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protocols::rosetta_scripts::ParsedProtocol Class Reference

#include <ParsedProtocol.hh>

Inheritance diagram for protocols::rosetta_scripts::ParsedProtocol:
Inheritance graph


struct  ParsedProtocolStep
 Represents a step in the ParsedProtocol Note that one or more of mover/filter/metrics may be null/empty. More...

Public Types

enum class  FilterReportTime { AT_END , AFTER_APPLY , NONE }
typedef core::Real Real
typedef core::pose::Pose Pose
typedef utility::vector1< ParsedProtocolStepParsedProtocolStepVector
typedef ParsedProtocolStepVector::iterator iterator
typedef ParsedProtocolStepVector::const_iterator const_iterator
- 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

 ParsedProtocol ()
 ~ParsedProtocol () override
void apply (Pose &pose) override
core::pose::PoseOP get_additional_output () override
void final_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
core::scoring::ScoreFunctionCOP final_scorefxn () const
void final_score (core::pose::Pose &pose) const
void report_all (Pose const &pose) const
void report_filters_to_pose (Pose &pose) const
void add_values_to_job (Pose const &pose, protocols::jd2::Job &) const override
protocols::moves::MoverCOP get_mover (core::Size const mover_number) const
ParsedProtocolStep get_step (core::Size const step_number) const
void add_step (protocols::moves::MoverOP mover, std::string const &mover_name, protocols::filters::FilterOP filter, bool const report_filter_at_end=false)
 Add a mover-filter pair. More...
void add_step (ParsedProtocolStep const &step)
 Add a step to the protocol. More...
void set_resid (core::Size const resid) override
void set_resid (core::pose::ResidueIndexDescriptionCOP r) override
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void clear ()
std::string mode () const
iterator begin ()
const_iterator begin () const
iterator end ()
const_iterator end () const
void apply_probability (utility::vector1< core::Real > const &a)
utility::vector1< core::Realapply_probability ()
core::Size size ()
core::Size last_attempted_mover_idx ()
void last_attempted_mover_idx (core::Size const s)
bool report_call_order () const
void report_call_order (bool const c)
std::string call_order () const
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
void provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
 Provide the citation. More...
core::Size n_steps_passed_in_previous_run () const
bool get_filter_status () const
 Get the status of any filters after running. 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...
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...
- Public Member Functions inherited from protocols::moves::ResId
 ResId ()=default
 ResId (core::Size const r)
virtual ~ResId ()=default
virtual core::Size get_resid (core::pose::Pose const &) const
bool modifiable () const
 should another method be able to modify resid_. This is used by modify_ResId_based_object as a test More...
void modifiable (bool const u)
- Public Member Functions inherited from protocols::jd2::JobOutputterObserver
virtual ~JobOutputterObserver ()=default

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 finish_protocol (Pose &pose)
bool apply_step (Pose &pose, ParsedProtocolStep const &step, bool skip_mover=false)
 apply the components of the step More...
bool apply_mover (Pose &pose, ParsedProtocolStep const &step)
 apply the mover of the step More...
bool apply_filter (Pose &pose, ParsedProtocolStep const &step)
 apply the filter of the step More...
void apply_metrics (Pose &pose, ParsedProtocolStep const &step)
 apply the metric of the step More...
void sequence_protocol (Pose &pose, ParsedProtocolStepVector::const_iterator mover_it_in)
void random_order_protocol (Pose &pose)
void random_single_protocol (Pose &pose)

Private Attributes

ParsedProtocolStepVector steps_
core::scoring::ScoreFunctionCOP final_scorefxn_
std::string mode_ = "sequence"
utility::vector1< core::Realapply_probability_
core::Size last_attempted_mover_idx_ = 0
bool report_call_order_ = false
std::string call_order_
protocols::moves::MoverOP last_mover_
bool resume_support_ = false
core::Size n_steps_passed_in_previous_run_ = 0
bool filter_status_ = true

Additional Inherited Members

- 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

◆ const_iterator

typedef ParsedProtocolStepVector::const_iterator protocols::rosetta_scripts::ParsedProtocol::const_iterator

◆ iterator

typedef ParsedProtocolStepVector::iterator protocols::rosetta_scripts::ParsedProtocol::iterator

◆ ParsedProtocolStepVector

◆ Pose

◆ Real

Member Enumeration Documentation

◆ FilterReportTime


Constructor & Destructor Documentation

◆ ParsedProtocol()

protocols::rosetta_scripts::ParsedProtocol::ParsedProtocol ( )

◆ ~ParsedProtocol()

protocols::rosetta_scripts::ParsedProtocol::~ParsedProtocol ( )

Member Function Documentation

◆ add_step() [1/2]

void protocols::rosetta_scripts::ParsedProtocol::add_step ( ParsedProtocolStep const &  step)

Add a step to the protocol.

Indended for use OUTSIDE of a RosettaScripts context.

References steps_.

◆ add_step() [2/2]

void protocols::rosetta_scripts::ParsedProtocol::add_step ( protocols::moves::MoverOP  mover,
std::string const &  mover_name,
protocols::filters::FilterOP  filter,
bool const  report_filter_at_end = false 

◆ add_values_to_job()

void protocols::rosetta_scripts::ParsedProtocol::add_values_to_job ( Pose const &  pose,
protocols::jd2::Job job 
) const

◆ apply()

void protocols::rosetta_scripts::ParsedProtocol::apply ( Pose pose)

◆ apply_filter()

bool protocols::rosetta_scripts::ParsedProtocol::apply_filter ( Pose pose,
ParsedProtocolStep const &  step 

◆ apply_metrics()

void protocols::rosetta_scripts::ParsedProtocol::apply_metrics ( Pose pose,
ParsedProtocolStep const &  step 

◆ apply_mover()

bool protocols::rosetta_scripts::ParsedProtocol::apply_mover ( Pose pose,
ParsedProtocolStep const &  step 

◆ apply_probability() [1/2]

utility::vector1< core::Real > protocols::rosetta_scripts::ParsedProtocol::apply_probability ( )

◆ apply_probability() [2/2]

void protocols::rosetta_scripts::ParsedProtocol::apply_probability ( utility::vector1< core::Real > const &  a)

◆ apply_step()

bool protocols::rosetta_scripts::ParsedProtocol::apply_step ( Pose pose,
ParsedProtocolStep const &  step,
bool  skip_mover = false 

◆ begin() [1/2]

ParsedProtocol::iterator protocols::rosetta_scripts::ParsedProtocol::begin ( )

References steps_.

◆ begin() [2/2]

ParsedProtocol::const_iterator protocols::rosetta_scripts::ParsedProtocol::begin ( ) const

References steps_.

◆ call_order()

std::string protocols::rosetta_scripts::ParsedProtocol::call_order ( ) const

References call_order_.

◆ clear()

void protocols::rosetta_scripts::ParsedProtocol::clear ( )

References steps_.

◆ clone()

protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::clone ( ) const

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

◆ end() [1/2]

ParsedProtocol::iterator protocols::rosetta_scripts::ParsedProtocol::end ( )

References steps_.

Referenced by apply_mover().

◆ end() [2/2]

ParsedProtocol::const_iterator protocols::rosetta_scripts::ParsedProtocol::end ( ) const

References steps_.

◆ final_score()

void protocols::rosetta_scripts::ParsedProtocol::final_score ( core::pose::Pose pose) const

References final_scorefxn().

Referenced by apply(), and get_additional_output().

◆ final_scorefxn() [1/2]

core::scoring::ScoreFunctionCOP protocols::rosetta_scripts::ParsedProtocol::final_scorefxn ( ) const

References final_scorefxn_.

Referenced by final_score().

◆ final_scorefxn() [2/2]

void protocols::rosetta_scripts::ParsedProtocol::final_scorefxn ( core::scoring::ScoreFunctionCOP  scorefxn)

References final_scorefxn_.

◆ finish_protocol()

void protocols::rosetta_scripts::ParsedProtocol::finish_protocol ( Pose pose)

◆ fresh_instance()

protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::fresh_instance ( ) const

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_additional_output()

core::pose::PoseOP protocols::rosetta_scripts::ParsedProtocol::get_additional_output ( )

Looks for any submovers that have additional output poses to process. If any are found, run remainder of parsed protocol.

Reimplemented from protocols::moves::Mover.

References apply_step(), final_score(), mode_, protocols::moves::MS_SUCCESS, report_all(), report_filters_to_pose(), resume_support_, protocols::moves::Mover::set_last_move_status(), steps_, protocols::rosetta_scripts::TR(), and protocols::rosetta_scripts::TR_report().

◆ get_filter_status()

bool protocols::rosetta_scripts::ParsedProtocol::get_filter_status ( ) const

Get the status of any filters after running.

References filter_status_.

◆ get_mover()

protocols::moves::MoverCOP protocols::rosetta_scripts::ParsedProtocol::get_mover ( core::Size const  mover_number) const

References steps_.

◆ get_name()

std::string protocols::rosetta_scripts::ParsedProtocol::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_step()

ParsedProtocolStep protocols::rosetta_scripts::ParsedProtocol::get_step ( core::Size const  step_number) const

References steps_.

◆ last_attempted_mover_idx() [1/2]

core::Size protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx ( )

◆ last_attempted_mover_idx() [2/2]

void protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx ( core::Size const  s)

◆ mode()

std::string protocols::rosetta_scripts::ParsedProtocol::mode ( ) const

References mode_.

◆ mover_name()

std::string protocols::rosetta_scripts::ParsedProtocol::mover_name ( )

◆ n_steps_passed_in_previous_run()

core::Size protocols::rosetta_scripts::ParsedProtocol::n_steps_passed_in_previous_run ( ) const

◆ parse_my_tag()

void protocols::rosetta_scripts::ParsedProtocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References AFTER_APPLY, apply_probability(), AT_END, core::simple_metrics::get_metrics_from_datamap_and_subtags(), protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::metric_labels, protocols::rosetta_scripts::ParsedProtocol::ParsedProtocolStep::metrics, mode_, mover_name(), NONE, protocols::rosetta_scripts::parse_filter_or_null(), protocols::rosetta_scripts::parse_mover_subtag(), report_call_order(), resume_support_, steps_, and protocols::rosetta_scripts::TR().

◆ provide_citation_info()

void protocols::rosetta_scripts::ParsedProtocol::provide_citation_info ( basic::citation_manager::CitationCollectionList &  citations) const

Provide the citation.

Reimplemented from protocols::moves::Mover.

References last_mover_, and steps_.

◆ provide_xml_schema()

void protocols::rosetta_scripts::ParsedProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ random_order_protocol()

void protocols::rosetta_scripts::ParsedProtocol::random_order_protocol ( Pose pose)

References apply_step(), finish_protocol(), core::scoring::rg, and steps_.

Referenced by apply().

◆ random_single_protocol()

void protocols::rosetta_scripts::ParsedProtocol::random_single_protocol ( Pose pose)

◆ report_all()

void protocols::rosetta_scripts::ParsedProtocol::report_all ( Pose const &  pose) const

◆ report_call_order() [1/2]

bool protocols::rosetta_scripts::ParsedProtocol::report_call_order ( ) const

References report_call_order_.

Referenced by finish_protocol(), and parse_my_tag().

◆ report_call_order() [2/2]

void protocols::rosetta_scripts::ParsedProtocol::report_call_order ( bool const  c)

References report_call_order_.

◆ report_filters_to_pose()

void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose ( Pose pose) const

◆ sequence_protocol()

void protocols::rosetta_scripts::ParsedProtocol::sequence_protocol ( Pose pose,
ParsedProtocolStepVector::const_iterator  mover_it_in 

References apply_step(), finish_protocol(), and steps_.

Referenced by apply().

◆ set_resid() [1/2]

void protocols::rosetta_scripts::ParsedProtocol::set_resid ( core::pose::ResidueIndexDescriptionCOP  r)

sets resid for the constituent filters and movers

Reimplemented from protocols::moves::ResId.

References protocols::moves::modify_ResId_based_object(), and steps_.

◆ set_resid() [2/2]

void protocols::rosetta_scripts::ParsedProtocol::set_resid ( core::Size const  resid)

sets resid for the constituent filters and movers

Reimplemented from protocols::moves::ResId.

References protocols::moves::modify_ResId_based_object(), and steps_.

◆ size()

core::Size protocols::rosetta_scripts::ParsedProtocol::size ( )

References steps_.

Member Data Documentation

◆ apply_probability_

utility::vector1< core::Real > protocols::rosetta_scripts::ParsedProtocol::apply_probability_

Referenced by apply_probability().

◆ call_order_

std::string protocols::rosetta_scripts::ParsedProtocol::call_order_

Referenced by call_order().

◆ filter_status_

bool protocols::rosetta_scripts::ParsedProtocol::filter_status_ = true

Referenced by apply_filter(), and get_filter_status().

◆ final_scorefxn_

core::scoring::ScoreFunctionCOP protocols::rosetta_scripts::ParsedProtocol::final_scorefxn_

Referenced by final_scorefxn().

◆ last_attempted_mover_idx_

core::Size protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx_ = 0

◆ last_mover_

protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::last_mover_

◆ mode_

std::string protocols::rosetta_scripts::ParsedProtocol::mode_ = "sequence"

◆ n_steps_passed_in_previous_run_

core::Size protocols::rosetta_scripts::ParsedProtocol::n_steps_passed_in_previous_run_ = 0

◆ report_call_order_

bool protocols::rosetta_scripts::ParsedProtocol::report_call_order_ = false

Referenced by report_call_order().

◆ resume_support_

bool protocols::rosetta_scripts::ParsedProtocol::resume_support_ = false

◆ steps_

ParsedProtocolStepVector protocols::rosetta_scripts::ParsedProtocol::steps_

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