), and protocols::loops::loop_mover::LoopMover::init().

protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::LoopMover_Refine_KIC	(	protocols::loops::LoopsOP const	loops_in,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

Definition at line 111 of file LoopMover_KIC.cc.

References protocols::loops::loop_mover::LoopMover::init().

protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::~LoopMover_Refine_KIC ( )

Definition at line 120 of file LoopMover_KIC.cc.

Member Function Documentation

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply ( core::pose::Pose & pose)

virtual

detailed Refines the polypeptide segments in the LoopMover_Refine_KIC::loops_ class variable from their current conformations. Uses Rosetta's all-atom respresentation and high-resolution scoring function (score12 with an upweighted chain break term). At the beginning of this stage, unless the flag -loops:fix_natsc has been set, all residues within the neighbor distance of a loop (defined by -loops:neighbor_dist) are repacked and then subject to rotamer trials. The backbones of all loop residues, and the side-chains of all loop residues and neighbors are then subject to DFPmin. If -loops:fix_natsc is set, only the loop residues (and not the neighbors) will be subject to repacking, rotamer trials, and minimization. Consequently, if this stage has been preceeded by LoopMover_Perturb_KIC:model_loop, and the -loops:fix_natsc flag is omitted, the side-chains surrounding the loop will be optimized for the perturbed loop conformation, rather than the starting conformation that preceded the call to model_loop.

Implements protocols::loops::loop_mover::LoopMover.

Definition at line 165 of file LoopMover_KIC.cc.

Referenced by protocols::protein_interface_design::movers::LoopMoverFromCommandLine::apply(), protocols::protein_interface_design::movers::LoopRemodel::apply(), protocols::antibody2::RefineOneCDRLoop::apply(), protocols::comparative_modeling::LoopRelaxMover::apply(), protocols::abinitio::AbrelaxMover::close_with_idealization(), protocols::forge::remodel::RemodelMover::confirm_sequence(), protocols::forge::remodel::RemodelMover::design_refine(), protocols::abinitio::AbrelaxApplication::fold(), and protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub().

protocols::moves::MoverOP protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::clone ( ) const

virtual

Clone this object.

Reimplemented from protocols::moves::Mover.

Definition at line 123 of file LoopMover_KIC.cc.

References LoopMover_Refine_KIC().

std::string protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_name ( ) const

virtual

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

Reimplemented from protocols::loops::loop_mover::LoopMover.

Definition at line 753 of file LoopMover_KIC.cc.

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_redesign_loop ( )

inline

Definition at line 64 of file LoopMover_KIC.hh.

References redesign_loop_.

bool protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::get_task_factory ( )

Definition at line 152 of file LoopMover_KIC.cc.

References task_factory.

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::init ( core::scoring::ScoreFunctionCOP scorefxn)

Definition at line 127 of file LoopMover_KIC.cc.

References set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_default_settings ( )

Definition at line 135 of file LoopMover_KIC.cc.

References fix_natsc_, flank_residue_min_, max_seglen_, min_after_repack_, neighbor_dist_, optimize_only_kic_region_sidechains_after_move_, recover_low_, and redesign_loop_.

Referenced by init().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_flank_residue_min ( bool value)

inline

Definition at line 65 of file LoopMover_KIC.hh.

References flank_residue_min_.

Referenced by protocols::antibody2::RefineOneCDRLoop::apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_movemap_from_kic_segment	(	core::pose::Pose &	pose,
		core::kinematics::MoveMap &	cur_mm,
		Size	kic_start,
		Size	kic_end
	)

detailed Sets the MoveMap for minimization used in LoopMover_Refine_KIC::apply() to only minimize the neighborhood around KIC segment that moved. May slightly hurt performance in de novo loop reconstruction, but may yield a speedup of 2X or more in cases of modeling very large or multiple segments (loop definitions), in conjunction with set_movemap_from_kic_segment(), which are both used when optimize_only_kic_region_sidechains_after_move_ is set to true.

Definition at line 820 of file LoopMover_KIC.cc.

References protocols::loops::Loops::add_loop(), fix_natsc_, protocols::loops::loops_set_move_map(), and neighbor_dist_.

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop ( bool value = true)

inline

Definition at line 63 of file LoopMover_KIC.hh.

References redesign_loop_.

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

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_rottrials_from_kic_segment	(	core::pose::Pose &	pose,
		core::pack::task::PackerTaskOP &	rottrials_packer_task,
		Size	kic_start,
		Size	kic_end
	)

detailed Sets the rotamer trials packer task used in LoopMover_Refine_KIC::apply() to only rotamer trial the neighborhood around KIC segment that moved. May slightly hurt performance in de novo loop reconstruction, but may yield a speedup of 2X or more in cases of modeling very large or multiple segments (loop definitions), in conjunction with set_movemap_from_kic_segment(), which are both used when optimize_only_kic_region_sidechains_after_move_ is set to true.

Definition at line 800 of file LoopMover_KIC.cc.

References neighbor_dist_, protocols::loops::select_loop_residues(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_task_factory ( core::pack::task::TaskFactoryOP value)

Definition at line 151 of file LoopMover_KIC.cc.

References task_factory.

Referenced by protocols::protein_interface_design::movers::PlaceOnLoop::minimize_toward_stub().

basic::Tracer & protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::tr ( ) const

protectedvirtual

Implements protocols::loops::loop_mover::LoopMover.

Definition at line 831 of file LoopMover_KIC.cc.

References protocols::loops::loop_mover::refine::TR().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_allow_sc_vectors	(	core::pose::Pose &	pose,
		utility::vector1< utility::vector1< bool > > &	allow_sc_vectors
	)

update the vector of vectors of moveable side-chain positions, one for each loop in loops_

detailed Update the allow_sc_vectors that define, for each loop in loops_, which residue side-chains may be subject to rotamer trials. Allows for rotamer trials to apply only to the neighborhood around the segment that KIC moved, in cases where multiple segments (loops) are defined.

Definition at line 780 of file LoopMover_KIC.cc.

References protocols::loops::Loops::add_loop(), fix_natsc_, protocols::loops::loop_mover::LoopMover::loops(), neighbor_dist_, protocols::loops::select_loop_residues(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::update_movemap_vectors	(	core::pose::Pose &	pose,
		utility::vector1< core::kinematics::MoveMap > &	move_maps
	)

update the vector of movemaps, one for each loop in loops_

detailed Update the MoveMaps that define, for each loop in loops_, which residues may be minimized. Allows for minimization to apply only to the neighborhood around the segment that KIC moved, in cases where multiple segments (loops) are defined.

Definition at line 762 of file LoopMover_KIC.cc.

References protocols::loops::Loops::add_loop(), fix_natsc_, protocols::loops::loop_mover::LoopMover::loops(), protocols::loops::loops_set_move_map(), and neighbor_dist_.

Referenced by apply().