Public Types | Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::design_opt::GreedyOptMutationMover Class Reference

#include <GreedyOptMutationMover.hh>

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

Public Types

typedef core::pose::Pose Pose
- 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::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, bool diversify=false, bool incl_nonopt=false, protocols::filters::FilterOP stopping_condition=protocols::filters::FilterOP(nullptr))
bool pose_coords_are_same (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
void filter_seqpos_pareto_opt_ptmuts ()
void filter_pareto_opt_poses ()
void downsample_pfront_poses ()
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) override
 Main Method. More...
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 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)
 ~GreedyOptMutationMover () override
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::FilterOPfilters () 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)
utility::vector1< protocols::simple_filters::DeltaFilterOPdelta_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)
bool diversify () const
void diversify (bool const b)
bool incl_nonopt () const
void incl_nonopt (bool const b)
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual MoverOP create ()
MoverCOP get_self_ptr () const
MoverOP get_self_ptr ()
MoverCAP get_self_weak_ptr () const
MoverAP get_self_weak_ptr ()
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
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...
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...
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...
void set_type (std::string const &setting)
 Set the 'type' string. More...
std::string get_type () const
void type (const std::string &type_in)
 Set the 'type' string. More...
std::string const & type () const
 Get the set 'type' string. More...
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
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const
virtual void set_current_tag (std::string const &new_tag)
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...
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
virtual core::Real last_proposal_density_ratio ()
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions

static std::string mover_name ()
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
static std::string subelement_ct_namer (std::string tag_name)
static std::string subsubelement_ct_namer (std::string tag_name)
static utility::tag::XMLSchemaRepeatableCTNodeOP root_node_for_greedy_opt (utility::tag::AttributeList &attlist1, utility::tag::XMLSchemaDefinition &xsd)
- 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...

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
core::scoring::ScoreFunctionOP scorefxn_
utility::vector1< protocols::filters::FilterOPfilters_
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::Realfilter_deltas_
core::pose::Pose ref_pose_
utility::vector1< core::pose::Posepfront_poses_
utility::vector1< utility::vector1< core::Real > > pfront_poses_filter_vals_
utility::vector1< utility::vector1< core::Size > > pfront_poses_filter_ranks_
core::Size nstruct_iter_
bool stop_before_condition_
bool skip_best_check_
utility::vector1< protocols::simple_filters::DeltaFilterOPreset_delta_filters_
bool rtmin_
core::Real design_shell_
core::Real repack_shell_
bool shuffle_order_
bool diversify_
bool incl_nonopt_

Additional Inherited Members

- 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

◆ Pose

Constructor & Destructor Documentation

◆ GreedyOptMutationMover() [1/2]

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

default ctor

◆ GreedyOptMutationMover() [2/2]

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,
bool  diversify = false,
bool  incl_nonopt = false,
protocols::filters::FilterOP  stopping_condition = protocols::filters::FilterOP(nullptr) 

◆ ~GreedyOptMutationMover()

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

Member Function Documentation

◆ add_filter()

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().

◆ apply()

void protocols::design_opt::GreedyOptMutationMover::apply ( Pose )

◆ calc_pfront_poses_filter_ranks()

void protocols::design_opt::GreedyOptMutationMover::calc_pfront_poses_filter_ranks ( )

◆ clear_cached_data()

void protocols::design_opt::GreedyOptMutationMover::clear_cached_data ( )

◆ clone()

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::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.

◆ delta_filters() [1/2]

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

References reset_delta_filters_.

◆ delta_filters() [2/2]

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

References reset_delta_filters_.

◆ diversify() [1/2]

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

References diversify_.

Referenced by parse_my_tag().

◆ diversify() [2/2]

void protocols::design_opt::GreedyOptMutationMover::diversify ( bool const  b)

◆ downsample_pfront_poses()

void protocols::design_opt::GreedyOptMutationMover::downsample_pfront_poses ( )

◆ dump_pdb() [1/2]

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

References dump_pdb_.

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

◆ dump_pdb() [2/2]

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

◆ dump_scoring_table()

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

◆ dump_table() [1/2]

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

References dump_table_.

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

◆ dump_table() [2/2]

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

◆ filter_deltas() [1/2]

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

References filter_deltas_.

◆ filter_deltas() [2/2]

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

◆ filter_pareto_opt_poses()

void protocols::design_opt::GreedyOptMutationMover::filter_pareto_opt_poses ( )

◆ filter_seqpos_pareto_opt_ptmuts()

void protocols::design_opt::GreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts ( )

◆ filters() [1/2]

vector1< protocols::filters::FilterOP > protocols::design_opt::GreedyOptMutationMover::filters ( ) const

References filters_.

Referenced by apply().

◆ filters() [2/2]

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

◆ fresh_instance()

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::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.

◆ get_name()

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

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

Implements protocols::moves::Mover.

References mover_name().

◆ incl_nonopt() [1/2]

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

References incl_nonopt_.

Referenced by parse_my_tag().

◆ incl_nonopt() [2/2]

void protocols::design_opt::GreedyOptMutationMover::incl_nonopt ( bool const  b)

◆ mover_name()

std::string protocols::design_opt::GreedyOptMutationMover::mover_name ( )

◆ parallel() [1/2]

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

References parallel_.

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

◆ parallel() [2/2]

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

References parallel(), and parallel_.

◆ parse_my_tag()

void protocols::design_opt::GreedyOptMutationMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References add_filter(), design_shell_, diversify(), dump_pdb(), dump_table(), filters_, incl_nonopt(), parallel(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), relax_mover(), repack_shell_, reset_delta_filters_, rtmin(), scorefxn(), shuffle_order(), skip_best_check(), stop_before_condition(), stopping_condition(), task_factory(), and protocols::design_opt::TR().

◆ pose_coords_are_same()

bool protocols::design_opt::GreedyOptMutationMover::pose_coords_are_same ( core::pose::Pose const &  pose1,
core::pose::Pose const &  pose2 

◆ provide_xml_schema()

void protocols::design_opt::GreedyOptMutationMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ relax_mover() [1/2]

protocols::moves::MoverOP protocols::design_opt::GreedyOptMutationMover::relax_mover ( ) const

References relax_mover_.

Referenced by apply(), and parse_my_tag().

◆ relax_mover() [2/2]

void protocols::design_opt::GreedyOptMutationMover::relax_mover ( protocols::moves::MoverOP  relax_mover)

◆ root_node_for_greedy_opt()

utility::tag::XMLSchemaRepeatableCTNodeOP protocols::design_opt::GreedyOptMutationMover::root_node_for_greedy_opt ( utility::tag::AttributeList &  attlist1,
utility::tag::XMLSchemaDefinition &  xsd 

◆ rtmin() [1/2]

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

References rtmin_.

Referenced by parse_my_tag().

◆ rtmin() [2/2]

void protocols::design_opt::GreedyOptMutationMover::rtmin ( bool const  b)

◆ sample_types() [1/2]

vector1< std::string > protocols::design_opt::GreedyOptMutationMover::sample_types ( ) const

References sample_types_.

Referenced by apply().

◆ sample_types() [2/2]

void protocols::design_opt::GreedyOptMutationMover::sample_types ( utility::vector1< std::string > const  sample_types)

◆ scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::design_opt::GreedyOptMutationMover::scorefxn ( ) const

References scorefxn_.

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

◆ scorefxn() [2/2]

void protocols::design_opt::GreedyOptMutationMover::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)

◆ shuffle_order() [1/2]

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

References shuffle_order_.

Referenced by apply(), and parse_my_tag().

◆ shuffle_order() [2/2]

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

◆ skip_best_check() [1/2]

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

References skip_best_check_.

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

◆ skip_best_check() [2/2]

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

◆ stop_before_condition() [1/2]

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

◆ stop_before_condition() [2/2]

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

◆ stopping_condition() [1/2]

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

References stopping_condition_.

Referenced by apply(), and parse_my_tag().

◆ stopping_condition() [2/2]

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

References stopping_condition_.

◆ subelement_ct_namer()

std::string protocols::design_opt::GreedyOptMutationMover::subelement_ct_namer ( std::string  tag_name)

◆ subsubelement_ct_namer()

std::string protocols::design_opt::GreedyOptMutationMover::subsubelement_ct_namer ( std::string  tag_name)

◆ task_factory() [1/2]

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

References task_factory_.

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

◆ task_factory() [2/2]

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

Member Data Documentation

◆ design_shell_

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

Referenced by parse_my_tag().

◆ diversify_

bool protocols::design_opt::GreedyOptMutationMover::diversify_

◆ dump_pdb_

bool protocols::design_opt::GreedyOptMutationMover::dump_pdb_

Referenced by dump_pdb().

◆ dump_table_

bool protocols::design_opt::GreedyOptMutationMover::dump_table_

Referenced by dump_table().

◆ filter_deltas_

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

◆ filters_

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

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

◆ incl_nonopt_

bool protocols::design_opt::GreedyOptMutationMover::incl_nonopt_

◆ nstruct_iter_

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

Referenced by apply().

◆ parallel_

bool protocols::design_opt::GreedyOptMutationMover::parallel_

Referenced by parallel().

◆ pfront_poses_

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

◆ pfront_poses_filter_ranks_

utility::vector1< utility::vector1< core::Size > > protocols::design_opt::GreedyOptMutationMover::pfront_poses_filter_ranks_

◆ pfront_poses_filter_vals_

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

◆ ref_pose_

core::pose::Pose protocols::design_opt::GreedyOptMutationMover::ref_pose_

Referenced by apply(), and clear_cached_data().

◆ relax_mover_

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

Referenced by relax_mover().

◆ repack_shell_

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

Referenced by parse_my_tag().

◆ reset_delta_filters_

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

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

◆ rtmin_

bool protocols::design_opt::GreedyOptMutationMover::rtmin_

Referenced by rtmin().

◆ sample_types_

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

Referenced by add_filter(), and sample_types().

◆ scorefxn_

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

Referenced by scorefxn().

◆ seqpos_aa_vals_vec_

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_

◆ shuffle_order_

bool protocols::design_opt::GreedyOptMutationMover::shuffle_order_

Referenced by shuffle_order().

◆ skip_best_check_

bool protocols::design_opt::GreedyOptMutationMover::skip_best_check_

Referenced by skip_best_check().

◆ stop_before_condition_

bool protocols::design_opt::GreedyOptMutationMover::stop_before_condition_

Referenced by stop_before_condition().

◆ stopping_condition_

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

Referenced by stopping_condition().

◆ task_factory_

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: