protocols::rosetta_scripts::ParsedProtocol Class Reference

#include <ParsedProtocol.hh>

Classes
class	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 protocols::filters::Filters_map	Filters_map
typedef std::list< std::string >	Strings

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::Real >	apply_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)
Mover &	operator= (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 Strings &	info ()
	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::Size &	get_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::Real >	apply_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

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

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

typedef utility::vector1< MoverFilterPair > protocols::rosetta_scripts::ParsedProtocol::MoverFilterVector

typedef core::pose::Pose protocols::rosetta_scripts::ParsedProtocol::Pose

typedef core::Real protocols::rosetta_scripts::ParsedProtocol::Real

Constructor & Destructor Documentation

protocols::rosetta_scripts::ParsedProtocol::ParsedProtocol

(

)

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

virtual

Member Function Documentation

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

virtual

Implements protocols::jd2::JobOutputterObserver.

References protocols::jd2::Job::add_string_real_pair(), and movers_.

Referenced by report_filters_to_job().

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

virtual

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(), checkpoint, protocols::moves::FAIL_RETRY, final_score(), protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_last_move_status(), protocols::jd2::jd2_used(), mode_, movers_, protocols::moves::MS_SUCCESS, random_order_protocol(), random_single_protocol(), resume_support_, sequence_protocol(), protocols::moves::Mover::set_last_move_status(), core::pose::Pose::update_residue_neighbors(), and utility_exit_with_message.

bool protocols::rosetta_scripts::ParsedProtocol::apply_filter ( Pose &  pose, MoverFilterPair const &  mover_pair  )

private

apply the filter of the pair

References protocols::jd2::Job::add_string_real_pair(), protocols::filters::Filter::apply(), protocols::nonlocal::current_job(), end(), protocols::moves::FAIL_RETRY, protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::filter(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::first, protocols::jd2::JobDistributor::get_instance(), protocols::filters::Filter::get_user_defined_name(), protocols::moves::Mover::info(), protocols::moves::MS_SUCCESS, protocols::filters::Filter::report(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::report_filter_at_end_, protocols::filters::Filter::report_sm(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::second, protocols::moves::Mover::set_last_move_status(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply(), get_additional_output(), random_order_protocol(), random_single_protocol(), and sequence_protocol().

void protocols::rosetta_scripts::ParsedProtocol::apply_mover ( Pose &  pose, MoverFilterPair const &  mover_pair  )

private

apply the mover of the pair

References protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::first, protocols::moves::Mover::get_name(), protocols::moves::Mover::get_native_pose(), and last_mover_.

Referenced by get_additional_output(), random_order_protocol(), random_single_protocol(), and sequence_protocol().

void protocols::rosetta_scripts::ParsedProtocol::apply_probability

(

utility::vector1< core::Real > const

a

)

References apply_probability_, movers_, runtime_assert, and sum().

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

(

)

References apply_probability_, runtime_assert, and sum().

Referenced by parse_my_tag(), and random_single_protocol().

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

virtual

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(), core::pose::symmetry::is_symmetric(), and core::scoring::symmetry::symmetrize_scorefunction().

Referenced by apply().

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

References protocols::nonlocal::current_job(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::first, protocols::jd2::JobDistributor::get_instance(), movers_, protocols::moves::MS_SUCCESS, report_all(), report_call_order(), report_filters_to_pose(), and protocols::moves::Mover::set_last_move_status().

Referenced by random_order_protocol(), random_single_protocol(), and sequence_protocol().

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

inlinevirtual

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 ( )

virtual

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(), checkpoint, protocols::moves::Mover::get_additional_output(), protocols::moves::Mover::get_name(), mode_, movers_, protocols::moves::MS_SUCCESS, report_all(), report_filters_to_pose(), resume_support_, protocols::moves::Mover::set_last_move_status(), and utility_exit_with_message.

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

inline

References movers_, and runtime_assert.

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

virtual

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 ( )

inline

References last_attempted_mover_idx_.

Referenced by random_single_protocol().

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

inline

References last_attempted_mover_idx_.

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

inline

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  )

virtual

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 )

private

References apply_filter(), apply_mover(), finish_protocol(), movers_, numeric::random::random_permutation(), and protocols::rosetta_scripts::RG.

Referenced by apply().

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

private

References apply_filter(), apply_mover(), apply_probability(), finish_protocol(), last_attempted_mover_idx(), movers_, sum(), and numeric::random::RandomGenerator::uniform().

Referenced by apply().

void protocols::rosetta_scripts::ParsedProtocol::report_all

(

Pose const &

pose

)

const

References protocols::filters::Filter::get_user_defined_name(), movers_, protocols::filters::Filter::report(), protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::report_filter_at_end_, and protocols::rosetta_scripts::ParsedProtocol::MoverFilterPair::second.

Referenced by finish_protocol(), and get_additional_output().

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

References report_call_order_.

void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_job

(

Pose const &

pose

)

const

References add_values_to_job(), protocols::nonlocal::current_job(), and protocols::jd2::JobDistributor::get_instance().

void protocols::rosetta_scripts::ParsedProtocol::report_filters_to_pose

(

Pose &

pose

)

References movers_, and setPoseExtraScore().

Referenced by finish_protocol(), and get_additional_output().

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

private

References apply_filter(), apply_mover(), finish_protocol(), and movers_.

Referenced by apply().

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

virtual

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_

private

Referenced by final_scorefxn().

core::Size protocols::rosetta_scripts::ParsedProtocol::last_attempted_mover_idx_

private

Referenced by last_attempted_mover_idx().

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

private

Referenced by apply_mover().

std::string protocols::rosetta_scripts::ParsedProtocol::mode_

private

Referenced by apply(), get_additional_output(), mode(), and parse_my_tag().

MoverFilterVector protocols::rosetta_scripts::ParsedProtocol::movers_

private

Referenced by add_values_to_job(), apply(), apply_probability(), begin(), clear(), end(), finish_protocol(), get_additional_output(), get_mover(), parse_my_tag(), random_order_protocol(), random_single_protocol(), report_all(), report_filters_to_pose(), sequence_protocol(), set_resid(), and size().

bool protocols::rosetta_scripts::ParsedProtocol::report_call_order_

private

Referenced by report_call_order().

bool protocols::rosetta_scripts::ParsedProtocol::resume_support_

private

Referenced by apply(), get_additional_output(), and parse_my_tag().

---

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

• src/protocols/rosetta_scripts/ParsedProtocol.hh
• src/protocols/rosetta_scripts/ParsedProtocol.cc