protocols::design_opt::ParetoOptMutationMover Class Reference

#include <ParetoOptMutationMover.hh>

Inheritance diagram for protocols::design_opt::ParetoOptMutationMover:

Collaboration diagram for protocols::design_opt::ParetoOptMutationMover:

Public Types
typedef core::pose::Pose	Pose
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr
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
	ParetoOptMutationMover ()
	default ctor More...
	ParetoOptMutationMover (core::pack::task::TaskFactoryOP task_factory, core::scoring::ScoreFunctionOP scorefxn, protocols::moves::MoverOP relax_mover, utility::vector1< protocols::filters::FilterOP > filters, utility::vector1< std::string > sample_types, utility::vector1< core::Real > filter_deltas, bool dump_pdb=false, bool dump_table=false, bool parallel=false, bool stop_before_condition=false, bool skip_best_check=false, bool rtmin=false, bool shuffle_order=false, protocols::filters::FilterOP stopping_condition=protocols::filters::FilterOP(NULL))
void	apply (Pose &pose)
protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...
virtual std::string	get_name () const
	Each derived class must specify its name. The class name. 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...
void	parse_my_tag (utility::tag::TagPtr const tag, 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	add_filter (protocols::filters::FilterOP, std::string const sample_type, core::Real filter_delta)
virtual	~ParetoOptMutationMover ()
core::pack::task::TaskFactoryOP	task_factory () const
void	task_factory (core::pack::task::TaskFactoryOP task_factory)
core::scoring::ScoreFunctionOP	scorefxn () const
void	scorefxn (core::scoring::ScoreFunctionOP scorefxn)
utility::vector1 < protocols::filters::FilterOP >	filters () const
void	filters (utility::vector1< protocols::filters::FilterOP > filters)
protocols::moves::MoverOP	relax_mover () const
void	relax_mover (protocols::moves::MoverOP relax_mover)
bool	dump_pdb () const
void	dump_pdb (bool const dump_pdb)
bool	dump_table () const
void	dump_table (bool const dump_table)
bool	parallel () const
void	parallel (bool const parallel)
utility::vector1< std::string >	sample_types () const
void	sample_types (utility::vector1< std::string > const sample_types)
utility::vector1< core::Real >	filter_deltas () const
void	filter_deltas (utility::vector1< core::Real > const filter_deltas)
void	stopping_condition (protocols::filters::FilterOP f)
protocols::filters::FilterOP	stopping_condition () const
bool	stop_before_condition () const
void	stop_before_condition (bool const stop_before_condition)
bool	skip_best_check () const
void	skip_best_check (bool const skip_best_check)
utility::vector1 < protocols::simple_filters::DeltaFilterOP >	delta_filters () const
void	delta_filters (utility::vector1< protocols::simple_filters::DeltaFilterOP > const d)
bool	rtmin () const
void	rtmin (bool const b)
bool	shuffle_order () const
void	shuffle_order (bool const b)
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
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 core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. 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
	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

Private Attributes
core::pack::task::TaskFactoryOP	task_factory_
core::scoring::ScoreFunctionOP	scorefxn_
utility::vector1 < protocols::filters::FilterOP >	filters_
protocols::moves::MoverOP	relax_mover_
utility::vector1< std::string >	sample_types_
bool	dump_pdb_
bool	dump_table_
bool	parallel_
protocols::filters::FilterOP	stopping_condition_
utility::vector1< std::pair < core::Size, utility::vector1 < std::pair < core::chemical::AA, utility::vector1< core::Real > > > > >	seqpos_aa_vals_vec_
utility::vector1< core::Real >	filter_deltas_
bool	stop_before_condition_
bool	skip_best_check_
utility::vector1 < protocols::simple_filters::DeltaFilterOP >	reset_delta_filters_
bool	rtmin_
core::Real	design_shell_
core::Real	repack_shell_
bool	shuffle_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...

Detailed Description

Definition at line 34 of file ParetoOptMutationMover.hh.

Member Typedef Documentation

typedef core::pose::Pose protocols::design_opt::ParetoOptMutationMover::Pose

Definition at line 37 of file ParetoOptMutationMover.hh.

Constructor & Destructor Documentation

protocols::design_opt::ParetoOptMutationMover::ParetoOptMutationMover

(

)

default ctor

Definition at line 73 of file ParetoOptMutationMover.cc.

Referenced by clone().

protocols::design_opt::ParetoOptMutationMover::ParetoOptMutationMover	(	core::pack::task::TaskFactoryOP	task_factory,
		core::scoring::ScoreFunctionOP	scorefxn,
		protocols::moves::MoverOP	relax_mover,
		utility::vector1< protocols::filters::FilterOP >	filters,
		utility::vector1< std::string >	sample_types,
		utility::vector1< core::Real >	filter_deltas,
		bool	dump_pdb = false,
		bool	dump_table = false,
		bool	parallel = false,
		bool	stop_before_condition = false,
		bool	skip_best_check = false,
		bool	rtmin = false,
		bool	shuffle_order = false,
		protocols::filters::FilterOP	stopping_condition = protocols::filters::FilterOP(NULL)
	)

protocols::design_opt::ParetoOptMutationMover::~ParetoOptMutationMover ( )

virtual

Definition at line 125 of file ParetoOptMutationMover.cc.

Member Function Documentation

void protocols::design_opt::ParetoOptMutationMover::add_filter	(	protocols::filters::FilterOP	filter,
		std::string const	sample_type,
		core::Real	filter_delta
	)

Definition at line 311 of file ParetoOptMutationMover.cc.

References filter_deltas_, filters_, and sample_types_.

Referenced by parse_my_tag().

void protocols::design_opt::ParetoOptMutationMover::apply ( Pose &  pose)

virtual

Implements protocols::moves::Mover.

Definition at line 296 of file ParetoOptMutationMover.cc.

References dump_pdb(), dump_table(), filter_deltas(), filters(), parallel(), relax_mover(), rtmin(), sample_types(), scorefxn(), shuffle_order(), skip_best_check(), stop_before_condition(), stopping_condition(), and task_factory().

protocols::moves::MoverOP protocols::design_opt::ParetoOptMutationMover::clone ( ) const

virtual

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.

Definition at line 134 of file ParetoOptMutationMover.cc.

References ParetoOptMutationMover().

utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::design_opt::ParetoOptMutationMover::delta_filters

(

)

const

Definition at line 245 of file ParetoOptMutationMover.cc.

References reset_delta_filters_.

void protocols::design_opt::ParetoOptMutationMover::delta_filters

(

utility::vector1< protocols::simple_filters::DeltaFilterOP > const

d)

Definition at line 250 of file ParetoOptMutationMover.cc.

References reset_delta_filters_.

bool protocols::design_opt::ParetoOptMutationMover::dump_pdb

(

)

const

Definition at line 194 of file ParetoOptMutationMover.cc.

References dump_pdb_.

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

void protocols::design_opt::ParetoOptMutationMover::dump_pdb

(

bool const

dump_pdb)

Definition at line 189 of file ParetoOptMutationMover.cc.

References dump_pdb(), and dump_pdb_.

bool protocols::design_opt::ParetoOptMutationMover::dump_table

(

)

const

Definition at line 204 of file ParetoOptMutationMover.cc.

References dump_table_.

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

void protocols::design_opt::ParetoOptMutationMover::dump_table

(

bool const

dump_table)

Definition at line 199 of file ParetoOptMutationMover.cc.

References dump_table(), and dump_table_.

vector1< core::Real > protocols::design_opt::ParetoOptMutationMover::filter_deltas

(

)

const

Definition at line 270 of file ParetoOptMutationMover.cc.

References filter_deltas_.

Referenced by apply(), and filter_deltas().

void protocols::design_opt::ParetoOptMutationMover::filter_deltas

(

utility::vector1< core::Real > const

filter_deltas)

Definition at line 265 of file ParetoOptMutationMover.cc.

References filter_deltas(), and filter_deltas_.

vector1< protocols::filters::FilterOP > protocols::design_opt::ParetoOptMutationMover::filters

(

)

const

Definition at line 172 of file ParetoOptMutationMover.cc.

References filters_.

Referenced by apply(), and filters().

void protocols::design_opt::ParetoOptMutationMover::filters

(

utility::vector1< protocols::filters::FilterOP >

filters)

Definition at line 168 of file ParetoOptMutationMover.cc.

References filters(), and filters_.

protocols::moves::MoverOP protocols::design_opt::ParetoOptMutationMover::fresh_instance ( ) const

inlinevirtual

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.

Definition at line 60 of file ParetoOptMutationMover.hh.

std::string protocols::design_opt::ParetoOptMutationMover::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 152 of file ParetoOptMutationMover.cc.

References protocols::design_opt::ParetoOptMutationMoverCreator::mover_name().

bool protocols::design_opt::ParetoOptMutationMover::parallel

(

)

const

Definition at line 290 of file ParetoOptMutationMover.cc.

References parallel_.

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

void protocols::design_opt::ParetoOptMutationMover::parallel

(

bool const

parallel)

Definition at line 285 of file ParetoOptMutationMover.cc.

References parallel(), and parallel_.

void protocols::design_opt::ParetoOptMutationMover::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  )

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.

Definition at line 322 of file ParetoOptMutationMover.cc.

References add_filter(), design_shell_, dump_pdb(), dump_table(), filters_, parallel(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), relax_mover(), repack_shell_, reset_delta_filters_, rtmin(), scorefxn(), shuffle_order(), skip_best_check(), stop_before_condition(), stopping_condition(), and task_factory().

protocols::moves::MoverOP protocols::design_opt::ParetoOptMutationMover::relax_mover

(

)

const

Definition at line 163 of file ParetoOptMutationMover.cc.

References relax_mover_.

Referenced by apply(), and parse_my_tag().

void protocols::design_opt::ParetoOptMutationMover::relax_mover

(

protocols::moves::MoverOP

relax_mover)

Definition at line 158 of file ParetoOptMutationMover.cc.

References relax_mover_.

bool protocols::design_opt::ParetoOptMutationMover::rtmin

(

)

const

Definition at line 234 of file ParetoOptMutationMover.cc.

References rtmin_.

Referenced by apply(), and parse_my_tag().

void protocols::design_opt::ParetoOptMutationMover::rtmin

(

bool const

b)

Definition at line 229 of file ParetoOptMutationMover.cc.

References protocols::match::upstream::b, and rtmin_.

vector1< std::string > protocols::design_opt::ParetoOptMutationMover::sample_types

(

)

const

Definition at line 260 of file ParetoOptMutationMover.cc.

References sample_types_.

Referenced by apply().

void protocols::design_opt::ParetoOptMutationMover::sample_types

(

utility::vector1< std::string > const

sample_types)

core::scoring::ScoreFunctionOP protocols::design_opt::ParetoOptMutationMover::scorefxn

(

)

const

Definition at line 280 of file ParetoOptMutationMover.cc.

References scorefxn_.

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

void protocols::design_opt::ParetoOptMutationMover::scorefxn

(

core::scoring::ScoreFunctionOP

scorefxn)

Definition at line 275 of file ParetoOptMutationMover.cc.

References scorefxn(), and scorefxn_.

bool protocols::design_opt::ParetoOptMutationMover::shuffle_order

(

)

const

Definition at line 242 of file ParetoOptMutationMover.cc.

References shuffle_order_.

Referenced by apply(), and parse_my_tag().

void protocols::design_opt::ParetoOptMutationMover::shuffle_order

(

bool const

b)

Definition at line 237 of file ParetoOptMutationMover.cc.

References protocols::match::upstream::b, and shuffle_order_.

bool protocols::design_opt::ParetoOptMutationMover::skip_best_check

(

)

const

Definition at line 224 of file ParetoOptMutationMover.cc.

References skip_best_check_.

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

void protocols::design_opt::ParetoOptMutationMover::skip_best_check

(

bool const

skip_best_check)

Definition at line 219 of file ParetoOptMutationMover.cc.

References skip_best_check(), and skip_best_check_.

bool protocols::design_opt::ParetoOptMutationMover::stop_before_condition

(

)

const

Definition at line 214 of file ParetoOptMutationMover.cc.

References stop_before_condition_.

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

void protocols::design_opt::ParetoOptMutationMover::stop_before_condition

(

bool const

stop_before_condition)

Definition at line 209 of file ParetoOptMutationMover.cc.

References stop_before_condition(), and stop_before_condition_.

void protocols::design_opt::ParetoOptMutationMover::stopping_condition ( protocols::filters::FilterOP  f)

inline

Definition at line 87 of file ParetoOptMutationMover.hh.

References stopping_condition_.

protocols::filters::FilterOP protocols::design_opt::ParetoOptMutationMover::stopping_condition ( ) const

inline

Definition at line 88 of file ParetoOptMutationMover.hh.

References stopping_condition_.

Referenced by apply(), and parse_my_tag().

core::pack::task::TaskFactoryOP protocols::design_opt::ParetoOptMutationMover::task_factory

(

)

const

Definition at line 183 of file ParetoOptMutationMover.cc.

References task_factory_.

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

void protocols::design_opt::ParetoOptMutationMover::task_factory

(

core::pack::task::TaskFactoryOP

task_factory)

Definition at line 177 of file ParetoOptMutationMover.cc.

References task_factory(), and task_factory_.

Member Data Documentation

core::Real protocols::design_opt::ParetoOptMutationMover::design_shell_

private

Definition at line 117 of file ParetoOptMutationMover.hh.

Referenced by parse_my_tag().

bool protocols::design_opt::ParetoOptMutationMover::dump_pdb_

private

Definition at line 106 of file ParetoOptMutationMover.hh.

Referenced by dump_pdb().

bool protocols::design_opt::ParetoOptMutationMover::dump_table_

private

Definition at line 107 of file ParetoOptMutationMover.hh.

Referenced by dump_table().

utility::vector1< core::Real > protocols::design_opt::ParetoOptMutationMover::filter_deltas_

private

Definition at line 112 of file ParetoOptMutationMover.hh.

Referenced by add_filter(), and filter_deltas().

utility::vector1< protocols::filters::FilterOP > protocols::design_opt::ParetoOptMutationMover::filters_

private

Definition at line 103 of file ParetoOptMutationMover.hh.

Referenced by add_filter(), filters(), and parse_my_tag().

bool protocols::design_opt::ParetoOptMutationMover::parallel_

private

Definition at line 108 of file ParetoOptMutationMover.hh.

Referenced by parallel().

protocols::moves::MoverOP protocols::design_opt::ParetoOptMutationMover::relax_mover_

private

Definition at line 104 of file ParetoOptMutationMover.hh.

Referenced by relax_mover().

core::Real protocols::design_opt::ParetoOptMutationMover::repack_shell_

private

Definition at line 118 of file ParetoOptMutationMover.hh.

Referenced by parse_my_tag().

utility::vector1<protocols::simple_filters::DeltaFilterOP> protocols::design_opt::ParetoOptMutationMover::reset_delta_filters_

private

Definition at line 115 of file ParetoOptMutationMover.hh.

Referenced by delta_filters(), and parse_my_tag().

bool protocols::design_opt::ParetoOptMutationMover::rtmin_

private

Definition at line 116 of file ParetoOptMutationMover.hh.

Referenced by rtmin().

utility::vector1< std::string > protocols::design_opt::ParetoOptMutationMover::sample_types_

private

Definition at line 105 of file ParetoOptMutationMover.hh.

Referenced by add_filter(), and sample_types().

core::scoring::ScoreFunctionOP protocols::design_opt::ParetoOptMutationMover::scorefxn_

private

Definition at line 102 of file ParetoOptMutationMover.hh.

Referenced by scorefxn().

utility::vector1< std::pair< core::Size, utility::vector1< std::pair< core::chemical::AA, utility::vector1< core::Real > > > > > protocols::design_opt::ParetoOptMutationMover::seqpos_aa_vals_vec_

private

Definition at line 111 of file ParetoOptMutationMover.hh.

bool protocols::design_opt::ParetoOptMutationMover::shuffle_order_

private

Definition at line 119 of file ParetoOptMutationMover.hh.

Referenced by shuffle_order().

bool protocols::design_opt::ParetoOptMutationMover::skip_best_check_

private

Definition at line 114 of file ParetoOptMutationMover.hh.

Referenced by skip_best_check().

bool protocols::design_opt::ParetoOptMutationMover::stop_before_condition_

private

Definition at line 113 of file ParetoOptMutationMover.hh.

Referenced by stop_before_condition().

protocols::filters::FilterOP protocols::design_opt::ParetoOptMutationMover::stopping_condition_

private

Definition at line 109 of file ParetoOptMutationMover.hh.

Referenced by stopping_condition().

core::pack::task::TaskFactoryOP protocols::design_opt::ParetoOptMutationMover::task_factory_

private

Definition at line 101 of file ParetoOptMutationMover.hh.

Referenced by task_factory().

---

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

• src/protocols/design_opt/ParetoOptMutationMover.hh
• src/protocols/design_opt/ParetoOptMutationMover.cc