Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::loophash::LoopHashDiversifier Class Reference

#include <LoopHashDiversifier.hh>

Public Member Functions

 LoopHashDiversifier ()
 LoopHashDiversifier (LoopHashLibraryOP library, core::Real min_inter_ss_bbrms, core::Real max_inter_ss_bbrms, core::Real min_intra_ss_bbrms, core::Real max_intra_ss_bbrms, core::Real min_rms, core::Real max_rms, core::Size start_res, core::Size stop_res, core::Size window_size, core::Size max_radius, core::Size max_struct, core::Size num_iterations, core::Size num_try_div, bool diversify_loop_only, bool ideal, bool filter_by_phipsi, protocols::filters::FilterOP cenfilter, protocols::filters::FilterOP ranking_cenfilter, core::scoring::ScoreFunctionOP scorefxn_cen_cst, core::scoring::ScoreFunctionOP scorefxn_rama_cst)
void apply (core::pose::Pose &pose)
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void parse_my_tag (utility::tag::TagCOP tag, 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...
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 ~LoopHashDiversifier ()
 ****End Creator Methods****/// More...
Real min_inter_ss_bbrms () const
void min_inter_ss_bbrms (Real const min_inter_ss_bbrms)
Real max_inter_ss_bbrms () const
void max_inter_ss_bbrms (Real const max_inter_ss_bbrms)
Real min_intra_ss_bbrms () const
void min_intra_ss_bbrms (Real const min_intra_ss_bbrms)
Real max_intra_ss_bbrms () const
void max_intra_ss_bbrms (Real const max_intra_ss_bbrms)
Real min_rms () const
void min_rms (Real const min_rms)
Real max_rms () const
void max_rms (Real const max_rms)
Size num_iterations () const
void num_iterations (Size const num_iterations)
Size num_try_div () const
void num_try_div (Size const num_try_div)
utility::vector1< Sizeloop_sizes () const
void add_loop_size (Size const loop_size)
void cenfilter (protocols::filters::FilterOP cenfilter)
void ranking_cenfilter (protocols::filters::FilterOP filter)
protocols::filters::FilterOP ranking_cenfilter () 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)
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)
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...
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...

Private Attributes

utility::vector1< Sizeloop_sizes_
LoopHashLibraryOP library_
Real min_inter_ss_bbrms_
Real max_inter_ss_bbrms_
Real min_intra_ss_bbrms_
Real max_intra_ss_bbrms_
Real min_rms_
Real max_rms_
Size start_res_
Size stop_res_
Size window_size_
Size max_radius_
Size max_struct_
Size num_iterations_
Size num_try_div_
bool diversify_loop_only_
bool ideal_
bool filter_by_phipsi_
protocols::filters::FilterOP cenfilter_
protocols::filters::FilterOP ranking_cenfilter_
core::scoring::ScoreFunctionOP scorefxn_cen_cst_
core::scoring::ScoreFunctionOP scorefxn_rama_cst_
std::vector< std::pair< Real,
core::io::silent::SilentStructOP > > 

Additional Inherited Members

- 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::stringStrings
- 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...

Constructor & Destructor Documentation

protocols::loophash::LoopHashDiversifier::LoopHashDiversifier ( )
protocols::loophash::LoopHashDiversifier::LoopHashDiversifier ( LoopHashLibraryOP  library,
core::Real  min_inter_ss_bbrms,
core::Real  max_inter_ss_bbrms,
core::Real  min_intra_ss_bbrms,
core::Real  max_intra_ss_bbrms,
core::Real  min_rms,
core::Real  max_rms,
core::Size  start_res,
core::Size  stop_res,
core::Size  window_size,
core::Size  max_radius,
core::Size  max_struct,
core::Size  num_iterations,
core::Size  num_try_div,
bool  diversify_loop_only,
bool  ideal,
bool  filter_by_phipsi,
protocols::filters::FilterOP  cenfilter,
protocols::filters::FilterOP  ranking_cenfilter,
core::scoring::ScoreFunctionOP  scorefxn_cen_cst,
core::scoring::ScoreFunctionOP  scorefxn_rama_cst 
protocols::loophash::LoopHashDiversifier::~LoopHashDiversifier ( )

****End Creator Methods****///

Member Function Documentation

void protocols::loophash::LoopHashDiversifier::add_loop_size ( Size const  loop_size)

References loop_sizes_.

Referenced by parse_my_tag().

void protocols::loophash::LoopHashDiversifier::apply ( core::pose::Pose pose)

Implements protocols::moves::Mover.

References all_structs_, protocols::filters::Filter::apply(), protocols::loophash::LoopHashSampler::build_structures(), cenfilter_, core::chemical::CENTROID, core::pose::Pose::conformation(), diversify_loop_only_, core::chemical::FA_STANDARD, protocols::moves::FAIL_RETRY, core::io::silent::SilentStruct::fill_struct(), filter_by_phipsi_, core::io::silent::SilentStructFactory::get_instance(), core::io::silent::SilentStructFactory::get_silent_struct(), core::io::silent::SilentStructFactory::get_silent_struct_out(), ideal_, library_, max_inter_ss_bbrms(), max_intra_ss_bbrms(), max_radius_, max_rms(), max_struct_, min_inter_ss_bbrms(), min_intra_ss_bbrms(), min_rms(), protocols::moves::MS_SUCCESS, num_iterations_, num_try_div_, numeric::random::random_range(), ranking_cenfilter(), protocols::filters::Filter::report_sm(), runtime_assert, scorefxn_cen_cst_, scorefxn_rama_cst_, core::conformation::Conformation::secstruct(), protocols::loophash::LoopHashSampler::set_filter_by_phipsi(), protocols::moves::Mover::set_last_move_status(), protocols::loophash::LoopHashSampler::set_max_bbrms(), protocols::loophash::LoopHashSampler::set_max_radius(), protocols::loophash::LoopHashSampler::set_max_rms(), protocols::loophash::LoopHashSampler::set_max_struct(), protocols::loophash::LoopHashSampler::set_min_bbrms(), protocols::loophash::LoopHashSampler::set_min_rms(), protocols::loophash::LoopHashSampler::set_nonideal(), core::pose::set_ss_from_phipsi(), protocols::loophash::LoopHashSampler::set_start_res(), protocols::loophash::LoopHashSampler::set_stop_res(), start_res_, stop_res_, core::util::switch_to_residue_type_set(), protocols::loophash::TR, and window_size_.

void protocols::loophash::LoopHashDiversifier::cenfilter ( protocols::filters::FilterOP  cenfilter)

References cenfilter_.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::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.

References LoopHashDiversifier().

protocols::moves::MoverOP protocols::loophash::LoopHashDiversifier::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.

std::string protocols::loophash::LoopHashDiversifier::get_name ( ) const

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

Implements protocols::moves::Mover.

References protocols::loophash::LoopHashDiversifierCreator::mover_name().

utility::vector1< Size > protocols::loophash::LoopHashDiversifier::loop_sizes ( ) const

References loop_sizes_.

Referenced by LoopHashDiversifier(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( ) const

References max_inter_ss_bbrms_.

Referenced by apply(), and max_inter_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms ( Real const  max_inter_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( ) const

References max_intra_ss_bbrms_.

Referenced by apply(), and max_intra_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms ( Real const  max_intra_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::max_rms ( ) const

References max_rms_.

Referenced by apply(), and max_rms().

void protocols::loophash::LoopHashDiversifier::max_rms ( Real const  max_rms)

References max_rms(), and max_rms_.

Real protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( ) const

References min_inter_ss_bbrms_.

Referenced by apply(), and min_inter_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms ( Real const  min_inter_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( ) const

References min_intra_ss_bbrms_.

Referenced by apply(), and min_intra_ss_bbrms().

void protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms ( Real const  min_intra_ss_bbrms)
Real protocols::loophash::LoopHashDiversifier::min_rms ( ) const

References min_rms_.

Referenced by apply(), and min_rms().

void protocols::loophash::LoopHashDiversifier::min_rms ( Real const  min_rms)

References min_rms(), and min_rms_.

Size protocols::loophash::LoopHashDiversifier::num_iterations ( ) const

References num_iterations_.

Referenced by num_iterations().

void protocols::loophash::LoopHashDiversifier::num_iterations ( Size const  num_iterations)
Size protocols::loophash::LoopHashDiversifier::num_try_div ( ) const

References num_try_div_.

Referenced by num_try_div().

void protocols::loophash::LoopHashDiversifier::num_try_div ( Size const  num_try_div)

References num_try_div(), and num_try_div_.

void protocols::loophash::LoopHashDiversifier::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 
void protocols::loophash::LoopHashDiversifier::ranking_cenfilter ( protocols::filters::FilterOP  filter)

References ranking_cenfilter_.

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::ranking_cenfilter ( ) const

References ranking_cenfilter_.

Referenced by apply(), and parse_my_tag().

Member Data Documentation

std::vector< std::pair< Real, core::io::silent::SilentStructOP > > protocols::loophash::LoopHashDiversifier::all_structs_

Referenced by apply().

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::cenfilter_

Referenced by apply(), and cenfilter().

bool protocols::loophash::LoopHashDiversifier::diversify_loop_only_

Referenced by apply(), and parse_my_tag().

bool protocols::loophash::LoopHashDiversifier::filter_by_phipsi_

Referenced by apply(), and parse_my_tag().

bool protocols::loophash::LoopHashDiversifier::ideal_

Referenced by apply(), and parse_my_tag().

LoopHashLibraryOP protocols::loophash::LoopHashDiversifier::library_
utility::vector1< Size > protocols::loophash::LoopHashDiversifier::loop_sizes_
Real protocols::loophash::LoopHashDiversifier::max_inter_ss_bbrms_

Referenced by max_inter_ss_bbrms(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::max_intra_ss_bbrms_

Referenced by max_intra_ss_bbrms(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::max_radius_

Referenced by apply(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::max_rms_

Referenced by max_rms(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::max_struct_

Referenced by apply(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::min_inter_ss_bbrms_

Referenced by min_inter_ss_bbrms(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::min_intra_ss_bbrms_

Referenced by min_intra_ss_bbrms(), and parse_my_tag().

Real protocols::loophash::LoopHashDiversifier::min_rms_

Referenced by min_rms(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::num_iterations_

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

Size protocols::loophash::LoopHashDiversifier::num_try_div_

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

protocols::filters::FilterOP protocols::loophash::LoopHashDiversifier::ranking_cenfilter_

Referenced by ranking_cenfilter().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashDiversifier::scorefxn_cen_cst_

Referenced by apply(), and parse_my_tag().

core::scoring::ScoreFunctionOP protocols::loophash::LoopHashDiversifier::scorefxn_rama_cst_

Referenced by apply(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::start_res_

Referenced by apply(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::stop_res_

Referenced by apply(), and parse_my_tag().

Size protocols::loophash::LoopHashDiversifier::window_size_

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