Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::dna::DnaInterfacePacker Class Reference

#include <DnaInterfacePacker.hh>

Inheritance diagram for protocols::dna::DnaInterfacePacker:
Inheritance graph
[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::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.) 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...
 
- 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 Stringsinfo ()
 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 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

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

Constructor & Destructor Documentation

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

lightweight default constructor

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

destructor

Member Function Documentation

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

References allowed_types_.

Referenced by protein_scan().

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().

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().

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

References initialization_state_.

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().

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

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

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

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().

ResTypeSequence protocols::dna::DnaInterfacePacker::get_targeted_sequence ( Pose const &  pose) const
void protocols::dna::DnaInterfacePacker::init_standard ( Pose pose)
private
bool protocols::dna::DnaInterfacePacker::initialized ( ) const
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().

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.)

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().

std::string protocols::dna::DnaInterfacePacker::mover_name ( )
static
void protocols::dna::DnaInterfacePacker::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
std::string protocols::dna::DnaInterfacePacker::pdbname ( )
inline

References pdbname_.

Referenced by measure_specificities().

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

References pdboutput_.

void protocols::dna::DnaInterfacePacker::post_packing ( Pose pose,
ResTypeSequence const &  dnaseq,
core::Size  trial 
)
private
void protocols::dna::DnaInterfacePacker::protein_scan ( Pose pose)
private
void protocols::dna::DnaInterfacePacker::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
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_.

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

References reference_pose_.

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.) 
)
void protocols::dna::DnaInterfacePacker::set_filename_root ( std::string const &  name)
inline
void protocols::dna::DnaInterfacePacker::standard_packing ( Pose pose)
private
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 = "" 
)

Member Data Documentation

std::string protocols::dna::DnaInterfacePacker::allowed_types_
private
bool protocols::dna::DnaInterfacePacker::base_only_
private
bool protocols::dna::DnaInterfacePacker::binding_E_
private
DnaChainsOP protocols::dna::DnaInterfacePacker::dna_chains_
private
ResTypeSequences protocols::dna::DnaInterfacePacker::dna_sequences_
private
std::string protocols::dna::DnaInterfacePacker::filename_root_
private
bool protocols::dna::DnaInterfacePacker::include_dna_potentials_in_specificity_calculations_
private
bool protocols::dna::DnaInterfacePacker::initialization_state_
private
core::kinematics::MoveMapOP protocols::dna::DnaInterfacePacker::min_movemap_
private
bool protocols::dna::DnaInterfacePacker::minimize_
private
core::optimization::MinimizerOptionsOP protocols::dna::DnaInterfacePacker::minimize_options_
private
core::Size protocols::dna::DnaInterfacePacker::num_repacks_
private
std::string protocols::dna::DnaInterfacePacker::pdbname_
private

Referenced by pdbname(), and post_packing().

PDBOutputOP protocols::dna::DnaInterfacePacker::pdboutput_
private
bool protocols::dna::DnaInterfacePacker::probe_specificity_
private
bool protocols::dna::DnaInterfacePacker::protein_scan_
private
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
bool protocols::dna::DnaInterfacePacker::reversion_scan_
private
core::Size protocols::dna::DnaInterfacePacker::specificity_repacks_
private
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: