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

#include <LoopAnalyzerMover.hh>

Inheritance diagram for protocols::analysis::LoopAnalyzerMover:
Inheritance graph
[legend]

Public Member Functions

 LoopAnalyzerMover (protocols::loops::Loops const &loops, bool const tracer=false)
 
 LoopAnalyzerMover ()
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
bool reinitialize_for_new_input () const override
 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 apply (core::pose::Pose &input_pose) override
 apply function will calculate data about the input pose. It is not intended to modify the pose itself (conformation and energies objects) although it may toss data into the DataCache or a Job object. More...
 
void set_loops (protocols::loops::LoopsCOP loops)
 set loops object, because public setters/getters are a rule More...
 
protocols::loops::LoopsCOP get_loops (void) const
 get loops object, because public setters/getters are a rule More...
 
void set_use_tracer (bool tracer)
 set tracer bool, because public setters/getters are a rule More...
 
bool get_use_tracer (void) const
 get tracer bool, because public setters/getters are a rule More...
 
core::Real get_total_score () const
 Return the total score found from the last apply call. More...
 
core::Real get_max_rama () const
 
core::Real get_max_omega () const
 
core::Real get_max_pbond () const
 
core::Real get_max_chainbreak () const
 
utility::vector1< core::Realget_chainbreak_scores ()
 Return the vector of chainbreak scores. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
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 void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. 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::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 reset ()
 reset stored data More...
 
void calculate_all_chainbreaks (core::pose::Pose &pose)
 places cutpoints in the loops, scores chainbreak, removes cutpoints More...
 
void set_sf ()
 ctor helper: create scorefunction More...
 
void find_positions (core::pose::Pose const &pose)
 convert loops into positions (must wait until pose, thus not in ctor) More...
 

Private Attributes

utility::pointer::DeepCopyOP
< protocols::loops::Loops
const > 
loops_
 used to store a copy of the input loops More...
 
bool tracer_ = true
 output to tracer or PDB/silent file More...
 
utility::vector1< core::Sizepositions_
 used to calculate positions to examine - loops +- 1 position are interesting, but vary w/termini, etc More...
 
utility::pointer::DeepCopyOP
< core::scoring::ScoreFunction
sf_
 scorefunction used to apply multiple individual terms at once, not as a cohesive unit More...
 
utility::pointer::DeepCopyOP
< core::scoring::ScoreFunction
chbreak_sf_
 scorefunction for chainbreak score More...
 
utility::vector1< core::Realscores_
 brief remember chainbreak scores More...
 
core::Real total_score_ = 0
 
core::Real max_rama_ = REAL_FAKE_MIN
 
core::Real max_chainbreak_ = REAL_FAKE_MIN
 
core::Real max_omega_ = REAL_FAKE_MIN
 
core::Real max_pbond_ = REAL_FAKE_MIN
 

Static Private Attributes

static constexpr core::Real REAL_FAKE_MIN = -1000000
 

Additional Inherited Members

- 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
 
- 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...
 

Constructor & Destructor Documentation

protocols::analysis::LoopAnalyzerMover::LoopAnalyzerMover ( protocols::loops::Loops const &  loops,
bool const  tracer = false 
)
protocols::analysis::LoopAnalyzerMover::LoopAnalyzerMover ( )

Member Function Documentation

void protocols::analysis::LoopAnalyzerMover::apply ( core::pose::Pose input_pose)
overridevirtual
void protocols::analysis::LoopAnalyzerMover::calculate_all_chainbreaks ( core::pose::Pose pose)
private
protocols::moves::MoverOP protocols::analysis::LoopAnalyzerMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

void protocols::analysis::LoopAnalyzerMover::find_positions ( core::pose::Pose const &  pose)
private

convert loops into positions (must wait until pose, thus not in ctor)

References core::sequence::end, core::conformation::Residue::is_terminus(), loops_, positions_, core::pose::Pose::residue(), scores_, core::pose::Pose::size(), protocols::loops::start, and protocols::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::analysis::LoopAnalyzerMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

utility::vector1< core::Real > protocols::analysis::LoopAnalyzerMover::get_chainbreak_scores ( )

Return the vector of chainbreak scores.

References scores_.

protocols::loops::LoopsCOP protocols::analysis::LoopAnalyzerMover::get_loops ( void  ) const

get loops object, because public setters/getters are a rule

References loops_.

core::Real protocols::analysis::LoopAnalyzerMover::get_max_chainbreak ( ) const

References max_chainbreak_.

core::Real protocols::analysis::LoopAnalyzerMover::get_max_omega ( ) const

References max_omega_.

core::Real protocols::analysis::LoopAnalyzerMover::get_max_pbond ( ) const

References max_pbond_.

core::Real protocols::analysis::LoopAnalyzerMover::get_max_rama ( ) const

References max_rama_.

std::string protocols::analysis::LoopAnalyzerMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Real protocols::analysis::LoopAnalyzerMover::get_total_score ( ) const

Return the total score found from the last apply call.

References total_score_.

Referenced by protocols::loops::filters::LoopAnalyzerFilter::report_sm().

bool protocols::analysis::LoopAnalyzerMover::get_use_tracer ( void  ) const
inline

get tracer bool, because public setters/getters are a rule

References tracer_.

std::string protocols::analysis::LoopAnalyzerMover::mover_name ( )
static
void protocols::analysis::LoopAnalyzerMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References protocols::loop_modeling::utilities::parse_loops_from_tag(), set_loops(), and set_use_tracer().

void protocols::analysis::LoopAnalyzerMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
bool protocols::analysis::LoopAnalyzerMover::reinitialize_for_new_input ( ) const
inlineoverridevirtual

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).

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

void protocols::analysis::LoopAnalyzerMover::reset ( )
private

reset stored data

References max_chainbreak_, max_omega_, max_pbond_, max_rama_, REAL_FAKE_MIN, and scores_.

Referenced by apply().

void protocols::analysis::LoopAnalyzerMover::set_loops ( protocols::loops::LoopsCOP  loops)

set loops object, because public setters/getters are a rule

getters, setters/////////////

getters, setters/////////////////////

References loops_.

Referenced by parse_my_tag().

void protocols::analysis::LoopAnalyzerMover::set_sf ( )
private
void protocols::analysis::LoopAnalyzerMover::set_use_tracer ( bool  tracer)
inline

set tracer bool, because public setters/getters are a rule

References protocols::frag_picker::tracer(), and tracer_.

Referenced by parse_my_tag().

Member Data Documentation

utility::pointer::DeepCopyOP< core::scoring::ScoreFunction > protocols::analysis::LoopAnalyzerMover::chbreak_sf_
private

scorefunction for chainbreak score

Referenced by set_sf().

utility::pointer::DeepCopyOP< protocols::loops::Loops const > protocols::analysis::LoopAnalyzerMover::loops_
private

used to store a copy of the input loops

Referenced by apply(), find_positions(), get_loops(), and set_loops().

core::Real protocols::analysis::LoopAnalyzerMover::max_chainbreak_ = REAL_FAKE_MIN
private

Referenced by apply(), get_max_chainbreak(), and reset().

core::Real protocols::analysis::LoopAnalyzerMover::max_omega_ = REAL_FAKE_MIN
private

Referenced by apply(), get_max_omega(), and reset().

core::Real protocols::analysis::LoopAnalyzerMover::max_pbond_ = REAL_FAKE_MIN
private

Referenced by apply(), get_max_pbond(), and reset().

core::Real protocols::analysis::LoopAnalyzerMover::max_rama_ = REAL_FAKE_MIN
private

Referenced by apply(), get_max_rama(), and reset().

utility::vector1< core::Size > protocols::analysis::LoopAnalyzerMover::positions_
private

used to calculate positions to examine - loops +- 1 position are interesting, but vary w/termini, etc

Referenced by apply(), calculate_all_chainbreaks(), and find_positions().

constexpr core::Real protocols::analysis::LoopAnalyzerMover::REAL_FAKE_MIN = -1000000
staticprivate

Referenced by reset().

utility::vector1< core::Real > protocols::analysis::LoopAnalyzerMover::scores_
private

brief remember chainbreak scores

Referenced by apply(), calculate_all_chainbreaks(), find_positions(), get_chainbreak_scores(), and reset().

utility::pointer::DeepCopyOP< core::scoring::ScoreFunction > protocols::analysis::LoopAnalyzerMover::sf_
private

scorefunction used to apply multiple individual terms at once, not as a cohesive unit

Referenced by set_sf().

core::Real protocols::analysis::LoopAnalyzerMover::total_score_ = 0
private

Referenced by apply(), and get_total_score().

bool protocols::analysis::LoopAnalyzerMover::tracer_ = true
private

output to tracer or PDB/silent file

Referenced by apply(), get_use_tracer(), and set_use_tracer().


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