#include <DnaInterfacePacker.hh>

Inheritance diagram for protocols::dna::DnaInterfacePacker:

[legend]

Public Types
typedef utility::tag::TagCOP	TagCOP

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

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 std::list< std::string >	Strings

Public Member Functions
	DnaInterfacePacker ()
	lightweight default constructor More...

	DnaInterfacePacker (ScoreFunctionOP, bool minimize=false, std::string const &filename_root="dnapacker")
	functional constructor More...

	~DnaInterfacePacker () override
	destructor 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...

void	apply (Pose &) override
	runs the packer, with support for efficiently looping over multiple explicit DNA sequences (provided that they can be represented by the RotamerSets/InteractionGraph) More...

bool	initialized () const

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

core::Real	unbound_score (Pose const &, bool output_pdb=false, std::string pdbname="")

std::pair< core::Real, core::Real >	measure_specificity (Pose &)
	This method returns the overall bolztmann probabilities for target bound and binding(if enabled) states vs. all single-basepair variant competitors. (For this + specifities for individual basepair positions, use the measure_bp_specificities method instead.) More...

std::pair< SequenceScores, SequenceScores >	measure_bp_specificities (Pose &)
	Measures and calculates bound and binding specificities of the current protein sequence for its target DNA sequence, vs. single-basepair variant competitors. Also returns specificity scores for each individual basepair in a multiple-basepair target region. More...

std::pair< SequenceScores, SequenceScores >	measure_specificities (Pose &, ResTypeSequences const &)
	This requires that all DNA states to be searched are already represented in the rotamer set and interaction graph. More...

void	reversion_scan (Pose &, core::Real bound_score=0., core::Real binding_score=0., std::pair< core::Real, core::Real > specificities=std::make_pair(0., 0.))

void	reference_pose (Pose const &)
	makes hard copy to guarantee that the reference pose isn't changed from elsewhere More...

PoseCOP	reference_pose () const

void	targeted_dna (DnaDesignDefOPs const &)

DnaDesignDefOPs const &	targeted_dna () const

void	pdboutput (PDBOutputOP)

void	set_filename_root (std::string const &name)

std::string	dna_seq_tag (Pose const &, ResTypeSequence const &) const

ResTypeSequence	get_targeted_sequence (Pose const &) const

ResTypeSequence	current_working_sequence (Pose const &) const
	current TOP-STRANDED DNA sequence of the pose, at PackerTask's 'targeted' or 'scan' positions More...

std::string	current_dna_design_string (Pose const &) const

std::string	allowed_types () const

void	clear_initialization ()

std::string	pdbname ()

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 &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

virtual void	parse_score_function (TagCOP, basic::datacache::DataMap const &)
	parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...

virtual void	parse_task_operations (TagCOP, basic::datacache::DataMap 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...

void	set_annealer_observer (core::pack::annealer::AnnealerObserverOP observer)

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 void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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	standard_packing (Pose &)

void	post_packing (Pose &, ResTypeSequence const &, core::Size)

void	protein_scan (Pose &)
	runs a single-residue scan of user-defined amino acid possibilities to estimate affinity and specificity of single mutants w/ respect to relevant DNA More...

void	init_standard (Pose &)
	standard initialization of the necessary member data More...

void	make_dna_sequence_combinations (core::chemical::ResidueTypeSet const &)

void	add_complementary_sequence (ResTypeSequence &, core::chemical::ResidueTypeSet const &)

core::Real	calculate_specificity (Pose const &, ResTypeSequence const &, SequenceScores const &)
	calculates specificity as a Boltzmann probability of the target sequence in the presence of competitors More...

Private Attributes
PoseCOP	reference_pose_

DnaDesignDefOPs	targeted_dna_

DnaChainsOP	dna_chains_

ResTypeSequences	dna_sequences_

bool	minimize_

std::string	filename_root_

bool	binding_E_

bool	probe_specificity_

bool	reversion_scan_

bool	protein_scan_

std::string	allowed_types_

bool	base_only_

bool	include_dna_potentials_in_specificity_calculations_

core::Size	num_repacks_

core::Size	specificity_repacks_

core::optimization::MinimizerOptionsOP	minimize_options_

core::kinematics::MoveMapOP	min_movemap_

PDBOutputOP	pdboutput_

utility::vector1< core::chemical::ResidueTypeCOP >	reference_residue_types_

bool	initialization_state_

std::string	pdbname_

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

◆ ScoreFunctionOP

typedef core::scoring::ScoreFunctionOP protocols::dna::DnaInterfacePacker::ScoreFunctionOP

◆ TagCOP

typedef utility::tag::TagCOP protocols::dna::DnaInterfacePacker::TagCOP

Constructor & Destructor Documentation

◆ DnaInterfacePacker() [1/2]

protocols::dna::DnaInterfacePacker::DnaInterfacePacker ( )

lightweight default constructor

◆ DnaInterfacePacker() [2/2]

protocols::dna::DnaInterfacePacker::DnaInterfacePacker	(	ScoreFunctionOP	scorefxn_in,
		bool	minimize = `false`,
		std::string const &	filename_root = `"dnapacker"`
	)

functional constructor

References allowed_types_, base_only_, binding_E_, include_dna_potentials_in_specificity_calculations_, num_repacks_, probe_specificity_, protein_scan_, reversion_scan_, protocols::minimization_packing::PackRotamersMover::score_function(), and specificity_repacks_.

◆ ~DnaInterfacePacker()

protocols::dna::DnaInterfacePacker::~DnaInterfacePacker ( )

overridedefault

destructor

Member Function Documentation

◆ add_complementary_sequence()

void protocols::dna::DnaInterfacePacker::add_complementary_sequence	(	ResTypeSequence &	sequence,
		core::chemical::ResidueTypeSet const &	typeset
	)

private

turns single-stranded DNA sequences into double-stranded ones

Author: ashworth

References protocols::dna::DnaPosition::bottom(), protocols::dna::dna_base_partner(), dna_chains_, core::chemical::ResidueTypeSet::get_representative_type_aa(), protocols::dna::DnaPosition::paired(), protocols::dna::DnaPosition::top(), and protocols::moves::Mover::type().

Referenced by make_dna_sequence_combinations(), measure_bp_specificities(), and measure_specificity().

◆ allowed_types()

std::string protocols::dna::DnaInterfacePacker::allowed_types ( ) const

References allowed_types_.

Referenced by protein_scan().

◆ apply()

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

overridevirtual

runs the packer, with support for efficiently looping over multiple explicit DNA sequences (provided that they can be represented by the RotamerSets/InteractionGraph)

Author: ashworth

Implements protocols::moves::Mover.

References protocols::moves::Mover::info(), init_standard(), initialized(), protein_scan(), protein_scan_, and standard_packing().

◆ calculate_specificity()

Real protocols::dna::DnaInterfacePacker::calculate_specificity	(	Pose const &	pose,
		ResTypeSequence const &	target_sequence,
		SequenceScores const &	sequence_scores
	)

private

calculates specificity as a Boltzmann probability of the target sequence in the presence of competitors

Author: ashworth

References core::pose::Pose::chain(), protocols::cryst::denom(), protocols::dna::dna_full_name3(), core::pose::Pose::pdb_info(), protocols::dna::PRECISION(), protocols::hybridization::score, and protocols::dna::TR_spec().

Referenced by measure_bp_specificities(), and measure_specificity().

◆ clear_initialization()

void protocols::dna::DnaInterfacePacker::clear_initialization ( )

References initialization_state_.

◆ clone()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

Referenced by measure_specificities(), and unbound_score().

◆ current_dna_design_string()

std::string protocols::dna::DnaInterfacePacker::current_dna_design_string ( Pose const & pose ) const

References current_working_sequence(), and dna_seq_tag().

◆ current_working_sequence()

ResTypeSequence protocols::dna::DnaInterfacePacker::current_working_sequence ( Pose const & pose ) const

current TOP-STRANDED DNA sequence of the pose, at PackerTask's 'targeted' or 'scan' positions

Author: ashworth

References dna_chains_, core::pack::task::ResidueLevelTask::has_behavior(), core::pose::Pose::residue_type_ptr(), and protocols::minimization_packing::PackRotamersMover::task().

Referenced by current_dna_design_string(), measure_bp_specificities(), measure_specificities(), measure_specificity(), post_packing(), and protein_scan().

◆ dna_seq_tag()

std::string protocols::dna::DnaInterfacePacker::dna_seq_tag	(	Pose const &	pose,
		ResTypeSequence const &	sequence
	)		const

similar to basic::dna_seq_str, but returns only top stranded sequence, delimited by "_". (safe for filenames)

Author: ashworth

References core::pose::Pose::chain(), dna_chains_, protocols::dna::dna_full_name3(), and core::pose::Pose::pdb_info().

Referenced by current_dna_design_string(), measure_specificities(), post_packing(), and protein_scan().

◆ fresh_instance()

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

overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_targeted_sequence()

ResTypeSequence protocols::dna::DnaInterfacePacker::get_targeted_sequence ( Pose const & pose ) const

returns DNA sequence that the PackerTask is configured to target (if any)

Author: ashworth

References protocols::dna::DnaPosition::bottom(), dna_chains_, core::sequence::end, core::pack::task::ResidueLevelTask::has_behavior(), protocols::dna::DnaPosition::paired(), core::pose::Pose::residue_type_ptr(), core::pack::task::ResidueLevelTask::target_type(), protocols::minimization_packing::PackRotamersMover::task(), and protocols::dna::DnaPosition::top().

Referenced by init_standard().

◆ init_standard()

void protocols::dna::DnaInterfacePacker::init_standard ( Pose & pose )

private

standard initialization of the necessary member data

Author: ashworth

pose is nonconst because it is so in pack_rotamers::setup()

References base_only_, core::pose::Pose::chain(), dna_chains_, dna_sequences_, core::sequence::end, protocols::dna::find_basepairs(), get_targeted_sequence(), initialization_state_, initialized(), core::chemical::ResidueTypeBase::is_protein(), make_dna_sequence_combinations(), min_movemap_, minimize_, minimize_options_, core::pose::Pose::pdb_info(), pdboutput_, protocols::dna::PRECISION(), protocols::dna::print_sequences_pdb_nums(), reference_pose_, reference_residue_types_, core::pose::Pose::residue_type(), core::pose::Pose::residue_type_ptr(), core::pose::Pose::residue_type_set_for_pose(), protocols::minimization_packing::PackRotamersMover::setup(), core::pose::Pose::size(), targeted_dna_, protocols::minimization_packing::PackRotamersMover::task(), protocols::minimization_packing::PackRotamersMover::task_factory(), and protocols::dna::TR().

Referenced by apply(), and reversion_scan().

◆ initialized()

bool protocols::dna::DnaInterfacePacker::initialized ( ) const

References dna_chains_, initialization_state_, min_movemap_, minimize_, minimize_options_, reference_residue_types_, protocols::minimization_packing::PackRotamersMover::rotamer_sets(), protocols::minimization_packing::PackRotamersMover::score_function(), protocols::minimization_packing::PackRotamersMover::task(), and protocols::minimization_packing::PackRotamersMover::task_factory().

Referenced by apply(), init_standard(), and reversion_scan().

◆ make_dna_sequence_combinations()

void protocols::dna::DnaInterfacePacker::make_dna_sequence_combinations ( core::chemical::ResidueTypeSet const & typeset )

private

looks for rotable DNA positions in the RotamerSets, generates a list of all canonical sequence combinations for them

Author: ashworth

References add_complementary_sequence(), dna_chains_, dna_sequences_, protocols::dna::make_sequence_combinations(), protocols::minimization_packing::PackRotamersMover::rotamer_sets(), and protocols::minimization_packing::PackRotamersMover::task().

Referenced by init_standard().

◆ measure_bp_specificities()

std::pair< SequenceScores, SequenceScores > protocols::dna::DnaInterfacePacker::measure_bp_specificities ( Pose & pose )

Measures and calculates bound and binding specificities of the current protein sequence for its target DNA sequence, vs. single-basepair variant competitors. Also returns specificity scores for each individual basepair in a multiple-basepair target region.

Author: ashworth

References add_complementary_sequence(), core::chemical::ADDUCT_VARIANT, core::pack::task::ResidueLevelTask::allowed_residue_types_begin(), core::pack::task::ResidueLevelTask::allowed_residue_types_end(), binding_E_, calculate_specificity(), current_working_sequence(), core::sequence::end, protocols::moves::Mover::info(), measure_specificities(), protocols::dna::PRECISION(), probe_specificity_, core::pose::Pose::residue_type_set_for_pose(), protocols::dna::seq_pdb_str(), protocols::minimization_packing::PackRotamersMover::task(), protocols::dna::TR(), protocols::dna::TR_spec(), and protocols::moves::Mover::type().

Referenced by post_packing().

◆ measure_specificities()

std::pair< SequenceScores, SequenceScores > protocols::dna::DnaInterfacePacker::measure_specificities	(	Pose &	pose,
		ResTypeSequences const &	dna_sequences
	)

This requires that all DNA states to be searched are already represented in the rotamer set and interaction graph.

Author: ashworth

References binding_E_, clone(), current_working_sequence(), core::scoring::dna_bp, core::scoring::dna_bs, dna_seq_tag(), core::sequence::end, filename_root_, include_dna_potentials_in_specificity_calculations_, min_movemap_, minimize_options_, pdbname(), pdboutput_, core::pose::Pose::residue_type_ptr(), protocols::dna::restrict_to_single_sequence(), protocols::minimization_packing::PackRotamersMover::rotamer_sets(), protocols::minimization_packing::PackRotamersMover::run(), core::optimization::AtomTreeMinimizer::run(), protocols::minimization_packing::PackRotamersMover::score_function(), core::pose::Pose::size(), specificity_repacks_, and unbound_score().

Referenced by measure_bp_specificities(), and measure_specificity().

◆ measure_specificity()

std::pair< Real, Real > protocols::dna::DnaInterfacePacker::measure_specificity ( Pose & pose )

This method returns the overall bolztmann probabilities for target bound and binding(if enabled) states vs. all single-basepair variant competitors. (For this + specifities for individual basepair positions, use the measure_bp_specificities method instead.)

Author: ashworth

References add_complementary_sequence(), binding_E_, calculate_specificity(), current_working_sequence(), protocols::dna::make_single_mutants(), measure_specificities(), probe_specificity_, core::pose::Pose::residue_type_set_for_pose(), protocols::minimization_packing::PackRotamersMover::task(), protocols::dna::TR(), and protocols::dna::TR_spec().

Referenced by protein_scan(), and reversion_scan().

◆ mover_name()

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

static

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

◆ parse_my_tag()

void protocols::dna::DnaInterfacePacker::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References allowed_types_, base_only_, binding_E_, minimize_, protocols::minimization_packing::PackRotamersMover::parse_score_function(), protocols::minimization_packing::PackRotamersMover::parse_task_operations(), pdboutput_, probe_specificity_, protein_scan_, reversion_scan_, and specificity_repacks_.

◆ pdbname()

std::string protocols::dna::DnaInterfacePacker::pdbname ( )

inline

References pdbname_.

Referenced by measure_specificities(), and unbound_score().

◆ pdboutput()

void protocols::dna::DnaInterfacePacker::pdboutput ( PDBOutputOP pdboutput )

References pdboutput_.

◆ post_packing()

void protocols::dna::DnaInterfacePacker::post_packing	(	Pose &	pose,
		ResTypeSequence const &	dnaseq,
		core::Size	trial
	)

private

◆ protein_scan()

void protocols::dna::DnaInterfacePacker::protein_scan ( Pose & pose )

private

runs a single-residue scan of user-defined amino acid possibilities to estimate affinity and specificity of single mutants w/ respect to relevant DNA

Author: ashworth

References core::chemical::aa_from_oneletter_code(), core::pack::task::ResidueLevelTask::allowed_residue_types(), allowed_types(), core::pack::task::ResidueLevelTask::being_packed(), binding_E_, core::pose::Pose::chain(), current_working_sequence(), protocols::dna::dna_full_name3(), dna_seq_tag(), core::sequence::end, protocols::abinitio::filename(), filename_root_, core::chemical::ResidueTypeBase::is_DNA(), measure_specificity(), min_movemap_, minimize_options_, core::chemical::ResidueTypeBase::name3(), num_repacks_, core::pose::Pose::pdb_info(), protocols::dna::PRECISION(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_ptr(), core::pose::Pose::residue_type_set_for_pose(), protocols::dna::restrict_to_single_sequence(), protocols::minimization_packing::PackRotamersMover::rotamer_sets(), protocols::minimization_packing::PackRotamersMover::run(), core::optimization::AtomTreeMinimizer::run(), protocols::hybridization::score, protocols::minimization_packing::PackRotamersMover::score_function(), core::pose::Pose::size(), protocols::frag_picker::quota::ss_index(), protocols::minimization_packing::PackRotamersMover::task(), protocols::dna::TR(), and unbound_score().

Referenced by apply().

◆ provide_xml_schema()

void protocols::dna::DnaInterfacePacker::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), core::pack::task::attributes_for_parse_task_operations(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::dna::DnaInterfacePackerCreator::provide_xml_schema().

◆ reference_pose() [1/2]

PoseCOP protocols::dna::DnaInterfacePacker::reference_pose ( ) const

References reference_pose_.

◆ reference_pose() [2/2]

void protocols::dna::DnaInterfacePacker::reference_pose ( Pose const & pose )

makes hard copy to guarantee that the reference pose isn't changed from elsewhere

References reference_pose_.

◆ reversion_scan()

void protocols::dna::DnaInterfacePacker::reversion_scan	(	Pose &	pose,
		core::Real	bound_score = `0.`,
		core::Real	binding_score = `0.`,
		std::pair< core::Real, core::Real >	specificities = `std::make_pair(0.,0.)`
	)