Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::loop_modeling::LoopModeler Class Reference

#include <LoopModeler.hh>

Public Member Functions

 LoopModeler ()
 Default constructor. More...
 ~LoopModeler ()
 Default destructor. More...
string get_name () const
 Return the class name of this mover. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
void enable_build_stage ()
void disable_build_stage ()
void enable_centroid_stage ()
void disable_centroid_stage ()
void enable_fullatom_stage ()
void disable_fullatom_stage ()
LoopBuilderOP build_stage ()
LoopProtocolOP centroid_stage ()
LoopProtocolOP fullatom_stage ()
void repack_everything_before_fullatom (bool setting)
void setup_empty_config ()
void setup_kic_config ()
void setup_next_gen_kic_config ()
void add_shared_mover (LoopMoverOP mover)
void add_shared_refiner (LoopMoverOP refiner)
void add_shared_filter (protocols::filters::FilterOP filter)
void clear_movers ()
void clear_refiners ()
void clear_movers_and_refiners ()
void mark_as_default ()
- Public Member Functions inherited from protocols::loop_modeling::LoopMover
 LoopMover ()
 Default constructor. More...
 ~LoopMover ()
 Default destructor. More...
void apply (Pose &pose)
 Sample the pose in the regions specified by get_loops(). More...
bool was_successful () const
 Return true if the previous move was successful. More...
Loops get_loops () const
 Return the loops to be sampled on the next call to apply(). More...
core::scoring::ScoreFunctionCOP get_score_function () const
 Return the score function to be used on the next call to apply(). More...
core::scoring::ScoreFunctionOP get_score_function ()
 Return the score function to be used on the next call to apply() (non-const access). More...
void set_loop (Loop const &loop)
 Set the loop to be sampled on the next call to apply(). More...
void set_loops (Loops const &loops)
 Set the loops to be sampled on the next call to apply(). More...
void set_score_function (core::scoring::ScoreFunctionOP sfxn)
 Set the score function to be used on the next call to apply(). More...
virtual FoldTreeRequest request_fold_tree () const
 Return an enum representing the kind of fold tree that is compatible with this mover. More...
void trust_fold_tree ()
 Promise that the calling code will setup a fold tree compatible with request_fold_tree(). If this method is not called, most movers will setup a fold tree on their own the first time apply() is called. 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...
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 do_apply (Pose &pose)
 Perform the loop sampling move. This method can be overwritten in child classes. More...
- Protected Member Functions inherited from protocols::loop_modeling::LoopMover
virtual bool do_apply (Pose &pose, Loop const &loop)
 Perform the loop sampling move. This method can be overwritten in child classes. More...
void dont_manage_score_function ()
 Disable all the LoopMover score function related methods. More...
template<class LoopMoverSubclassOP >
LoopMoverSubclassOP register_nested_loop_mover (LoopMoverSubclassOP mover)
 Indicate that the given loop mover is used within do_apply(). More...
void deregister_nested_loop_movers ()
 Drop association with any currently registered loop movers. More...
vector1< LoopMoverOP > const & get_nested_loop_movers () const
 Return a reference to the list of nested loop movers. 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 Member Functions

void convert_to_centroid (Pose &pose)
void convert_to_fullatom (Pose &pose, Pose &original_pose)

Private Attributes

LoopBuilderOP build_stage_
LoopProtocolOP centroid_stage_
LoopProtocolOP fullatom_stage_
bool is_build_stage_enabled_
bool is_centroid_stage_enabled_
bool is_fullatom_stage_enabled_
bool repack_everything_before_fullatom_

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::loop_modeling::LoopMover
static void setup_fold_tree (Pose &pose, Loops const &loops, FoldTreeRequest request)
 Setup the given pose with a fold tree that is compatible with the given loops and requests. More...
- 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...

Constructor & Destructor Documentation

protocols::loop_modeling::LoopModeler::LoopModeler ( )

Default constructor.

protocols::loop_modeling::LoopModeler::~LoopModeler ( )

Default destructor.

Member Function Documentation

void protocols::loop_modeling::LoopModeler::add_shared_filter ( protocols::filters::FilterOP  filter)
void protocols::loop_modeling::LoopModeler::add_shared_mover ( LoopMoverOP  mover)
void protocols::loop_modeling::LoopModeler::add_shared_refiner ( LoopMoverOP  refiner)
LoopBuilderOP protocols::loop_modeling::LoopModeler::build_stage ( )
LoopProtocolOP protocols::loop_modeling::LoopModeler::centroid_stage ( )
void protocols::loop_modeling::LoopModeler::clear_movers ( )
void protocols::loop_modeling::LoopModeler::clear_movers_and_refiners ( )
void protocols::loop_modeling::LoopModeler::clear_refiners ( )
void protocols::loop_modeling::LoopModeler::convert_to_centroid ( Pose pose)
void protocols::loop_modeling::LoopModeler::convert_to_fullatom ( Pose pose,
Pose original_pose 
void protocols::loop_modeling::LoopModeler::disable_build_stage ( )
void protocols::loop_modeling::LoopModeler::disable_centroid_stage ( )
void protocols::loop_modeling::LoopModeler::disable_fullatom_stage ( )
bool protocols::loop_modeling::LoopModeler::do_apply ( Pose pose)

Perform the loop sampling move. This method can be overwritten in child classes.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::loop_modeling::LoopModeler::enable_build_stage ( )
void protocols::loop_modeling::LoopModeler::enable_centroid_stage ( )
void protocols::loop_modeling::LoopModeler::enable_fullatom_stage ( )
LoopProtocolOP protocols::loop_modeling::LoopModeler::fullatom_stage ( )
string protocols::loop_modeling::LoopModeler::get_name ( ) const

Return the class name of this mover.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::loop_modeling::LoopModeler::mark_as_default ( )
void protocols::loop_modeling::LoopModeler::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
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 config, loop_mover, and protocols::loop_modeling::utilities::loop_mover_from_tag().

void protocols::loop_modeling::LoopModeler::repack_everything_before_fullatom ( bool  setting)
void protocols::loop_modeling::LoopModeler::setup_empty_config ( )
void protocols::loop_modeling::LoopModeler::setup_kic_config ( )
void protocols::loop_modeling::LoopModeler::setup_next_gen_kic_config ( )

Member Data Documentation

LoopBuilderOP protocols::loop_modeling::LoopModeler::build_stage_
LoopProtocolOP protocols::loop_modeling::LoopModeler::centroid_stage_
LoopProtocolOP protocols::loop_modeling::LoopModeler::fullatom_stage_
bool protocols::loop_modeling::LoopModeler::is_build_stage_enabled_
bool protocols::loop_modeling::LoopModeler::is_centroid_stage_enabled_
bool protocols::loop_modeling::LoopModeler::is_fullatom_stage_enabled_
bool protocols::loop_modeling::LoopModeler::repack_everything_before_fullatom_

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