#include <DesignProteinBackboneAroundDNA.hh>

Inheritance diagram for protocols::dna::DesignProteinBackboneAroundDNA:

Collaboration diagram for protocols::dna::DesignProteinBackboneAroundDNA:

Public Types
typedef loops::Loops	Loops

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

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

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 (TagPtr const, moves::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)

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

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

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

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_

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. 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 36 of file DesignProteinBackboneAroundDNA.hh.

Member Typedef Documentation

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

Definition at line 38 of file DesignProteinBackboneAroundDNA.hh.

Constructor & Destructor Documentation

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

Definition at line 99 of file DesignProteinBackboneAroundDNA.cc.

Referenced by clone(), and fresh_instance().

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

virtual

Definition at line 130 of file DesignProteinBackboneAroundDNA.cc.

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

Definition at line 112 of file DesignProteinBackboneAroundDNA.cc.

References protocols::simple_moves::PackRotamersMover::score_function().

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.

Definition at line 141 of file DesignProteinBackboneAroundDNA.cc.

References backrub(), 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(), protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue_type(), set_loop_info(), spread_, targeted_dna_, protocols::simple_moves::PackRotamersMover::task_factory(), protocols::dna::TR(), and type_.

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

private

Definition at line 313 of file DesignProteinBackboneAroundDNA.cc.

References protocols::backrub::BackrubMover::add_segment(), protocols::backrub::BackrubMover::apply(), core::chemical::ResidueType::atom_index(), 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_, core::sequence::end, protocols::moves::MonteCarlo::last_accepted_pose(), core::scoring::mm_bend, core::pack::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

Definition at line 295 of file DesignProteinBackboneAroundDNA.cc.

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.

Definition at line 263 of file DesignProteinBackboneAroundDNA.cc.

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.

Definition at line 256 of file DesignProteinBackboneAroundDNA.cc.

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.

Definition at line 226 of file DesignProteinBackboneAroundDNA.cc.

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

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