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

#include <ParsedProtocol.hh>

Inheritance diagram for protocols::rosetta_scripts::ParsedProtocol:
Inheritance graph
[legend]

Classes

struct  MoverFilterPair
 

Public Types

typedef core::Real Real
 
typedef core::pose::Pose Pose
 
typedef utility::vector1
< MoverFilterPair
MoverFilterVector
 
typedef MoverFilterVector::iterator iterator
 
typedef
MoverFilterVector::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
 
MoverFilterPair get_mover_filter_pair (core::Size const mover_number) const
 
void add_mover_filter_pair (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 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...
 
bool mover_provides_citation_info () const override
 This mover does not provide citation info for itself, though it might for movers or filters that it invokes. It therefore returns false. More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provide the citation. More...
 
bool mover_is_unpublished () const override
 This mover is not unpublished. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 This mover does provide information for unpublished movers and filters that it invokes. More...
 
core::Size n_filters_passed_in_previous_run () const
 
- 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 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)
 

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)
 
void apply_mover (Pose &pose, MoverFilterPair const &mover_pair)
 apply the mover of the pair More...
 
bool apply_filter (Pose &pose, MoverFilterPair const &mover_pair)
 apply the filter of the pair More...
 
void sequence_protocol (Pose &pose, MoverFilterVector::const_iterator mover_it_in)
 
void random_order_protocol (Pose &pose)
 
void random_single_protocol (Pose &pose)
 

Private Attributes

MoverFilterVector movers_
 
core::scoring::ScoreFunctionCOP final_scorefxn_ = nullptr
 
std::string mode_
 
utility::vector1< core::Realapply_probability_
 
core::Size last_attempted_mover_idx_
 
bool report_call_order_
 
std::string call_order_
 
protocols::moves::MoverOP last_mover_
 
bool resume_support_
 
core::Size n_filters_passed_in_previous_run_ = 0
 

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

typedef MoverFilterVector::const_iterator protocols::rosetta_scripts::ParsedProtocol::const_iterator
typedef MoverFilterVector::iterator protocols::rosetta_scripts::ParsedProtocol::iterator

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::rosetta_scripts::ParsedProtocol::add_mover_filter_pair ( 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.

Indended for use OUTSIDE of a RosettaScripts context.

Author
Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References movers_.

Referenced by protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_helix_update_moves(), and protocols::helical_bundle_predict::HBP_HelixCoilMoveGenerator::add_nonhelix_small_moves().

void protocols::rosetta_scripts::ParsedProtocol::add_values_to_job ( Pose const &  pose,
protocols::jd2::Job job 
) const
overridevirtual
void protocols::rosetta_scripts::ParsedProtocol::apply ( Pose pose)
overridevirtual
bool protocols::rosetta_scripts::ParsedProtocol::apply_filter ( Pose pose,
MoverFilterPair const &  mover_pair 
)
private
void protocols::rosetta_scripts::ParsedProtocol::apply_mover ( Pose pose,
MoverFilterPair const &  mover_pair 
)
private
void protocols::rosetta_scripts::ParsedProtocol::apply_probability ( utility::vector1< core::Real > const &  a)
utility::vector1< core::Real > protocols::rosetta_scripts::ParsedProtocol::apply_probability ( )
ParsedProtocol::iterator protocols::rosetta_scripts::ParsedProtocol::begin ( )

References movers_.

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

References movers_.

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

References call_order_.

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

References movers_.

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

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.

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

References movers_.

Referenced by apply_filter().

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

References movers_.

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

References final_scorefxn().

Referenced by apply(), and get_additional_output().

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

References final_scorefxn_.

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

References final_scorefxn_.

Referenced by final_score().

void protocols::rosetta_scripts::ParsedProtocol::finish_protocol ( Pose pose)
private
protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::fresh_instance ( ) const
inlineoverridevirtual

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.

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

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_filter(), apply_mover(), final_score(), mode_, movers_, protocols::moves::MS_SUCCESS, report_all(), report_filters_to_pose(), resume_support_, protocols::moves::Mover::set_last_move_status(), protocols::rosetta_scripts::TR(), and protocols::rosetta_scripts::TR_report().

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

References movers_.

MoverFilterPair protocols::rosetta_scripts::ParsedProtocol::get_mover_filter_pair ( core::Size const  mover_number) const
inline

References movers_.

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

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx ( )
inline
void protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx ( core::Size const  s)
inline
std::string protocols::rosetta_scripts::ParsedProtocol::mode ( ) const
inline

References mode_.

bool protocols::rosetta_scripts::ParsedProtocol::mover_is_unpublished ( ) const
overridevirtual

This mover is not unpublished.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

std::string protocols::rosetta_scripts::ParsedProtocol::mover_name ( )
static
bool protocols::rosetta_scripts::ParsedProtocol::mover_provides_citation_info ( ) const
overridevirtual

This mover does not provide citation info for itself, though it might for movers or filters that it invokes. It therefore returns false.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

core::Size protocols::rosetta_scripts::ParsedProtocol::n_filters_passed_in_previous_run ( ) const
inline
void protocols::rosetta_scripts::ParsedProtocol::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 apply_probability(), mode_, mover_name(), movers_, protocols::rosetta_scripts::parse_filter_or_null(), protocols::rosetta_scripts::parse_mover_subtag(), report_call_order(), resume_support_, and protocols::rosetta_scripts::TR().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::rosetta_scripts::ParsedProtocol::provide_authorship_info_for_unpublished ( ) const
overridevirtual

This mover does provide information for unpublished movers and filters that it invokes.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References last_mover_, and movers_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::rosetta_scripts::ParsedProtocol::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.
Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References last_mover_, and movers_.

void protocols::rosetta_scripts::ParsedProtocol::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::rosetta_scripts::ParsedProtocol::random_order_protocol ( Pose pose)
private
void protocols::rosetta_scripts::ParsedProtocol::random_single_protocol ( Pose pose)
private
void protocols::rosetta_scripts::ParsedProtocol::report_all ( Pose const &  pose) const
bool protocols::rosetta_scripts::ParsedProtocol::report_call_order ( ) const
inline

References report_call_order_.

Referenced by finish_protocol(), and parse_my_tag().

void protocols::rosetta_scripts::ParsedProtocol::report_call_order ( bool const  c)
inline
void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose ( Pose pose) const
void protocols::rosetta_scripts::ParsedProtocol::sequence_protocol ( Pose pose,
MoverFilterVector::const_iterator  mover_it_in 
)
private
void protocols::rosetta_scripts::ParsedProtocol::set_resid ( core::Size const  resid)
overridevirtual

sets resid for the constituent filters and movers

Reimplemented from protocols::moves::ResId.

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

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

sets resid for the constituent filters and movers

Reimplemented from protocols::moves::ResId.

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

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

References movers_.

Member Data Documentation

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

Referenced by apply_probability().

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

Referenced by call_order().

core::scoring::ScoreFunctionCOP protocols::rosetta_scripts::ParsedProtocol::final_scorefxn_ = nullptr
private

Referenced by final_scorefxn().

core::Size protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx_
private
protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::last_mover_
private
std::string protocols::rosetta_scripts::ParsedProtocol::mode_
private
MoverFilterVector protocols::rosetta_scripts::ParsedProtocol::movers_
private
core::Size protocols::rosetta_scripts::ParsedProtocol::n_filters_passed_in_previous_run_ = 0
private
bool protocols::rosetta_scripts::ParsedProtocol::report_call_order_
private

Referenced by report_call_order().

bool protocols::rosetta_scripts::ParsedProtocol::resume_support_
private

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