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protocols::design_opt::GreedyOptMutationMover Class Reference

#include <GreedyOptMutationMover.hh>

Inheritance diagram for protocols::design_opt::GreedyOptMutationMover:
Inheritance graph
Collaboration diagram for protocols::design_opt::GreedyOptMutationMover:
Collaboration graph

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 std::list< std::string > Strings

Public Member Functions

 GreedyOptMutationMover ()
 default ctor More...
 GreedyOptMutationMover (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))
bool pose_coords_are_same (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
void filter_seqpos_pareto_opt_ptmuts ()
void clear_cached_data ()
void calc_pfront_poses_filter_ranks ()
void dump_scoring_table (std::string filename, core::pose::Pose const &ref_pose) const
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 ~GreedyOptMutationMover ()
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)
< 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::Realfilter_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)
< 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)
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 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 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

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
core::scoring::ScoreFunctionOP scorefxn_
< protocols::filters::FilterOP
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 > > > > > 
utility::vector1< core::Realfilter_deltas_
core::pose::Pose ref_pose_
< core::pose::Pose
< utility::vector1< core::Real > > 
< utility::vector1< core::Size > > 
core::Size nstruct_iter_
bool stop_before_condition_
bool skip_best_check_
< protocols::simple_filters::DeltaFilterOP
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...

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::design_opt::GreedyOptMutationMover::GreedyOptMutationMover ( )

default ctor

Referenced by clone().

protocols::design_opt::GreedyOptMutationMover::GreedyOptMutationMover ( 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::GreedyOptMutationMover::~GreedyOptMutationMover ( )

Member Function Documentation

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

References filter_deltas_, filters_, and sample_types_.

Referenced by parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::apply ( Pose pose)
void protocols::design_opt::GreedyOptMutationMover::calc_pfront_poses_filter_ranks ( )
void protocols::design_opt::GreedyOptMutationMover::clear_cached_data ( )
protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::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.

References GreedyOptMutationMover().

utility::vector1< protocols::simple_filters::DeltaFilterOP > protocols::design_opt::GreedyOptMutationMover::delta_filters ( ) const

References reset_delta_filters_.

void protocols::design_opt::GreedyOptMutationMover::delta_filters ( utility::vector1< protocols::simple_filters::DeltaFilterOP > const  d)

References reset_delta_filters_.

bool protocols::design_opt::GreedyOptMutationMover::dump_pdb ( ) const

References dump_pdb_.

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

void protocols::design_opt::GreedyOptMutationMover::dump_pdb ( bool const  dump_pdb)
void protocols::design_opt::GreedyOptMutationMover::dump_scoring_table ( std::string  filename,
core::pose::Pose const &  ref_pose 
) const
bool protocols::design_opt::GreedyOptMutationMover::dump_table ( ) const

References dump_table_.

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

void protocols::design_opt::GreedyOptMutationMover::dump_table ( bool const  dump_table)
vector1< core::Real > protocols::design_opt::GreedyOptMutationMover::filter_deltas ( ) const

References filter_deltas_.

Referenced by filter_deltas().

void protocols::design_opt::GreedyOptMutationMover::filter_deltas ( utility::vector1< core::Real > const  filter_deltas)
void protocols::design_opt::GreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts ( )
vector1< protocols::filters::FilterOP > protocols::design_opt::GreedyOptMutationMover::filters ( ) const

References filters_.

Referenced by apply(), and filters().

void protocols::design_opt::GreedyOptMutationMover::filters ( utility::vector1< protocols::filters::FilterOP filters)
protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::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.

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

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

Implements protocols::moves::Mover.

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

bool protocols::design_opt::GreedyOptMutationMover::parallel ( ) const

References parallel_.

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

void protocols::design_opt::GreedyOptMutationMover::parallel ( bool const  parallel)

References parallel(), and parallel_.

void protocols::design_opt::GreedyOptMutationMover::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 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().

bool protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 
protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::relax_mover ( ) const

References relax_mover_.

Referenced by apply(), and parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::relax_mover ( protocols::moves::MoverOP  relax_mover)
bool protocols::design_opt::GreedyOptMutationMover::rtmin ( ) const

References rtmin_.

Referenced by parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::rtmin ( bool const  b)
vector1< std::string > protocols::design_opt::GreedyOptMutationMover::sample_types ( ) const

References sample_types_.

Referenced by apply().

void protocols::design_opt::GreedyOptMutationMover::sample_types ( utility::vector1< std::string > const  sample_types)
core::scoring::ScoreFunctionOP protocols::design_opt::GreedyOptMutationMover::scorefxn ( ) const

References scorefxn_.

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

void protocols::design_opt::GreedyOptMutationMover::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
bool protocols::design_opt::GreedyOptMutationMover::shuffle_order ( ) const

References shuffle_order_.

Referenced by apply(), and parse_my_tag().

void protocols::design_opt::GreedyOptMutationMover::shuffle_order ( bool const  b)
bool protocols::design_opt::GreedyOptMutationMover::skip_best_check ( ) const

References skip_best_check_.

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

void protocols::design_opt::GreedyOptMutationMover::skip_best_check ( bool const  skip_best_check)
bool protocols::design_opt::GreedyOptMutationMover::stop_before_condition ( ) const
void protocols::design_opt::GreedyOptMutationMover::stop_before_condition ( bool const  stop_before_condition)
void protocols::design_opt::GreedyOptMutationMover::stopping_condition ( protocols::filters::FilterOP  f)

References stopping_condition_.

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

References stopping_condition_.

Referenced by apply(), and parse_my_tag().

core::pack::task::TaskFactoryOP protocols::design_opt::GreedyOptMutationMover::task_factory ( ) const

References task_factory_.

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

void protocols::design_opt::GreedyOptMutationMover::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

Member Data Documentation

core::Real protocols::design_opt::GreedyOptMutationMover::design_shell_

Referenced by parse_my_tag().

bool protocols::design_opt::GreedyOptMutationMover::dump_pdb_

Referenced by dump_pdb().

bool protocols::design_opt::GreedyOptMutationMover::dump_table_

Referenced by dump_table().

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

Referenced by add_filter(), and filter_deltas().

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

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

core::Size protocols::design_opt::GreedyOptMutationMover::nstruct_iter_

Referenced by apply().

bool protocols::design_opt::GreedyOptMutationMover::parallel_

Referenced by parallel().

utility::vector1< core::pose::Pose > protocols::design_opt::GreedyOptMutationMover::pfront_poses_

Referenced by apply(), and clear_cached_data().

utility::vector1< utility::vector1< core::Size > > protocols::design_opt::GreedyOptMutationMover::pfront_poses_filter_ranks_
utility::vector1< utility::vector1< core::Real > > protocols::design_opt::GreedyOptMutationMover::pfront_poses_filter_vals_
core::pose::Pose protocols::design_opt::GreedyOptMutationMover::ref_pose_

Referenced by apply(), and clear_cached_data().

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::relax_mover_

Referenced by relax_mover().

core::Real protocols::design_opt::GreedyOptMutationMover::repack_shell_

Referenced by parse_my_tag().

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

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

bool protocols::design_opt::GreedyOptMutationMover::rtmin_

Referenced by rtmin().

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

Referenced by add_filter(), and sample_types().

core::scoring::ScoreFunctionOP protocols::design_opt::GreedyOptMutationMover::scorefxn_

Referenced by scorefxn().

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

Referenced by shuffle_order().

bool protocols::design_opt::GreedyOptMutationMover::skip_best_check_

Referenced by skip_best_check().

bool protocols::design_opt::GreedyOptMutationMover::stop_before_condition_

Referenced by stop_before_condition().

protocols::filters::FilterOP protocols::design_opt::GreedyOptMutationMover::stopping_condition_

Referenced by stopping_condition().

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

Referenced by task_factory().

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