#include <StepWiseProteinPacker.hh>

Inheritance diagram for protocols::swa::protein::StepWiseProteinPacker:

Collaboration diagram for protocols::swa::protein::StepWiseProteinPacker:

Public Member Functions
	StepWiseProteinPacker (utility::vector1< Size > const &moving_residues, protocols::swa::StepWisePoseSampleGeneratorOP sample_generator)

	~StepWiseProteinPacker ()

virtual void	apply (core::pose::Pose &pose_to_visualize)
	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	set_silent_file (std::string const &setting)

void	set_scorefxn (core::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	set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)

core::io::silent::SilentFileDataOP &	silent_file_data ()

void	set_pose_filter (protocols::swa::PoseFilterOP pose_filter)

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
	clone has to be overridden only if clone invocation is expected. More...

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

Private Member Functions
void	sample_residues (core::pose::Pose &pose)

void	print_tag (std::string const &tag, Size const k)

void	initialize_moving_residues_including_junction (Size const &nres)

void	initialize_green_packer (core::Size const &nres)

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

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

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

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

Additional Inherited Members
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

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::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...

Detailed Description

Definition at line 41 of file StepWiseProteinPacker.hh.

Constructor & Destructor Documentation

protocols::swa::protein::StepWiseProteinPacker::StepWiseProteinPacker	(	utility::vector1< Size > const &	moving_residues,
		protocols::swa::StepWisePoseSampleGeneratorOP	sample_generator
	)

Definition at line 94 of file StepWiseProteinPacker.cc.

protocols::swa::protein::StepWiseProteinPacker::~StepWiseProteinPacker ( )

Definition at line 112 of file StepWiseProteinPacker.cc.

Member Function Documentation

void protocols::swa::protein::StepWiseProteinPacker::apply ( core::pose::Pose & pose_to_visualize)

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 124 of file StepWiseProteinPacker.cc.

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

void protocols::swa::protein::StepWiseProteinPacker::apply_regular_packer ( core::pose::Pose & pose)

private

Definition at line 333 of file StepWiseProteinPacker.cc.

References figure_out_neighbors(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), pack_at_neighbors_only_, core::pack::pack_rotamers(), pack_task_, pose_init_, reinstate_side_chain_angles(), core::pose::Pose::residue(), core::pack::rotamer_trials(), scorefxn_, core::pose::Pose::total_residue(), and use_packer_instead_of_rotamer_trials_.

Referenced by sample_residues().

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

private

Definition at line 297 of file StepWiseProteinPacker.cc.

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

Referenced by apply_regular_packer().

std::string protocols::swa::protein::StepWiseProteinPacker::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 116 of file StepWiseProteinPacker.cc.

void protocols::swa::protein::StepWiseProteinPacker::initialize_for_regular_packer ( core::pose::Pose & pose)

private

Definition at line 263 of file StepWiseProteinPacker.cc.

References core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), pack_task_, pose_init_, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::swa::protein::StepWiseProteinPacker::initialize_green_packer ( core::Size const & nres)

private

Definition at line 212 of file StepWiseProteinPacker.cc.

References green_packer_, moving_residues_, scorefxn_, and protocols::TR().

Referenced by apply().

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

private

void protocols::swa::protein::StepWiseProteinPacker::print_tag	(	std::string const &	tag,
		Size const	k
	)

private

Definition at line 201 of file StepWiseProteinPacker.cc.

References sample_generator_, and use_packer_instead_of_rotamer_trials_.

Referenced by sample_residues().

void protocols::swa::protein::StepWiseProteinPacker::reinstate_side_chain_angles	(	core::pose::Pose &	pose,
		core::pose::Pose const &	src_pose
	)

private

Definition at line 323 of file StepWiseProteinPacker.cc.

References core::pose::Pose::chi(), 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::swa::protein::StepWiseProteinPacker::sample_residues ( core::pose::Pose & pose)

private

Definition at line 149 of file StepWiseProteinPacker.cc.

References apply_regular_packer(), calc_rms_res_, protocols::moves::Mover::get_native_pose(), green_packer_, core::pose::Pose::is_fullatom(), protocols::swa::protein::output_silent_struct(), pose_filter_, print_tag(), rescore_only_, sample_generator_, sfd_, silent_file_, protocols::TR(), and use_green_packer_.

Referenced by apply().

void protocols::swa::protein::StepWiseProteinPacker::set_calc_rms_res ( utility::vector1< core::Size > const & calc_rms_res)

Definition at line 418 of file StepWiseProteinPacker.cc.

References calc_rms_res_.

void protocols::swa::protein::StepWiseProteinPacker::set_pose_filter ( protocols::swa::PoseFilterOP pose_filter)

Definition at line 424 of file StepWiseProteinPacker.cc.

References pose_filter_.

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

inline

Definition at line 71 of file StepWiseProteinPacker.hh.

References rescore_only_.

void protocols::swa::protein::StepWiseProteinPacker::set_scorefxn ( core::scoring::ScoreFunctionOP const & scorefxn)

Definition at line 394 of file StepWiseProteinPacker.cc.

References scorefxn_.

void protocols::swa::protein::StepWiseProteinPacker::set_silent_file ( std::string const & setting)

Definition at line 388 of file StepWiseProteinPacker.cc.

References silent_file_.

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

Definition at line 400 of file StepWiseProteinPacker.cc.

References use_green_packer_.

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

Definition at line 406 of file StepWiseProteinPacker.cc.

References use_packer_instead_of_rotamer_trials_.

core::io::silent::SilentFileDataOP & protocols::swa::protein::StepWiseProteinPacker::silent_file_data ( )

Definition at line 412 of file StepWiseProteinPacker.cc.

References sfd_.

Member Data Documentation

utility::vector1< core::Size > protocols::swa::protein::StepWiseProteinPacker::calc_rms_res_

private

Definition at line 126 of file StepWiseProteinPacker.hh.

Referenced by sample_residues(), and set_calc_rms_res().

protocols::simple_moves::GreenPackerOP protocols::swa::protein::StepWiseProteinPacker::green_packer_

private

Definition at line 114 of file StepWiseProteinPacker.hh.

Referenced by initialize_green_packer(), and sample_residues().

utility::vector1< Size > const protocols::swa::protein::StepWiseProteinPacker::moving_residues_

private

Definition at line 111 of file StepWiseProteinPacker.hh.

Referenced by figure_out_neighbors(), and initialize_green_packer().

bool protocols::swa::protein::StepWiseProteinPacker::pack_at_neighbors_only_

private

Definition at line 117 of file StepWiseProteinPacker.hh.

Referenced by apply_regular_packer().

core::pack::task::PackerTaskOP protocols::swa::protein::StepWiseProteinPacker::pack_task_

private

Definition at line 119 of file StepWiseProteinPacker.hh.

Referenced by apply_regular_packer(), and initialize_for_regular_packer().

protocols::swa::PoseFilterOP protocols::swa::protein::StepWiseProteinPacker::pose_filter_

private

Definition at line 130 of file StepWiseProteinPacker.hh.

Referenced by sample_residues(), and set_pose_filter().

core::pose::PoseOP protocols::swa::protein::StepWiseProteinPacker::pose_init_

private

Definition at line 120 of file StepWiseProteinPacker.hh.

Referenced by apply_regular_packer(), and initialize_for_regular_packer().

bool protocols::swa::protein::StepWiseProteinPacker::rescore_only_

private

Definition at line 118 of file StepWiseProteinPacker.hh.

Referenced by sample_residues(), and set_rescore_only().

protocols::swa::StepWisePoseSampleGeneratorOP protocols::swa::protein::StepWiseProteinPacker::sample_generator_

private

Definition at line 128 of file StepWiseProteinPacker.hh.

Referenced by print_tag(), and sample_residues().

core::scoring::ScoreFunctionOP protocols::swa::protein::StepWiseProteinPacker::scorefxn_

private

Definition at line 113 of file StepWiseProteinPacker.hh.

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

core::io::silent::SilentFileDataOP protocols::swa::protein::StepWiseProteinPacker::sfd_

private

Definition at line 124 of file StepWiseProteinPacker.hh.

Referenced by sample_residues(), and silent_file_data().

std::string protocols::swa::protein::StepWiseProteinPacker::silent_file_

private

Definition at line 122 of file StepWiseProteinPacker.hh.

Referenced by sample_residues(), and set_silent_file().

bool protocols::swa::protein::StepWiseProteinPacker::use_green_packer_

private

Definition at line 115 of file StepWiseProteinPacker.hh.

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

bool protocols::swa::protein::StepWiseProteinPacker::use_packer_instead_of_rotamer_trials_

private

Definition at line 116 of file StepWiseProteinPacker.hh.

Referenced by apply_regular_packer(), print_tag(), and set_use_packer_instead_of_rotamer_trials().

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

src/protocols/swa/protein/StepWiseProteinPacker.hh
src/protocols/swa/protein/StepWiseProteinPacker.cc

Private Attributes
utility::vector1< Size > const	moving_residues_

core::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	rescore_only_

core::pack::task::PackerTaskOP	pack_task_

core::pose::PoseOP	pose_init_

std::string	silent_file_

core::io::silent::SilentFileDataOP	sfd_

utility::vector1< core::Size >	calc_rms_res_

protocols::swa::StepWisePoseSampleGeneratorOP	sample_generator_

protocols::swa::PoseFilterOP	pose_filter_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation