Rosetta Protocols  2014.35
Classes | Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::rosetta_scripts::ParsedProtocol Class Reference

#include <ParsedProtocol.hh>


class  MoverFilterPair

Public Types

typedef core::Real Real
typedef core::pose::Pose Pose
typedef utility::vector1
< MoverFilterPair
typedef MoverFilterVector::iterator 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::stringStrings

Public Member Functions

 ParsedProtocol ()
virtual ~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 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)
void report_filters_to_job (Pose const &pose) const
virtual void add_values_to_job (Pose const &pose, protocols::jd2::JobOP) const
protocols::moves::MoverCOP get_mover (core::Size const mover_number) const
void set_resid (core::Size const resid)
protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
virtual void parse_my_tag (utility::tag::TagCOP, basic::datacache::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
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
void set_type (std::string const &setting)
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
 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...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
- 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)
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_
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_

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

Member Function Documentation

void protocols::rosetta_scripts::ParsedProtocol::add_values_to_job ( Pose const &  pose,
protocols::jd2::JobOP  job 
) const
void protocols::rosetta_scripts::ParsedProtocol::apply ( Pose pose)
bool protocols::rosetta_scripts::ParsedProtocol::apply_filter ( Pose pose,
MoverFilterPair const &  mover_pair 
void protocols::rosetta_scripts::ParsedProtocol::apply_mover ( Pose pose,
MoverFilterPair const &  mover_pair 
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

References call_order_.

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

References movers_.

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.

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

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

References movers_, and runtime_assert.

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::TagCOP  tag,
basic::datacache::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 apply_probability(), protocols::moves::Mover::clone(), mode_, movers_, protocols::rosetta_scripts::parse_mover_subtag(), report_call_order(), resume_support_, and runtime_assert.

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
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)

References report_call_order_.

void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_job ( Pose const &  pose) const
void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose ( Pose pose)
void protocols::rosetta_scripts::ParsedProtocol::sequence_protocol ( Pose pose,
MoverFilterVector::const_iterator  mover_it_in 

References apply_filter(), apply_mover(), 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_
protocols::moves::MoverOP protocols::rosetta_scripts::ParsedProtocol::last_mover_

Referenced by apply_mover().

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().

bool protocols::rosetta_scripts::ParsedProtocol::resume_support_

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