#include <PrepackMover.hh>

Inheritance diagram for protocols::protein_interface_design::movers::PrepackMover:

Collaboration diagram for protocols::protein_interface_design::movers::PrepackMover:

Public Member Functions
	PrepackMover ()

	PrepackMover (core::scoring::ScoreFunctionCOP scorefxn, core::Size jump_num)

virtual	~PrepackMover ()

protocols::moves::MoverOP	clone () const
	required in the context of the parser/scripting scheme More...

protocols::moves::MoverOP	fresh_instance () const
	required in the context of the parser/scripting scheme 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	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	allow non-const access to the internal minimizer options object More...

bool	min_bb () const

void	min_bb (bool const m)

core::kinematics::MoveMapOP	mm () const

void	mm (core::kinematics::MoveMapOP mm)

Public Member Functions inherited from protocols::simple_moves::PackRotamersMover
	PackRotamersMover ()
	default constructor More...

	PackRotamersMover (std::string const &)
	constructor with typename More...

	PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)
	Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...

virtual	~PackRotamersMover ()

	PackRotamersMover (PackRotamersMover const &other)

bool	task_is_valid (Pose const &pose) const
	when the PackerTask was not generated locally, verify compatibility with pose More...

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

virtual void	parse_score_function (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
	parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...

void	score_function (ScoreFunctionCOP sf)
	Sets the ScoreFunction to <sf> More...

void	task_factory (TaskFactoryCOP tf)
	Sets the TaskFactory to <tf> More...

void	task (PackerTaskCOP t)
	Sets the PackerTask to <t> More...

void	nloop (core::Size nloop_in)

ScoreFunctionCOP	score_function () const
	Returns the ScoreFunction. More...

PackerTaskCOP	task () const
	Returns the PackerTask. More...

core::Size	nloop () const

TaskFactoryCOP	task_factory () const
	Returns the TaskFactory. More...

RotamerSetsCOP	rotamer_sets () const

InteractionGraphBaseCOP	ig () const

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	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

Private Attributes
core::scoring::ScoreFunctionCOP	scorefxn_

core::Size	jump_num_

bool	min_bb_

core::kinematics::MoveMapOP	mm_

Additional Inherited Members
Public Types inherited from protocols::simple_moves::PackRotamersMover
typedef core::pack::interaction_graph::InteractionGraphBaseOP	InteractionGraphBaseOP
	please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here! More...

typedef core::pack::interaction_graph::InteractionGraphBaseCOP	InteractionGraphBaseCOP

typedef core::pack::rotamer_set::RotamerSetsOP	RotamerSetsOP

typedef core::pack::rotamer_set::RotamerSetsCOP	RotamerSetsCOP

typedef core::pack::task::PackerTaskCOP	PackerTaskCOP

typedef core::pack::task::TaskFactoryCOP	TaskFactoryCOP

typedef core::scoring::ScoreFunctionCOP	ScoreFunctionCOP

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 inherited from protocols::simple_moves::PackRotamersMover
virtual void	setup (Pose &pose)
	get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...

virtual core::PackerEnergy	run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const

virtual void	note_packertask_settings (Pose const &)
	note PackerTask's packable and designable residues as string info More...

Detailed Description

Definition at line 33 of file PrepackMover.hh.

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::PrepackMover::PrepackMover ( )

Definition at line 76 of file PrepackMover.cc.

Referenced by clone().

protocols::protein_interface_design::movers::PrepackMover::PrepackMover	(	core::scoring::ScoreFunctionCOP	scorefxn,
		core::Size	jump_num
	)

Definition at line 84 of file PrepackMover.cc.

protocols::protein_interface_design::movers::PrepackMover::~PrepackMover ( )

virtual

Definition at line 104 of file PrepackMover.cc.

Member Function Documentation

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

virtual

separate bound partners (if any), minimize, do rotamer trials, and re-minimize.

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 107 of file PrepackMover.cc.

References protocols::simple_moves::RotamerTrialsMinMover::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::simple_moves::MinMover::apply(), core::kinematics::MoveMap::clear(), core::pose::Pose::conformation(), core::conformation::Residue::is_protein(), jump_num_, core::pack::dunbrack::load_unboundrot(), min_bb(), mm(), core::chemical::ResidueType::name(), core::conformation::Conformation::num_chains(), core::pack::task::TaskFactory::push_back(), core::pose::Pose::residue(), scorefxn_, protocols::simple_moves::PackRotamersMover::task(), protocols::simple_moves::PackRotamersMover::task_factory(), core::pose::Pose::total_residue(), protocols::protein_interface_design::movers::TR(), protocols::swa::translate(), and core::conformation::Residue::type().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 95 of file PrepackMover.cc.

References PrepackMover().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 100 of file PrepackMover.cc.

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

virtual

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

Reimplemented from protocols::simple_moves::PackRotamersMover.

Definition at line 202 of file PrepackMover.cc.

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

bool protocols::protein_interface_design::movers::PrepackMover::min_bb ( ) const

Definition at line 228 of file PrepackMover.cc.

References min_bb_.

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

void protocols::protein_interface_design::movers::PrepackMover::min_bb ( bool const m)

Definition at line 223 of file PrepackMover.cc.

References min_bb_.

core::kinematics::MoveMapOP protocols::protein_interface_design::movers::PrepackMover::mm ( ) const

Definition at line 233 of file PrepackMover.cc.

References min_bb(), mm_, and protocols::protein_interface_design::movers::TR().

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

void protocols::protein_interface_design::movers::PrepackMover::mm ( core::kinematics::MoveMapOP mm)

Definition at line 239 of file PrepackMover.cc.

References mm(), and mm_.

void protocols::protein_interface_design::movers::PrepackMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	datamap,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)