#include <DnaInterfacePacker.hh>

Public Types
typedef utility::tag::TagCOP	TagCOP

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

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
	DnaInterfacePacker ()
	lightweight default constructor More...

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

virtual	~DnaInterfacePacker ()
	destructor 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...

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

virtual void	apply (Pose &)
	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

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...

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 ()

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	standard_packing (Pose &)

void	post_packing (Pose &, ResTypeSequence const &, Size)
	DnaInterfacePacker::post_packing More...

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 ()

void	add_complementary_sequence (ResTypeSequence &)

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...

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

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

Constructor & Destructor Documentation

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

lightweight default constructor

References option, out, and prefix.

Referenced by clone(), and fresh_instance().

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

functional constructor

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

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

virtual

destructor

Member Function Documentation

void protocols::dna::DnaInterfacePacker::add_complementary_sequence ( ResTypeSequence & sequence )

private

DnaInterfacePacker::add_complementary_sequence

turns single-stranded DNA sequences into double-stranded ones

Authors: ashworth

References protocols::dna::DnaPosition::bottom(), protocols::dna::dna_base_partner(), dna_chains_, end, protocols::dna::DnaPosition::paired(), runtime_assert, protocols::dna::DnaPosition::top(), and protocols::moves::Mover::type().

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

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

References allowed_types_, and protein.

Referenced by protein_scan().

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

virtual

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

DnaInterfacePacker::apply

Author: ashworth

Reimplemented from protocols::simple_moves::PackRotamersMover.

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

Referenced by protocols::motifs::MotifDnaPacker::apply(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::motifs::MotifDnaPacker::expand_motifs(), and protocols::motifs::MotifDnaPacker::run_motifs().

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

DnaInterfacePacker::calculate_specificity

Author: ashworth

References core::pose::Pose::chain(), protocols::dna::dna_full_name3(), option, core::pose::Pose::pdb_info(), protocols::dna::PRECISION, score, sequence, and protocols::dna::TR_spec.

Referenced by measure_bp_specificities(), and measure_specificity().

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

References initialization_state_.

Referenced by protocols::motifs::MotifDnaPacker::apply(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::motifs::MotifDnaPacker::expand_motifs(), and protocols::motifs::MotifDnaPacker::run_motifs().

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

References DnaInterfacePacker().

Referenced by measure_specificities(), and unbound_score().

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

References current_working_sequence(), and dna_seq_tag().

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

current_working_sequence

Author: ashworth

References dna_chains_, core::pack::task::ResidueLevelTask::has_behavior(), core::pose::Pose::residue(), protocols::simple_moves::PackRotamersMover::task(), and core::conformation::Residue::type().

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

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

DnaInterfacePacker::dna_seq_tag

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

Authors: ashworth

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

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

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

virtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::simple_moves::PackRotamersMover.

References DnaInterfacePacker().

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

virtual

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

Reimplemented from protocols::simple_moves::PackRotamersMover.

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

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

DnaInterfacePacker::get_targeted_sequence()

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

Authors: ashworth

References protocols::dna::DnaPosition::bottom(), dna_chains_, end, protocols::dna::DnaPosition::paired(), core::pose::Pose::residue_type(), runtime_assert, sequence, protocols::simple_moves::PackRotamersMover::task(), and protocols::dna::DnaPosition::top().

Referenced by init_standard().

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

private

standard initialization of the necessary member data

DnaInterfacePacker::init_standard

Author: ashworth

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

References base_only_, core::pose::Pose::chain(), dna_chains_, dna_sequences_, end, protocols::dna::find_basepairs(), get_targeted_sequence(), initialization_state_, initialized(), core::chemical::ResidueType::is_protein(), make_dna_sequence_combinations(), min_movemap_, min_type, minimize_, minimize_options_, option, core::pose::Pose::pdb_info(), pdboutput_, protocols::dna::PRECISION, protocols::dna::print_sequences_pdb_nums(), core::pack::task::TaskFactory::push_back(), reference_pose_, reference_residue_types_, core::pose::Pose::residue_type(), runtime_assert, core::kinematics::MoveMap::set_chi(), protocols::simple_moves::PackRotamersMover::setup(), targeted_dna_, protocols::simple_moves::PackRotamersMover::task(), protocols::simple_moves::PackRotamersMover::task_factory(), tolerance, core::pose::Pose::total_residue(), protocols::dna::TR, and user.

Referenced by apply(), and reversion_scan().

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

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

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

void protocols::dna::DnaInterfacePacker::make_dna_sequence_combinations ( )

private

DnaInterfacePacker::make_dna_sequence_combinations

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

Authors: ashworth

References add_complementary_sequence(), dna_chains_, dna_sequences_, end, protocols::dna::make_sequence_combinations(), protocols::simple_moves::PackRotamersMover::rotamer_sets(), runtime_assert, sequence, and protocols::simple_moves::PackRotamersMover::task().

Referenced by init_standard().

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.

DnaInterfacePacker::measure_bp_specificities

Author: ashworth

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

Referenced by post_packing().

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.

DnaInterfacePacker::measure_specificities

Author: ashworth

References binding_E_, clone(), current_working_sequence(), dna_bp, dna_bs, dna_seq_tag(), end, filename_root_, include_dna_potentials_in_specificity_calculations_, min_movemap_, minimize_options_, option, pdbname(), pdboutput_, core::pose::Pose::residue_type(), protocols::dna::restrict_to_single_sequence(), protocols::simple_moves::PackRotamersMover::rotamer_sets(), protocols::simple_moves::PackRotamersMover::run(), protocols::simple_moves::PackRotamersMover::score_function(), specificity_repacks_, core::pose::Pose::total_residue(), and unbound_score().

Referenced by measure_bp_specificities(), and 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.)

DnaInterfacePacker::measure_specificity

Author: ashworth

References add_complementary_sequence(), binding_E_, calculate_specificity(), current_working_sequence(), end, protocols::dna::make_single_mutants(), measure_specificities(), probe_specificity_, sequence, protocols::simple_moves::PackRotamersMover::task(), protocols::dna::TR, and protocols::dna::TR_spec.

Referenced by protein_scan(), and reversion_scan().

void protocols::dna::DnaInterfacePacker::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 allowed_types_, base_only_, binding_E_, minimize_, protocols::simple_moves::PackRotamersMover::parse_score_function(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), pdboutput_, probe_specificity_, protein_scan_, reversion_scan_, runtime_assert, and specificity_repacks_.

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

inline

References pdbname_.

Referenced by protocols::motifs::MotifDnaPacker::apply(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::motifs::MotifDnaPacker::expand_motifs(), measure_specificities(), and protocols::motifs::MotifDnaPacker::run_motifs().

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

References pdboutput_.

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

private

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

DnaInterfacePacker::protein_scan

Author: ashworth

References 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(), utility::io::izstream::close(), current_working_sequence(), protocols::dna::dna_full_name3(), dna_seq_tag(), end, file, filename(), filename_root_, utility::io::izstream::getline(), core::chemical::ResidueType::is_DNA(), measure_specificity(), min_movemap_, minimize_options_, core::chemical::ResidueType::name3(), num_repacks_, utility::io::izstream::open(), option, core::pose::Pose::pdb_info(), protocols::dna::PRECISION, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::conformation::Residue::residue_type_set(), protocols::dna::restrict_to_single_sequence(), protocols::simple_moves::PackRotamersMover::rotamer_sets(), protocols::simple_moves::PackRotamersMover::run(), runtime_assert, score, protocols::simple_moves::PackRotamersMover::score_function(), protocols::frag_picker::quota::ss_index(), string_split(), t_warning, protocols::simple_moves::PackRotamersMover::task(), core::pose::Pose::total_residue(), protocols::dna::TR, unbound_score(), and user.

Referenced by apply().

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_.

Referenced by protocols::motifs::MotifDnaPacker::init_standard().

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

References reference_pose_.

void protocols::dna::DnaInterfacePacker::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 protocols::dna::DnaInterfacePacker::set_filename_root ( std::string const & name )

inline

References filename_root_, and protocols::moves::Mover::name().

Referenced by protocols::motifs::MotifDnaPacker::apply(), protocols::motifs::MotifDnaPacker::aromatic_motifs(), protocols::motifs::MotifDnaPacker::expand_motifs(), and protocols::motifs::MotifDnaPacker::run_motifs().

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

private

References dna_sequences_, end, num_repacks_, post_packing(), protocols::dna::print_sequence_pdb_nums(), protocols::dna::restrict_dna_rotamers(), protocols::simple_moves::PackRotamersMover::rotamer_sets(), protocols::simple_moves::PackRotamersMover::run(), and protocols::dna::TR.

Referenced by apply().

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

References targeted_dna_.

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

References targeted_dna_.

Real protocols::dna::DnaInterfacePacker::unbound_score	(	Pose const &	pose,
		bool	output_pdb = `false`,
		std::string	pdbname = `""`
	)

DnaInterfacePacker::unbound_score

Author: ashworth

References protocols::dna::SeparateDnaFromNonDna::apply(), atom_pair_constraint, clone(), pdboutput_, runtime_assert, and protocols::simple_moves::PackRotamersMover::score_function().

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

Member Data Documentation

std::string protocols::dna::DnaInterfacePacker::allowed_types_

private

Referenced by allowed_types(), DnaInterfacePacker(), and parse_my_tag().

bool protocols::dna::DnaInterfacePacker::base_only_

private

Referenced by DnaInterfacePacker(), init_standard(), and parse_my_tag().

bool protocols::dna::DnaInterfacePacker::binding_E_

private

Referenced by DnaInterfacePacker(), measure_bp_specificities(), measure_specificities(), measure_specificity(), parse_my_tag(), post_packing(), protein_scan(), and reversion_scan().

DnaChainsOP protocols::dna::DnaInterfacePacker::dna_chains_

private

Referenced by add_complementary_sequence(), current_working_sequence(), dna_seq_tag(), get_targeted_sequence(), init_standard(), initialized(), and make_dna_sequence_combinations().

ResTypeSequences protocols::dna::DnaInterfacePacker::dna_sequences_

private

Referenced by init_standard(), make_dna_sequence_combinations(), and standard_packing().

std::string protocols::dna::DnaInterfacePacker::filename_root_

private

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

bool protocols::dna::DnaInterfacePacker::include_dna_potentials_in_specificity_calculations_

private

Referenced by DnaInterfacePacker(), and measure_specificities().

bool protocols::dna::DnaInterfacePacker::initialization_state_

private

Referenced by clear_initialization(), init_standard(), and initialized().

core::kinematics::MoveMapOP protocols::dna::DnaInterfacePacker::min_movemap_

private

Referenced by init_standard(), initialized(), measure_specificities(), post_packing(), protein_scan(), and reversion_scan().

bool protocols::dna::DnaInterfacePacker::minimize_

private

Referenced by init_standard(), initialized(), and parse_my_tag().

core::optimization::MinimizerOptionsOP protocols::dna::DnaInterfacePacker::minimize_options_

private

Referenced by init_standard(), initialized(), measure_specificities(), post_packing(), protein_scan(), and reversion_scan().

core::Size protocols::dna::DnaInterfacePacker::num_repacks_

private

Referenced by DnaInterfacePacker(), protein_scan(), reversion_scan(), and standard_packing().

std::string protocols::dna::DnaInterfacePacker::pdbname_

private

Referenced by pdbname(), and post_packing().

PDBOutputOP protocols::dna::DnaInterfacePacker::pdboutput_

private

Referenced by init_standard(), measure_specificities(), parse_my_tag(), pdboutput(), post_packing(), and unbound_score().

bool protocols::dna::DnaInterfacePacker::probe_specificity_

private

Referenced by DnaInterfacePacker(), measure_bp_specificities(), measure_specificity(), parse_my_tag(), and post_packing().

bool protocols::dna::DnaInterfacePacker::protein_scan_

private

Referenced by apply(), DnaInterfacePacker(), and parse_my_tag().

PoseCOP protocols::dna::DnaInterfacePacker::reference_pose_

private

Referenced by init_standard(), and reference_pose().

utility::vector1< core::chemical::ResidueTypeCOP > protocols::dna::DnaInterfacePacker::reference_residue_types_

private

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

bool protocols::dna::DnaInterfacePacker::reversion_scan_

private

Referenced by DnaInterfacePacker(), parse_my_tag(), and post_packing().

core::Size protocols::dna::DnaInterfacePacker::specificity_repacks_

private

Referenced by DnaInterfacePacker(), measure_specificities(), and parse_my_tag().

DnaDesignDefOPs protocols::dna::DnaInterfacePacker::targeted_dna_

private

Referenced by init_standard(), and targeted_dna().

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

src/protocols/dna/DnaInterfacePacker.hh
src/protocols/dna/DnaInterfacePacker.cc

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_

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