protocols::protein_interface_design::movers::LoopRemodel Class Reference

#include <LoopRemodel.hh>

Public Member Functions
	LoopRemodel ()
	LoopRemodel (std::string const protocol, core::Size const loop_start, core::Size const loop_end, core::Size const cycles, bool const auto_loops, bool const perturb, bool const refine, bool const hurry, core::scoring::ScoreFunctionOP hires_score, core::scoring::ScoreFunctionOP lores_score, protocols::loops::LoopsCOP loops, core::fragment::FragSetOP frag1, core::fragment::FragSetOP frag3, core::fragment::FragSetOP frag9)
bool	perturb ()
void	perturb (bool const setting)
bool	refine ()
void	refine (bool const setting)
bool	hurry ()
void	hurry (bool const setting)
protocols::moves::MoverOP	clone () const
	Return a clone of the Mover object. More...
protocols::moves::MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...
void	apply (core::pose::Pose &pose)
	a dummy apply so that instantiation of this baseclass would be possible. More...
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
virtual	~LoopRemodel ()
Public Member Functions inherited from protocols::simple_moves::DesignRepackMover
	DesignRepackMover ()
	DesignRepackMover (std::string const name)
void	setup_packer_and_movemap (core::pose::Pose const &pose)
void	min_rb (utility::vector1< bool > const min_rb)
void	min_rb (bool const min_rb)
	in most cases, there would only be one rb dof making it useful to have a non-vector accessor to min_rb_. However, if the pose has multiple jumps, setting min_rb_ in this way might cause trouble in other parts of the code. More...
utility::vector1< bool > const &	min_rb () const
bool	min_rb_set () const
void	min_sc (utility::vector1< bool > const &min_sc)
utility::vector1< bool > const &	min_sc () const
bool	min_sc_set () const
void	min_bb (utility::vector1< bool > const &min_bb)
utility::vector1< bool > const &	min_bb () const
bool	min_bb_set () const
bool	optimize_foldtree () const
void	optimize_foldtree (bool const opt)
void	prevent_repacking (utility::vector1< core::Size > const p)
utility::vector1< core::Size > const &	prevent_repacking () const
void	restrict_to_repacking (utility::vector1< core::Size > const p)
utility::vector1< core::Size > const &	restrict_to_repacking () const
void	design (bool const des)
bool	design () const
void	set_scorefxn_repack (core::scoring::ScoreFunctionCOP scorefxn)
void	set_scorefxn_minimize (core::scoring::ScoreFunctionCOP scorefxn)
core::scoring::ScoreFunctionOP	scorefxn_repack () const
core::scoring::ScoreFunctionOP	scorefxn_minimize () const
core::pack::task::PackerTaskCOP	task () const
core::pack::task::PackerTaskOP &	task ()
void	clear_task ()
	after fiddling with a task from outside this mover, clear it, or else, on the next iteration through the mover the changes will be remembered More...
void	clear_task_factory ()
void	use_preset_task (bool const bt)
bool	use_preset_task () const
void	task_factory (core::pack::task::TaskFactoryOP p)
core::pack::task::TaskFactoryOP &	task_factory ()
core::pack::task::TaskFactoryOP	task_factory () const
virtual	~DesignRepackMover ()
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
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)
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...
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...

Private Member Functions
bool	pick_loop_frags (protocols::loops::LoopsCOP loops, std::string const full_seqeuence, std::string const full_ss)

Private Attributes
std::string	protocol_
core::scoring::ScoreFunctionOP	hires_score_
core::scoring::ScoreFunctionOP	lores_score_
core::Size	loop_start_
core::Size	loop_end_
core::Size	cycles_
bool	auto_loops_
bool	perturb_
bool	refine_
bool	hurry_
protocols::loops::LoopsOP	loops_
core::fragment::FragSetOP	frag1_
core::fragment::FragSetOP	frag3_
core::fragment::FragSetOP	frag9_

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...
Protected Attributes inherited from protocols::simple_moves::DesignRepackMover
core::scoring::ScoreFunctionOP	scorefxn_repack_
core::scoring::ScoreFunctionOP	scorefxn_minimize_
bool	repack_partner1_
bool	repack_partner2_
bool	design_partner1_
bool	design_partner2_
utility::vector1< bool >	min_sc_
utility::vector1< bool >	curr_min_sc_
utility::vector1< bool >	min_rb_
utility::vector1< bool >	min_bb_
utility::vector1< bool >	curr_min_bb_
utility::vector1< bool >	curr_min_rb_
bool	min_rb_set_
bool	min_sc_set_
bool	min_bb_set_
utility::vector1< core::Size >	target_residues_
core::Real	interface_distance_cutoff_
bool	repack_non_ala_
bool	optimize_foldtree_
bool	automatic_repacking_definition_
core::pack::task::PackerTaskOP	task_
bool	use_preset_task_
utility::vector1< bool >	allowed_aas_
utility::vector1< core::Size >	prevent_repacking_
utility::vector1< core::Size >	restrict_to_repacking_
core::pack::task::TaskFactoryOP	task_factory_
bool	symmetry_

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel

(

)

protocols::protein_interface_design::movers::LoopRemodel::LoopRemodel	(	std::string const	protocol,
		core::Size const	loop_start,
		core::Size const	loop_end,
		core::Size const	cycles,
		bool const	auto_loops,
		bool const	perturb,
		bool const	refine,
		bool const	hurry,
		core::scoring::ScoreFunctionOP	hires_score,
		core::scoring::ScoreFunctionOP	lores_score,
		protocols::loops::LoopsCOP	loops,
		core::fragment::FragSetOP	frag1,
		core::fragment::FragSetOP	frag3,
		core::fragment::FragSetOP	frag9
	)

References core::scoring::ScoreFunction::clone(), frag1_, frag3_, frag9_, hires_score_, loops_, and lores_score_.

protocols::protein_interface_design::movers::LoopRemodel::~LoopRemodel ( )

virtual

Member Function Documentation

void protocols::protein_interface_design::movers::LoopRemodel::apply ( core::pose::Pose &  )

virtual

a dummy apply so that instantiation of this baseclass would be possible.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::forge::methods::add_cutpoint_variants(), protocols::loops::loop_mover::LoopMover::add_fragments(), protocols::forge::remodel::RemodelLoopMover::add_fragments(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::allsc(), protocols::loops::loop_mover::IndependentLoopMover::apply(), protocols::protein_interface_design::movers::SaveAndRetrieveSidechains::apply(), protocols::loops::loop_closure::kinematic_closure::KinematicWrapper::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::simple_moves::MinMover::apply(), protocols::forge::remodel::RemodelLoopMover::apply(), protocols::moves::MonteCarlo::boltzmann(), core::chemical::CENTROID, core::scoring::chainbreak, core::scoring::ScoreFunction::clone(), core::pack::task::TaskFactory::create_task_and_apply_taskoperations(), cycles, cycles_, protocols::simple_moves::DesignRepackMover::design(), protocols::simple_filters::dssp(), core::chemical::FA_STANDARD, protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), frag1_, frag3_, frag9_, protocols::moves::Mover::get_last_move_status(), hires_score_, hurry_, core::scoring::dssp::Dssp::insert_ss_into_pose(), basic::options::OptionKeys::loops::kic_recover_last, protocols::moves::MonteCarlo::last_accepted_pose(), loops, loops_, protocols::loops::loops_set_move_map(), lores_score_, mc_kt, movemap, protocols::moves::MS_SUCCESS, core::pack::task::PackerTask::nonconst_residue_task(), core::scoring::omega, basic::options::option, outer_cycles, perturb(), perturb_, pick_loop_frags(), protocols::simple_moves::DesignRepackMover::prevent_repacking(), protocol_, core::pack::task::TaskFactory::push_back(), protocols::moves::MonteCarlo::recover_low(), refine(), refine_, remodel, basic::options::OptionKeys::loops::remodel_init_temp, remove_cutpoint_variants(), basic::options::OptionKeys::packing::resfile, core::pack::task::operation::OperateOnCertainResidues::residue_indices(), core::pack::task::ResidueLevelTask::restrict_to_repacking(), protocols::forge::remodel::RemodelLoopMover::scorefunction(), core::pose::Pose::secstruct(), core::pose::Pose::sequence(), protocols::moves::MonteCarlo::set_autotemp(), protocols::moves::Mover::set_last_move_status(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::set_redesign_loop(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_redesign_loop(), protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops(), protocols::moves::MonteCarlo::show_counters(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), core::util::switch_to_residue_type_set(), protocols::simple_moves::DesignRepackMover::task(), protocols::simple_moves::DesignRepackMover::task_factory(), protocols::moves::MonteCarlo::temperature(), core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR, core::pose::Pose::update_residue_neighbors(), and user.

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::clone ( ) const

virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Implements protocols::simple_moves::DesignRepackMover.

protocols::moves::MoverOP protocols::protein_interface_design::movers::LoopRemodel::fresh_instance ( ) const

inlinevirtual

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

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Implements protocols::simple_moves::DesignRepackMover.

std::string protocols::protein_interface_design::movers::LoopRemodel::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::protein_interface_design::movers::LoopRemodelCreator::mover_name().

bool protocols::protein_interface_design::movers::LoopRemodel::hurry ( )

inline

References hurry_.

void protocols::protein_interface_design::movers::LoopRemodel::hurry ( bool const  setting )

inline

References hurry_.

void protocols::protein_interface_design::movers::LoopRemodel::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data, protocols::filters::Filters_map const &  filters, protocols::moves::Movers_map const &  movers, core::pose::Pose const &  pose  )

virtual

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

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::simple_moves::DesignRepackMover.

References protocols::loops::Loops::add_loop(), auto_loops_, core::scoring::ScoreFunction::clone(), cycles_, protocols::simple_moves::DesignRepackMover::design(), basic::datacache::DataMap::get(), core::pose::get_resnum(), protocols::rosetta_scripts::get_score_function_name(), basic::datacache::DataMap::has(), hires_score_, hurry_, loop_end_, loop_start_, loops_, lores_score_, protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), perturb_, protocol_, refine_, runtime_assert, protocols::simple_moves::DesignRepackMover::task_factory(), core::pose::Pose::total_residue(), and protocols::protein_interface_design::movers::TR.

bool protocols::protein_interface_design::movers::LoopRemodel::perturb ( )

inline

References perturb_.

Referenced by apply().

void protocols::protein_interface_design::movers::LoopRemodel::perturb ( bool const  setting )

inline

References perturb_.

bool protocols::protein_interface_design::movers::LoopRemodel::pick_loop_frags ( protocols::loops::LoopsCOP  loops, std::string const  full_seqeuence, std::string const  full_ss  )

private

References core::fragment::Frame::add_fragment(), core::fragment::FragSet::begin(), protocols::simple_moves::DesignRepackMover::design(), core::fragment::FragSet::end(), frag1_, frag3_, frag9_, frame(), list, loops, protocols::forge::methods::smallmer_from_largemer(), ss, and protocols::protein_interface_design::movers::TR.

Referenced by apply().

bool protocols::protein_interface_design::movers::LoopRemodel::refine ( )

inline

References refine_.

Referenced by apply().

void protocols::protein_interface_design::movers::LoopRemodel::refine ( bool const  setting )

inline

References refine_.

Member Data Documentation

bool protocols::protein_interface_design::movers::LoopRemodel::auto_loops_

private

Referenced by parse_my_tag().

core::Size protocols::protein_interface_design::movers::LoopRemodel::cycles_

private

Referenced by apply(), and parse_my_tag().

core::fragment::FragSetOP protocols::protein_interface_design::movers::LoopRemodel::frag1_

private

Referenced by apply(), LoopRemodel(), and pick_loop_frags().

core::fragment::FragSetOP protocols::protein_interface_design::movers::LoopRemodel::frag3_

private

Referenced by apply(), LoopRemodel(), and pick_loop_frags().

core::fragment::FragSetOP protocols::protein_interface_design::movers::LoopRemodel::frag9_

private

Referenced by apply(), LoopRemodel(), and pick_loop_frags().

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::LoopRemodel::hires_score_

private

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

bool protocols::protein_interface_design::movers::LoopRemodel::hurry_

private

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

core::Size protocols::protein_interface_design::movers::LoopRemodel::loop_end_

private

Referenced by parse_my_tag().

core::Size protocols::protein_interface_design::movers::LoopRemodel::loop_start_

private

Referenced by parse_my_tag().

protocols::loops::LoopsOP protocols::protein_interface_design::movers::LoopRemodel::loops_

private

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

core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::LoopRemodel::lores_score_

private

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

bool protocols::protein_interface_design::movers::LoopRemodel::perturb_

private

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

std::string protocols::protein_interface_design::movers::LoopRemodel::protocol_

private

Referenced by apply(), and parse_my_tag().

bool protocols::protein_interface_design::movers::LoopRemodel::refine_

private

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

---

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

• src/protocols/protein_interface_design/movers/LoopRemodel.hh
• src/protocols/protein_interface_design/movers/LoopRemodel.cc