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protocols::rosetta_scripts::ParsedProtocol Class Reference

#include <ParsedProtocol.hh>

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

Public Types

typedef core::Real Real
typedef core::pose::Pose Pose
typedef std::pair< std::pair
< protocols::moves::MoverOP,
std::string >
, protocols::filters::FilterOP
typedef utility::vector1
< mover_filter_pair
typedef MoverFilterVector::iterator iterator
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::string > Strings

Public Member Functions

 ParsedProtocol ()
virtual void apply (Pose &pose)
virtual core::pose::PoseOP get_additional_output ()
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void add_mover (protocols::moves::MoverCOP mover, std::string const mover_name, protocols::filters::FilterOP filter)
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_job (Pose const &pose) const
void report_all_sm (std::map< std::string, core::Real > &score_map, Pose const &pose) const
protocols::moves::MoverCOP get_mover (core::Size const mover_number) const
void set_resid (core::Size const resid)
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
virtual void parse_my_tag (utility::tag::TagPtr const, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 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
virtual ~ParsedProtocol ()
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
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
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...
void set_current_tag (std::string const &new_tag)
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
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...
void type (const std::string &type_in)
std::string get_type () const
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 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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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 set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
- Public Member Functions inherited from protocols::moves::ResId
 ResId ()
 ResId (core::Size const r)
virtual core::Size get_resid () const
virtual core::Sizeget_resid ()
virtual bool modifiable () const
 should another method be able to modify resid_. This is used by modify_ResId_based_object as a test More...
virtual void modifiable (bool const u)
virtual ~ResId ()

Private Member Functions

void finish_protocol (Pose &pose)
bool apply_mover_filter_pair (Pose &pose, mover_filter_pair const &mover_pair)
bool apply_filter (Pose &pose, mover_filter_pair const &mover_pair)
void sequence_protocol (Pose &pose, utility::vector1< mover_filter_pair >::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_
std::string mode_
utility::vector1< core::Realapply_probability_
core::Size last_attempted_mover_idx_
bool report_call_order_
std::string call_order_

Additional Inherited Members

- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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 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 ( )

Member Function Documentation

void protocols::rosetta_scripts::ParsedProtocol::add_mover ( protocols::moves::MoverCOP  mover,
std::string const  mover_name,
protocols::filters::FilterOP  filter 

Tricky! movers are cloned into the protocol b/c their apply functions (which are nonconst) could accumulate state information. Filters are safe and are therefore merely registered. Under this state of affairs, a mover or filter may be called many times in the protocol, and it will be guaranteed to have no state accumulation.

References movers_.

Referenced by parse_my_tag().

void protocols::rosetta_scripts::ParsedProtocol::apply ( Pose pose)
Detailed: Takes care of the docking, design and filtering moves. pre_cycle and pose_cycle can
be setup in derived classes to setup variables before and after these cycles.

Implements protocols::moves::Mover.

References apply_filter(), protocols::moves::FAIL_RETRY, final_score(), protocols::moves::Mover::get_last_move_status(), mode_, movers_, protocols::moves::MS_SUCCESS, random_order_protocol(), random_single_protocol(), sequence_protocol(), protocols::moves::Mover::set_last_move_status(), and core::pose::Pose::update_residue_neighbors().

bool protocols::rosetta_scripts::ParsedProtocol::apply_filter ( Pose pose,
mover_filter_pair const &  mover_pair 
bool protocols::rosetta_scripts::ParsedProtocol::apply_mover_filter_pair ( Pose pose,
mover_filter_pair const &  mover_pair 
void protocols::rosetta_scripts::ParsedProtocol::apply_probability ( utility::vector1< core::Real > const  a)

References apply_probability_, and movers_.

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

References call_order_.

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

References movers_.

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

clone has to be overridden only if clone invocation is expected.

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

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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 ( )
Detailed: 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_filter_pair(), mode_, movers_, protocols::moves::MS_SUCCESS, report_all(), report_filters_to_job(), and protocols::moves::Mover::set_last_move_status().

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

References movers_.

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

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

Implements protocols::moves::Mover.

References protocols::rosetta_scripts::ParsedProtocolCreator::mover_name().

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

References mode_.

void protocols::rosetta_scripts::ParsedProtocol::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::moves::DataMap::add(), add_mover(), apply_probability(), protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), mode_, and report_call_order().

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

References movers_.

Referenced by finish_protocol(), and get_additional_output().

void protocols::rosetta_scripts::ParsedProtocol::report_all_sm ( std::map< std::string, core::Real > &  score_map,
Pose const &  pose 
) const

References movers_.

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

References report_call_order_.

Referenced by finish_protocol(), and parse_my_tag().

void protocols::rosetta_scripts::ParsedProtocol::report_call_order ( bool const  c)
void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_job ( Pose const &  pose) const
void protocols::rosetta_scripts::ParsedProtocol::sequence_protocol ( Pose pose,
utility::vector1< mover_filter_pair >::const_iterator  mover_it_in 

References apply_mover_filter_pair(), finish_protocol(), and movers_.

Referenced by apply().

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 movers_.

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

References movers_.

Member Data Documentation

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

Referenced by apply_probability().

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

Referenced by call_order().

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

Referenced by final_scorefxn().

core::Size protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx_
std::string protocols::rosetta_scripts::ParsedProtocol::mode_
MoverFilterVector protocols::rosetta_scripts::ParsedProtocol::movers_
bool protocols::rosetta_scripts::ParsedProtocol::report_call_order_

Referenced by report_call_order().

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