#include <DesignProteinBackboneAroundDNA.hh>

Inheritance diagram for protocols::dna::DesignProteinBackboneAroundDNA:

Public Types
typedef loops::Loops	Loops

Public Types inherited from protocols::minimization_packing::PackRotamersMover
typedef core::pack::interaction_graph::AnnealableGraphBaseOP	AnnealableGraphBaseOP

typedef core::pack::interaction_graph::AnnealableGraphBaseCOP	AnnealableGraphBaseCOP

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 ()

	~DesignProteinBackboneAroundDNA () override

	DesignProteinBackboneAroundDNA (std::string const &, ScoreFunctionCOP)

void	targeted_dna (DnaDesignDefOPs const &)

DnaDesignDefOPs const &	targeted_dna () const

void	apply (Pose &) override
	Main Method. More...

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

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

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

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

Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover
	PackRotamersMover ()
	default constructor; reads the nloop_ value from the global options system. More...

	PackRotamersMover (utility::options::OptionCollection const &options)
	constructor that reads from the (possibly local) options collection object More...

	PackRotamersMover (std::string const &)
	constructor with typename; reads the nloop_ value from the global options system. More...

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

	~PackRotamersMover () override

	PackRotamersMover (PackRotamersMover const &other)

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

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

void	show (std::ostream &output=std::cout) const override
	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...

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

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	initialize_task_factory_with_operations (std::list< core::pack::task::operation::TaskOperationCOP > const &)

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

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

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

virtual 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
	Returns the RotamerSets object being used for packing. More...

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

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...

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...

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...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

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

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

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...

virtual core::Real	last_proposal_density_ratio ()

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	mover_provides_citation_info () const
	Does this mover provide information about how to cite it? More...

virtual utility::vector1 < basic::citation_manager::CitationCollectionCOP >	provide_citation_info () const
	Provide the citation. More...

virtual bool	mover_is_unpublished () const
	Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...

virtual utility::vector1 < basic::citation_manager::UnpublishedModuleInfoCOP >	provide_authorship_info_for_unpublished () const
	Provide a list of authors and their e-mail addresses, as strings. More...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

Static Public Member Functions inherited from protocols::minimization_packing::PackRotamersMover
static std::string	mover_name ()

static utility::tag::XMLSchemaComplexTypeGeneratorOP	complex_type_generator_for_pack_rotamers_mover (utility::tag::XMLSchemaDefinition &xsd)

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static void	list_options_read (utility::options::OptionKeyList &opts)

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...

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
Protected Member Functions inherited from protocols::minimization_packing::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	cleanup (core::pose::Pose &pose)
	Clean up cached pose and mover data after the fact. More...

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 ( )

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

overridedefault

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

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

Member Function Documentation

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References backrub(), ccd(), designable_second_shell_, core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), gapspan_, core::chemical::ResidueTypeBase::is_protein(), protocols::loops::loops_around_residues(), protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue_type(), set_loop_info(), spread_, targeted_dna_, protocols::minimization_packing::PackRotamersMover::task_factory(), protocols::dna::TR(), and type_.

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::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_, 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::minimization_packing::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 clone(), cycles_inner_, cycles_outer_, repack_rate_, protocols::minimization_packing::PackRotamersMover::score_function(), temp_final_, and temp_initial_.

Referenced by apply().

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Referenced by backrub(), and ccd().

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::dna::DesignProteinBackboneAroundDNA::mover_name ( )

static

Referenced by get_name(), protocols::dna::DesignProteinBackboneAroundDNACreator::keyname(), and provide_xml_schema().

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
	)