Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::stepwise::sampler::StepWiseSamplerBase Class Referenceabstract

#include <StepWiseSamplerBase.hh>

Public Types

typedef utility::vector1
< core::Real
TorsionList
 
- 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::stringStrings
 

Public Member Functions

 StepWiseSamplerBase ()
 
virtual ~StepWiseSamplerBase ()
 
virtual void init ()=0
 Initialization. More...
 
virtual void reset ()=0
 Reset to the first (or random if random()) rotamer. More...
 
virtual void operator++ ()=0
 Move to next rotamer. More...
 
virtual bool not_end () const
 Check if there are more rotamers available. More...
 
virtual bool random () const
 Check if is random modeler. More...
 
virtual void set_random (bool const setting)
 Set the random modeler state. More...
 
virtual void apply (core::pose::Pose &)=0
 Apply the current rotamer to pose. More...
 
virtual std::string get_name () const =0
 Name of the class. More...
 
virtual StepWiseSamplerType type () const =0
 Type of class (see enum in StepWiseSamplerTypes.hh) More...
 
virtual void show (std::ostream &out, Size const indent=0) const
 output summary of class More...
 
- 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)
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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
 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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...
 

Protected Member Functions

bool is_init () const
 Check if the sampler has been initialized. More...
 
void set_init (bool const setting)
 Set the initialization state. More...
 
template<class T >
void set_and_reinit (T &params, T const &setting)
 Set value of a parameter, return to pre-init state. 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...
 

Private Attributes

bool is_init_
 
bool random_
 

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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::stepwise::sampler::StepWiseSamplerBase::StepWiseSamplerBase ( )
inline
virtual protocols::stepwise::sampler::StepWiseSamplerBase::~StepWiseSamplerBase ( )
inlinevirtual

Member Function Documentation

virtual void protocols::stepwise::sampler::StepWiseSamplerBase::apply ( core::pose::Pose )
pure virtual
virtual std::string protocols::stepwise::sampler::StepWiseSamplerBase::get_name ( ) const
pure virtual

Name of the class.

Implements protocols::moves::Mover.

Implemented in protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler, protocols::stepwise::sampler::rna::RNA_MC_Suite, protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerSizedComb, protocols::stepwise::sampler::MC_OneTorsion, protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerOneValue, protocols::stepwise::sampler::StepWiseSamplerAny, protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler, protocols::stepwise::sampler::rna::RNA_KIC_Sampler, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives, protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler, protocols::stepwise::sampler::rna::RNA_MC_Sugar, protocols::stepwise::sampler::StepWiseSamplerSizedAny, protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerOneTorsion, protocols::stepwise::sampler::MC_Comb, protocols::stepwise::sampler::rna::RNA_MC_MultiSuite, protocols::stepwise::sampler::StepWiseSamplerComb, protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb, protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerSized, protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler, protocols::stepwise::sampler::rna::RNA_KinematicCloser, protocols::stepwise::sampler::JumpStepWiseSampler, protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler, protocols::stepwise::sampler::MC_StepWiseSampler, protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler, protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerOneValueComb, protocols::stepwise::sampler::NoOpStepWiseSampler, and protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler.

Referenced by show().

virtual void protocols::stepwise::sampler::StepWiseSamplerBase::init ( )
pure virtual
bool protocols::stepwise::sampler::StepWiseSamplerBase::is_init ( ) const
inlineprotected

Check if the sampler has been initialized.

References is_init_.

Referenced by protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::apply(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::apply(), protocols::stepwise::sampler::StepWiseSamplerAny::apply(), protocols::stepwise::sampler::StepWiseSamplerComb::apply(), protocols::stepwise::sampler::MC_Comb::apply(), protocols::stepwise::sampler::rna::RNA_MC_Sugar::apply(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::apply(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::apply(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::id2list(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::id2state(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::list2id(), protocols::stepwise::sampler::StepWiseSamplerAny::not_end(), protocols::stepwise::sampler::StepWiseSamplerComb::not_end(), protocols::stepwise::sampler::StepWiseSamplerSized::not_end(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::not_end(), protocols::stepwise::sampler::rna::RNA_MC_Sugar::operator++(), protocols::stepwise::sampler::StepWiseSamplerComb::reset(), protocols::stepwise::sampler::MC_Comb::reset(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::reset(), protocols::stepwise::sampler::StepWiseSamplerAny::reset(), protocols::stepwise::sampler::StepWiseSamplerSized::reset(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::reset(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::reset(), protocols::stepwise::sampler::rna::RNA_MC_Suite::set_gaussian_stdev(), protocols::stepwise::sampler::rna::RNA_MC_Suite::set_pucker_flip_rate(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::set_random(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::size(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::size(), protocols::stepwise::sampler::StepWiseSamplerOneValue::size(), protocols::stepwise::sampler::MC_Comb::update(), and protocols::stepwise::sampler::StepWiseSamplerOneValue::value().

virtual bool protocols::stepwise::sampler::StepWiseSamplerBase::not_end ( ) const
inlinevirtual
virtual void protocols::stepwise::sampler::StepWiseSamplerBase::operator++ ( )
pure virtual
virtual bool protocols::stepwise::sampler::StepWiseSamplerBase::random ( ) const
inlinevirtual

Check if is random modeler.

References random_.

Referenced by protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler::apply(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::apply(), protocols::stepwise::sampler::StepWiseSamplerComb::init(), protocols::stepwise::sampler::StepWiseSamplerAny::init(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::init(), protocols::stepwise::sampler::StepWiseSamplerAny::not_end(), protocols::stepwise::sampler::StepWiseSamplerComb::not_end(), protocols::stepwise::sampler::StepWiseSamplerAny::operator++(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::operator++(), protocols::stepwise::sampler::StepWiseSamplerComb::operator++(), protocols::stepwise::sampler::StepWiseSamplerSized::operator++(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::operator++(), protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler::operator++(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::operator++(), protocols::stepwise::StepWiseSampleAndScreen::output_info_on_random_trials(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::reset(), protocols::stepwise::sampler::StepWiseSamplerSized::reset(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::reset(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::reset(), protocols::stepwise::StepWiseSampleAndScreen::run(), protocols::stepwise::sampler::StepWiseSamplerAny::set_random(), and protocols::stepwise::sampler::StepWiseSamplerComb::set_random().

virtual void protocols::stepwise::sampler::StepWiseSamplerBase::reset ( )
pure virtual
template<class T >
void protocols::stepwise::sampler::StepWiseSamplerBase::set_and_reinit ( T params,
T const &  setting 
)
inlineprotected
void protocols::stepwise::sampler::StepWiseSamplerBase::set_init ( bool const  setting)
inlineprotected

Set the initialization state.

References is_init_.

Referenced by protocols::stepwise::sampler::MC_Comb::add_external_loop_rotamer(), protocols::stepwise::sampler::StepWiseSamplerComb::add_external_loop_rotamer(), protocols::stepwise::sampler::StepWiseSamplerAny::add_external_loop_rotamer(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::add_external_loop_rotamer(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::add_external_loop_rotamer(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::add_internal_loop_rotamer(), protocols::stepwise::sampler::StepWiseSamplerComb::clear_rotamer(), protocols::stepwise::sampler::MC_Comb::clear_rotamer(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::clear_rotamer(), protocols::stepwise::sampler::StepWiseSamplerAny::clear_rotamer(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::clear_rotamer(), protocols::stepwise::sampler::MC_Comb::init(), protocols::stepwise::sampler::StepWiseSamplerComb::init(), protocols::stepwise::sampler::StepWiseSamplerSizedAny::init(), protocols::stepwise::sampler::StepWiseSamplerAny::init(), protocols::stepwise::sampler::StepWiseSamplerSized::init(), protocols::stepwise::sampler::MC_OneTorsion::init(), protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler::init(), protocols::stepwise::sampler::rna::RNA_MC_Sugar::init(), protocols::stepwise::sampler::StepWiseSamplerSizedComb::init(), protocols::stepwise::sampler::StepWiseSamplerOneValue::init(), protocols::stepwise::sampler::rna::RNA_MC_Suite::init(), protocols::stepwise::sampler::rna::RNA_KIC_Sampler::init(), protocols::stepwise::sampler::rna::RNA_KinematicCloser::init(), protocols::stepwise::sampler::rna::RNA_MC_Sugar::set_idealize_coord(), protocols::stepwise::sampler::rna::RNA_MC_Suite::set_init_from_pose(), protocols::stepwise::sampler::rna::RNA_MC_Suite::set_init_states(), protocols::stepwise::sampler::rna::RNA_MC_Sugar::set_skip_same_pucker(), and protocols::stepwise::sampler::StepWiseSamplerAny::set_weights().

virtual void protocols::stepwise::sampler::StepWiseSamplerBase::set_random ( bool const  setting)
inlinevirtual
virtual void protocols::stepwise::sampler::StepWiseSamplerBase::show ( std::ostream &  out,
Size const  indent = 0 
) const
inlinevirtual
virtual StepWiseSamplerType protocols::stepwise::sampler::StepWiseSamplerBase::type ( ) const
pure virtual

Type of class (see enum in StepWiseSamplerTypes.hh)

Implemented in protocols::stepwise::sampler::rna::RNA_MC_Suite, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler, protocols::stepwise::sampler::rna::RNA_SuiteStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerSizedComb, protocols::stepwise::sampler::MC_OneTorsion, protocols::stepwise::sampler::rna::RNA_ChiStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerOneValue, protocols::stepwise::sampler::StepWiseSamplerAny, protocols::stepwise::sampler::rna::RNA_KIC_Sampler, protocols::stepwise::sampler::rna::RNA_SugarStepWiseSampler, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueList, protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSamplerWithResidueAlternatives, protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSampler, protocols::stepwise::sampler::rna::RNA_MC_Sugar, protocols::stepwise::sampler::StepWiseSamplerSizedAny, protocols::stepwise::sampler::rna::RNA_NucleosideStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerOneTorsion, protocols::stepwise::sampler::rna::RNA_MC_MultiSuite, protocols::stepwise::sampler::StepWiseSamplerComb, protocols::stepwise::sampler::copy_dofs::ResidueAlternativeStepWiseSamplerComb, protocols::stepwise::sampler::input_streams::InputStreamStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerSized, protocols::stepwise::sampler::copy_dofs::CopyDofStepWiseSampler, protocols::stepwise::sampler::rna::RNA_KinematicCloser, protocols::stepwise::sampler::JumpStepWiseSampler, protocols::stepwise::sampler::protein::ProteinFragmentStepWiseSampler, protocols::stepwise::sampler::protein::ProteinMainChainStepWiseSampler, protocols::stepwise::sampler::copy_dofs::ResidueListStepWiseSampler, protocols::stepwise::sampler::StepWiseSamplerOneValueComb, protocols::stepwise::sampler::NoOpStepWiseSampler, and protocols::stepwise::sampler::protein::ProteinBetaAntiParallelStepWiseSampler.

Referenced by protocols::stepwise::StepWiseSampleAndScreen::early_exit_check(), protocols::stepwise::screener::IntegrationTestBreaker::fast_forward(), protocols::stepwise::screener::StubDistanceScreener::fast_forward(), protocols::stepwise::screener::CentroidDistanceScreener::fast_forward(), protocols::stepwise::screener::BaseCentroidScreener::fast_forward(), protocols::stepwise::screener::VDW_BinScreener::fast_forward(), protocols::stepwise::screener::StubApplier::get_update(), protocols::stepwise::screener::RNA_ChainClosableGeometryResidueBasedScreener::get_update(), protocols::stepwise::screener::BaseBinMapUpdater::get_update(), protocols::stepwise::screener::FastForwardToNextResidueAlternative::get_update(), protocols::stepwise::screener::FastForwardToNextRigidBody::get_update(), protocols::stepwise::screener::SampleApplier::get_update(), protocols::stepwise::screener::RNA_ChainClosableGeometryStubBasedScreener::get_update(), and protocols::stepwise::StepWiseSampleAndScreen::set_ok_to_increment().

Member Data Documentation

bool protocols::stepwise::sampler::StepWiseSamplerBase::is_init_
private

Referenced by is_init(), set_and_reinit(), and set_init().

bool protocols::stepwise::sampler::StepWiseSamplerBase::random_
private

Referenced by random(), and set_random().


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