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protocols::abinitio::abscript::AbscriptMover Class Reference

#include <AbscriptMover.hh>

Inheritance diagram for protocols::abinitio::abscript::AbscriptMover:
Inheritance graph
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Classes

class  StageTracker
 

Public Member Functions

 AbscriptMover ()
 
 AbscriptMover (AbscriptMover const &)
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
EnvClaims yield_claims (core::pose::Pose const &, basic::datacache::WriteableCacheableMapOP) override
 Returns a list of claims for this mover. More...
 
void yield_submovers (std::set< ClientMoverOP > &) const override
 this method is used to make sure any movers contained in this mover (that want to make claims) also get registered with the environment. More...
 
void initialize (Pose &) override
 this method is called by the broking system in response to a successful initialization claim by this mover. The passport will prevent any unauthorized changes. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::environment::ClientMover
 ClientMover ()
 
 ClientMover (ClientMover const &)
 
 ~ClientMover () override
 
- 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 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 stage_complex_namer (std::string)
 
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 Types

typedef
environment::claims::EnvClaims 
EnvClaims
 
typedef environment::ClientMoverOP ClientMoverOP
 
typedef std::set< ClientMoverOPMoverSet
 
typedef std::map< StageID,
MoverSet
IDMoverSetMap
 

Private Member Functions

void add_frags (std::string const &small_frags, std::string const &large_frags, core::select::residue_selector::ResidueSelectorCOP=nullptr, bool initialize=true)
 
void parse_subtags (utility::vector0< utility::tag::TagPtr > const &, basic::datacache::DataMap &data)
 
void register_submover (protocols::moves::MoverOP, StageIDs const &, core::Real weight)
 
void register_preparer (protocols::moves::MoverOP, StageIDs const &)
 
std::map< core::Size, core::Sizecalculate_iterations (core::pose::Pose const &)
 
StageIDs parse_stage_id (std::string const &) const
 

Private Attributes

std::map< std::string, StageIDid_map_
 
std::map< StageID,
AbscriptStageMoverOP
stage_movers_
 
moves::MonteCarloOP mc_
 
environment::claims::EnvClaims claims_
 

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::environment::ClientMover
void sandboxed_copy (core::pose::Pose const &sandbox_pose, core::pose::Pose &true_pose) const
 convience method that copies all changes from an unprotected pose to a protected pose. More...
 
virtual void passport_updated ()
 hook that is called each time the passport status is updated (presumably because there's a new subenvironment, or the sub- environment has expired). More...
 
virtual void broking_finished (EnvClaimBroker::BrokerResult const &)
 hook that provides information about the final result of broking at the very end, though this BrokerResult construct. More...
 
EnvironmentCAP active_environment () const
 return a pointer the active environment More...
 
core::environment::DofPassportCOP passport () const
 read-only access to the top passport in the passport stack. More...
 
bool has_passport () const
 
bool state_check (std::string const &method_name, bool test) const
 convienence method for failing a state-set call after brokering. 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

Constructor & Destructor Documentation

protocols::abinitio::abscript::AbscriptMover::AbscriptMover ( )
protocols::abinitio::abscript::AbscriptMover::AbscriptMover ( AbscriptMover const &  src)

Member Function Documentation

void protocols::abinitio::abscript::AbscriptMover::add_frags ( std::string const &  small_frags,
std::string const &  large_frags,
core::select::residue_selector::ResidueSelectorCOP  selector = nullptr,
bool  initialize = true 
)
private
void protocols::abinitio::abscript::AbscriptMover::apply ( core::pose::Pose )
overridevirtual
std::map< core::Size, core::Size > protocols::abinitio::abscript::AbscriptMover::calculate_iterations ( core::pose::Pose const &  pose)
private
moves::MoverOP protocols::abinitio::abscript::AbscriptMover::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.

Referenced by parse_my_tag().

moves::MoverOP protocols::abinitio::abscript::AbscriptMover::fresh_instance ( ) const
overridevirtual

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.

std::string protocols::abinitio::abscript::AbscriptMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Referenced by parse_my_tag().

void protocols::abinitio::abscript::AbscriptMover::initialize ( Pose conf)
inlineoverridevirtual

this method is called by the broking system in response to a successful initialization claim by this mover. The passport will prevent any unauthorized changes.

Reimplemented from protocols::environment::ClientMover.

std::string protocols::abinitio::abscript::AbscriptMover::mover_name ( )
static
void protocols::abinitio::abscript::AbscriptMover::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 add_frags(), clone(), get_name(), protocols::abinitio::abscript::I, id_map_, protocols::abinitio::abscript::II, protocols::abinitio::abscript::IIIa, protocols::abinitio::abscript::IIIb, protocols::abinitio::abscript::increment_stageid(), protocols::abinitio::abscript::IVa, protocols::abinitio::abscript::IVb, protocols::moves::Mover::name(), protocols::rosetta_scripts::parse_mover_or_null(), parse_stage_id(), register_preparer(), register_submover(), stage_movers_, core::id::to_string(), and tr().

StageIDs protocols::abinitio::abscript::AbscriptMover::parse_stage_id ( std::string const &  id_str) const
private
void protocols::abinitio::abscript::AbscriptMover::parse_subtags ( utility::vector0< utility::tag::TagPtr > const &  ,
basic::datacache::DataMap &  data 
)
private
void protocols::abinitio::abscript::AbscriptMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::abinitio::abscript::AbscriptMover::register_preparer ( protocols::moves::MoverOP  mover,
StageIDs const &  ids 
)
private

References stage_movers_, and tr().

Referenced by parse_my_tag().

void protocols::abinitio::abscript::AbscriptMover::register_submover ( protocols::moves::MoverOP  mover_in,
StageIDs const &  ids,
core::Real  weight 
)
private

References stage_movers_, and tr().

Referenced by parse_my_tag().

std::string protocols::abinitio::abscript::AbscriptMover::stage_complex_namer ( std::string  tag_name)
static

Referenced by provide_xml_schema().

EnvClaims protocols::abinitio::abscript::AbscriptMover::yield_claims ( core::pose::Pose const &  ,
basic::datacache::WriteableCacheableMapOP   
)
overridevirtual

Returns a list of claims for this mover.

The pose passed as an argument is used for reference informational purposes only (for example, you want to know the sequence) or access the pose cache. Any changes to the conformation will get overwritten!

Implements protocols::environment::ClientMover.

References claims_.

void protocols::abinitio::abscript::AbscriptMover::yield_submovers ( std::set< ClientMoverOP > &  ) const
overridevirtual

this method is used to make sure any movers contained in this mover (that want to make claims) also get registered with the environment.

Reimplemented from protocols::environment::ClientMover.

References stage_movers_.

Member Data Documentation

environment::claims::EnvClaims protocols::abinitio::abscript::AbscriptMover::claims_
private

Referenced by yield_claims().

std::map< std::string, StageID > protocols::abinitio::abscript::AbscriptMover::id_map_
private
moves::MonteCarloOP protocols::abinitio::abscript::AbscriptMover::mc_
private
std::map< StageID, AbscriptStageMoverOP > protocols::abinitio::abscript::AbscriptMover::stage_movers_
private

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