#include <DesignProteinBackboneAroundDNA.hh>

Public Types
typedef loops::Loops	Loops

Public Types inherited from protocols::simple_moves::PackRotamersMover
typedef core::pack::interaction_graph::InteractionGraphBaseOP	InteractionGraphBaseOP

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

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

Public Member Functions
	DesignProteinBackboneAroundDNA ()

virtual	~DesignProteinBackboneAroundDNA ()

	DesignProteinBackboneAroundDNA (std::string const &, ScoreFunctionCOP)

void	targeted_dna (DnaDesignDefOPs const &)

DnaDesignDefOPs const &	targeted_dna () const

virtual void	apply (Pose &)
	Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...

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

virtual void	parse_my_tag (TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, moves::Movers_map const &, Pose const &)
	parse XML (specifically in the context of the parser/scripting scheme) More...

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

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

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)

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

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 (TagCOP, basic::datacache::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 (TagCOP, basic::datacache::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

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

Private Member Functions
void	set_loop_info (Pose const &, Loops const &)

void	ccd (Pose &, loops::LoopsOP const, TaskFactoryCOP)

void	backrub (Pose &, loops::LoopsOP const, TaskFactoryCOP)

Additional Inherited Members
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::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...

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...

Member Typedef Documentation

typedef loops::Loops protocols::dna::DesignProteinBackboneAroundDNA::Loops

Constructor & Destructor Documentation

protocols::dna::DesignProteinBackboneAroundDNA::DesignProteinBackboneAroundDNA ( )

References cycles_inner, cycles_outer, design, designable_second_shell, dna, gapspan, loops, option, repack_rate, run, spread, temp_final, and temp_initial.

Referenced by clone(), and fresh_instance().

protocols::dna::DesignProteinBackboneAroundDNA::~DesignProteinBackboneAroundDNA ( )

virtual

protocols::dna::DesignProteinBackboneAroundDNA::DesignProteinBackboneAroundDNA	(	std::string const &	type,
		ScoreFunctionCOP	scorefxn
	)

References cycles_inner, cycles_outer, design, designable_second_shell, dna, gapspan, loops, option, repack_rate, run, protocols::simple_moves::PackRotamersMover::score_function(), spread, temp_final, and temp_initial.

Member Function Documentation

void protocols::dna::DesignProteinBackboneAroundDNA::apply ( Pose & pose )

virtual

Performs side-chain packing based on the input PackerTask using the input ScoreFunction.

example(s): packmover.apply(pose) See Also: PackerTask ScoreFunction

Reimplemented from protocols::simple_moves::PackRotamersMover.

References backrub(), core::pack::task::PackerTask::being_designed(), core::pack::task::PackerTask::being_packed(), ccd(), designable_second_shell_, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), gapspan_, core::chemical::ResidueType::is_protein(), protocols::loops::loops_around_residues(), option, core::pack::task::TaskFactory::push_back(), protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue_type(), set_loop_info(), protocols::loops::Loops::size(), spread_, t_debug, targeted_dna_, protocols::simple_moves::PackRotamersMover::task_factory(), core::pack::task::PackerTask::total_residue(), protocols::dna::TR, type_, and user.

void protocols::dna::DesignProteinBackboneAroundDNA::backrub	(	Pose &	pose,
		loops::LoopsOP const	loops,
		TaskFactoryCOP	task_factory2
	)

private

References protocols::backrub::BackrubMover::add_segment(), protocols::backrub::BackrubMover::apply(), core::chemical::ResidueType::atom_index(), protocols::loops::Loops::begin(), protocols::moves::MonteCarlo::boltzmann(), core::scoring::methods::EnergyMethodOptions::bond_angle_central_atoms_to_score(), protocols::backrub::BackrubMover::branchopt(), protocols::backrub::BackrubMover::clear_segments(), clone(), cycles_inner_, cycles_outer_, end, protocols::loops::Loops::end(), protocols::moves::MonteCarlo::last_accepted_pose(), mc, mm_bend, option, pack_rotamers(), protocols::branch_angle::BranchAngleOptimizer::read_database(), repack_rate_, core::pose::Pose::residue_type(), protocols::simple_moves::PackRotamersMover::score_function(), protocols::moves::Mover::set_input_pose(), protocols::moves::MonteCarlo::show_counters(), protocols::loops::start, protocols::loops::stop, temp_final_, and temp_initial_.

Referenced by apply().

void protocols::dna::DesignProteinBackboneAroundDNA::ccd	(	Pose &	pose,
		loops::LoopsOP const	loops,
		TaskFactoryCOP	task_factory2
	)

private

References protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), clone(), cycles_inner_, cycles_outer_, protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::max_inner_cycles(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::outer_cycles(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::repack_period(), repack_rate_, protocols::simple_moves::PackRotamersMover::score_function(), protocols::moves::Mover::set_native_pose(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final(), temp_final_, protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial(), and temp_initial_.

Referenced by apply().

moves::MoverOP protocols::dna::DesignProteinBackboneAroundDNA::clone ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

References DesignProteinBackboneAroundDNA().

Referenced by backrub(), and ccd().

moves::MoverOP protocols::dna::DesignProteinBackboneAroundDNA::fresh_instance ( ) const

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

References DesignProteinBackboneAroundDNA().

std::string protocols::dna::DesignProteinBackboneAroundDNA::get_name ( ) const

virtual

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

Reimplemented from protocols::simple_moves::PackRotamersMover.

References protocols::dna::DesignProteinBackboneAroundDNACreator::mover_name().

void protocols::dna::DesignProteinBackboneAroundDNA::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap,
		protocols::filters::Filters_map const &	filters,
		moves::Movers_map const &	movers,
		Pose const &	pose
	)

virtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::simple_moves::PackRotamersMover.

References cycles_inner_, cycles_outer_, designable_second_shell_, gapspan_, protocols::simple_moves::PackRotamersMover::parse_score_function(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), repack_rate_, spread_, temp_final_, temp_initial_, and type_.

void protocols::dna::DesignProteinBackboneAroundDNA::set_loop_info	(	Pose const &	pose,
		Loops const &	loops
	)

private

References protocols::loops::Loops::begin(), core::pose::Pose::chain(), end, protocols::loops::Loops::end(), protocols::moves::Mover::info(), core::pose::Pose::pdb_info(), protocols::loops::start, and protocols::loops::stop.

Referenced by apply().

void protocols::dna::DesignProteinBackboneAroundDNA::targeted_dna ( DnaDesignDefOPs const & defs )

References targeted_dna_.

DnaDesignDefOPs const & protocols::dna::DesignProteinBackboneAroundDNA::targeted_dna ( ) const

References targeted_dna_.

Member Data Documentation

core::Size protocols::dna::DesignProteinBackboneAroundDNA::cycles_inner_

private

Referenced by backrub(), ccd(), and parse_my_tag().

core::Size protocols::dna::DesignProteinBackboneAroundDNA::cycles_outer_

private

Referenced by backrub(), ccd(), and parse_my_tag().

bool protocols::dna::DesignProteinBackboneAroundDNA::designable_second_shell_

private

Referenced by apply(), and parse_my_tag().

core::Size protocols::dna::DesignProteinBackboneAroundDNA::gapspan_

private

Referenced by apply(), and parse_my_tag().

core::Size protocols::dna::DesignProteinBackboneAroundDNA::repack_rate_

private

Referenced by backrub(), ccd(), and parse_my_tag().

core::Size protocols::dna::DesignProteinBackboneAroundDNA::spread_

private

Referenced by apply(), and parse_my_tag().

DnaDesignDefOPs protocols::dna::DesignProteinBackboneAroundDNA::targeted_dna_

private

Referenced by apply(), and targeted_dna().

core::Real protocols::dna::DesignProteinBackboneAroundDNA::temp_final_

private

Referenced by backrub(), ccd(), and parse_my_tag().

core::Real protocols::dna::DesignProteinBackboneAroundDNA::temp_initial_

private

Referenced by backrub(), ccd(), and parse_my_tag().

std::string protocols::dna::DesignProteinBackboneAroundDNA::type_

private

Referenced by apply(), and parse_my_tag().

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

src/protocols/dna/DesignProteinBackboneAroundDNA.hh
src/protocols/dna/DesignProteinBackboneAroundDNA.cc

Private Attributes
std::string	type_

DnaDesignDefOPs	targeted_dna_

core::Size	gapspan_

core::Size	spread_

core::Size	cycles_outer_

core::Size	cycles_inner_

core::Size	repack_rate_

core::Real	temp_initial_

core::Real	temp_final_

bool	designable_second_shell_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation