#include <StepWiseProteinPacker.hh>

Public Member Functions
	StepWiseProteinPacker (utility::vector1< Size > const &moving_residues)

	~StepWiseProteinPacker ()

virtual void	apply (pose::Pose &pose)
	Apply the minimizer to one pose. More...

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

void	initialize (pose::Pose &pose)

void	set_scorefxn (scoring::ScoreFunctionOP const &scorefxn)

void	set_use_green_packer (bool const &setting)

void	set_use_packer_instead_of_rotamer_trials (bool const &setting)

void	set_rescore_only (bool const &setting)

void	do_prepack (pose::Pose &pose)

void	set_moving_res_list (utility::vector1< Size > const &setting)

void	set_allow_virtual_side_chains (bool const &setting)

bool	allow_virtual_side_chains () 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	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 MoverOP	clone () const
	Return a clone of the Mover object. More...

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

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Private Member Functions
void	initialize_moving_residues_including_junction (Size const &nres)

void	initialize_green_packer (Size const &nres)

void	initialize_for_regular_packer (pose::Pose const &pose)

void	figure_out_neighbors (pose::Pose &pose, utility::vector1< bool > &residues_allowed_to_be_packed)

void	reinstate_side_chain_angles (pose::Pose &pose, pose::Pose const &src_pose)

void	apply_regular_packer (pose::Pose &pose, bool const pack_at_neighbors_only)

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...

Constructor & Destructor Documentation

protocols::stepwise::sampling::protein::StepWiseProteinPacker::StepWiseProteinPacker ( utility::vector1< Size > const & moving_residues )

protocols::stepwise::sampling::protein::StepWiseProteinPacker::~StepWiseProteinPacker ( )

Member Function Documentation

bool protocols::stepwise::sampling::protein::StepWiseProteinPacker::allow_virtual_side_chains ( ) const

inline

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::apply ( pose::Pose & pose )

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References apply_regular_packer(), green_packer_, core::pose::Pose::is_fullatom(), pack_at_neighbors_only_, rescore_only_, and use_green_packer_.

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::apply_regular_packer	(	pose::Pose &	pose,
		bool const	pack_at_neighbors_only
	)

private

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::do_prepack ( pose::Pose & pose )

References apply_regular_packer(), copy_dofs_match_atom_names(), initialize_for_regular_packer(), protocols::stepwise::make_variants_match(), moving_res_list_, core::pose::Pose::remove_constraints(), protocols::stepwise::split_pose(), and core::pose::Pose::total_residue().

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::figure_out_neighbors	(	pose::Pose &	pose,
		utility::vector1< bool > &	residues_allowed_to_be_packed
	)

private

References core::graph::Node::const_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), core::graph::Edge::get_node(), j, and moving_residues_.

Referenced by apply_regular_packer().

std::string protocols::stepwise::sampling::protein::StepWiseProteinPacker::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::initialize ( pose::Pose & pose )

References initialize_for_regular_packer(), initialize_green_packer(), core::pose::Pose::is_fullatom(), core::pose::Pose::total_residue(), and use_green_packer_.

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::initialize_for_regular_packer ( pose::Pose const & pose )

private

Referenced by do_prepack(), and initialize().

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::initialize_green_packer ( Size const & nres )

private

References green_packer_, moving_residues_, core::pack::task::TaskFactory::push_back(), scorefxn_, and protocols::TR.

Referenced by initialize().

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::initialize_moving_residues_including_junction ( Size const & nres )

private

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::reinstate_side_chain_angles	(	pose::Pose &	pose,
		pose::Pose const &	src_pose
	)

private

References core::pose::Pose::chi(), protocols::stepwise::make_variants_match(), core::chemical::ResidueType::nchi(), core::pose::Pose::residue_type(), core::pose::Pose::set_chi(), and core::pose::Pose::total_residue().

Referenced by apply_regular_packer().

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::set_allow_virtual_side_chains ( bool const & setting )

inline

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::set_moving_res_list ( utility::vector1< Size > const & setting )

inline

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::set_rescore_only ( bool const & setting )

inline

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::set_scorefxn ( scoring::ScoreFunctionOP const & scorefxn )

References scorefxn_.

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::set_use_green_packer ( bool const & setting )

References use_green_packer_.

void protocols::stepwise::sampling::protein::StepWiseProteinPacker::set_use_packer_instead_of_rotamer_trials ( bool const & setting )

References use_packer_instead_of_rotamer_trials_.

Member Data Documentation

bool protocols::stepwise::sampling::protein::StepWiseProteinPacker::allow_virtual_side_chains_

private

Referenced by initialize_for_regular_packer().

protocols::simple_moves::GreenPackerOP protocols::stepwise::sampling::protein::StepWiseProteinPacker::green_packer_

private

Referenced by apply(), and initialize_green_packer().

utility::vector1< Size > protocols::stepwise::sampling::protein::StepWiseProteinPacker::moving_res_list_

private

Referenced by do_prepack().

utility::vector1< Size > const protocols::stepwise::sampling::protein::StepWiseProteinPacker::moving_residues_

private

Referenced by figure_out_neighbors(), and initialize_green_packer().

bool protocols::stepwise::sampling::protein::StepWiseProteinPacker::pack_at_neighbors_only_

private

Referenced by apply().

pack::task::PackerTaskOP protocols::stepwise::sampling::protein::StepWiseProteinPacker::pack_task_

private

Referenced by apply_regular_packer(), and initialize_for_regular_packer().

pose::PoseOP protocols::stepwise::sampling::protein::StepWiseProteinPacker::pose_init_

private

Referenced by apply_regular_packer(), and initialize_for_regular_packer().

bool protocols::stepwise::sampling::protein::StepWiseProteinPacker::rescore_only_

private

Referenced by apply().

scoring::ScoreFunctionOP protocols::stepwise::sampling::protein::StepWiseProteinPacker::scorefxn_

private

Referenced by apply_regular_packer(), initialize_green_packer(), and set_scorefxn().

bool protocols::stepwise::sampling::protein::StepWiseProteinPacker::use_green_packer_

private

Referenced by apply(), initialize(), and set_use_green_packer().

bool protocols::stepwise::sampling::protein::StepWiseProteinPacker::use_packer_instead_of_rotamer_trials_

private

Referenced by apply_regular_packer(), and set_use_packer_instead_of_rotamer_trials().

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

symlinks/rosetta/src/protocols/stepwise/sampling/protein/StepWiseProteinPacker.hh
symlinks/rosetta/src/protocols/stepwise/sampling/protein/StepWiseProteinPacker.cc

Private Attributes
utility::vector1< Size > const	moving_residues_

scoring::ScoreFunctionOP	scorefxn_

protocols::simple_moves::GreenPackerOP	green_packer_

bool	use_green_packer_

bool	use_packer_instead_of_rotamer_trials_

bool	pack_at_neighbors_only_

bool	allow_virtual_side_chains_

bool	rescore_only_

pack::task::PackerTaskOP	pack_task_

pose::PoseOP	pose_init_

utility::vector1< Size >	moving_res_list_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation