Rosetta 3.4
Public Types | Public Member Functions
protocols::dna::DnaInterfacePacker Class Reference

#include <DnaInterfacePacker.hh>

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List of all members.

Public Types

typedef utility::tag::TagPtr TagPtr
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP

Public Member Functions

 DnaInterfacePacker ()
 lightweight default constructor
 DnaInterfacePacker (ScoreFunctionOP, bool minimize=false, std::string filename_root="dnapacker")
 functional constructor
virtual ~DnaInterfacePacker ()
 destructor
virtual moves::MoverOP fresh_instance () const
 required in the context of the parser/scripting scheme
virtual moves::MoverOP clone () const
 required in the context of the parser/scripting scheme
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
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)
bool initialized () const
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)
core::Real unbound_score (Pose const &, bool output_pdb=false, std::string pdbname="")
std::pair< core::Real, core::Realmeasure_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.)
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.
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.
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
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
std::string current_dna_design_string (Pose const &) const
std::string allowed_types () const
void clear_initialization ()
std::string pdbname ()

Member Typedef Documentation

typedef utility::tag::TagPtr protocols::dna::DnaInterfacePacker::TagPtr

Reimplemented from protocols::moves::Mover.


Constructor & Destructor Documentation

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

lightweight default constructor

Referenced by clone(), and fresh_instance().

protocols::dna::DnaInterfacePacker::DnaInterfacePacker ( ScoreFunctionOP  scorefxn_in,
bool  minimize = false,
std::string  filename_root = "dnapacker" 
)
protocols::dna::DnaInterfacePacker::~DnaInterfacePacker ( ) [virtual]

destructor


Member Function Documentation

std::string protocols::dna::DnaInterfacePacker::allowed_types ( ) const
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(), and initialized().

void protocols::dna::DnaInterfacePacker::clear_initialization ( )
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
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 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(), and measure_specificity().

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

Referenced by current_dna_design_string(), and measure_specificities().

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
bool protocols::dna::DnaInterfacePacker::initialized ( ) const
std::pair< SequenceScores, SequenceScores > protocols::dna::DnaInterfacePacker::measure_bp_specificities ( Pose pose)
std::pair< SequenceScores, SequenceScores > protocols::dna::DnaInterfacePacker::measure_specificities ( Pose pose,
ResTypeSequences const &  dna_sequences 
)
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 current_working_sequence(), core::sequence::end, protocols::dna::make_single_mutants(), measure_specificities(), protocols::simple_moves::PackRotamersMover::task(), protocols::dna::TR(), and protocols::dna::TR_spec().

Referenced by reversion_scan().

void protocols::dna::DnaInterfacePacker::parse_my_tag ( TagPtr const  tag,
moves::DataMap datamap,
protocols::filters::Filters_map const &  filters,
moves::Movers_map const &  movers,
Pose const &  pose 
) [virtual]
std::string protocols::dna::DnaInterfacePacker::pdbname ( ) [inline]

Referenced by measure_specificities().

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

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

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]
void protocols::dna::DnaInterfacePacker::targeted_dna ( DnaDesignDefOPs const &  defs)
DnaDesignDefOPs const & protocols::dna::DnaInterfacePacker::targeted_dna ( ) const
Real protocols::dna::DnaInterfacePacker::unbound_score ( Pose const &  pose,
bool  output_pdb = false,
std::string  pdbname = "" 
)

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