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protocols::loops::loop_mover::IndependentLoopMover Class Referenceabstract

#include <IndependentLoopMover.hh>

Inheritance diagram for protocols::loops::loop_mover::IndependentLoopMover:
Inheritance graph
Collaboration diagram for protocols::loops::loop_mover::IndependentLoopMover:
Collaboration graph

Public Member Functions

 IndependentLoopMover ()
 IndependentLoopMover (LoopsOP loops_in)
 IndependentLoopMover (LoopsFileData const &lfd)
 IndependentLoopMover (GuardedLoopsFromFileOP guarded_loops)
virtual ~IndependentLoopMover ()
void set_defaults ()
virtual void apply (core::pose::Pose &pose)
 Apply the loop-build protocol to the input pose. More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
void set_build_attempts_ (int value)
 Accessors: More...
void set_grow_attempts_ (int value)
void set_accept_aborted_loops_ (bool value)
void set_strict_loops (bool value)
void set_random_order_ (bool value)
void set_build_all_loops_ (bool value)
void set_loop_combine_rate_ (core::Real value)
int get_build_attempts () const
int get_grow_attempts () const
bool get_accept_aborted_loops () const
bool get_strict_loops () const
bool get_random_order () const
bool get_build_all_loops () const
bool get_loop_combine_rate () const
bool get_all_loops_closed () const
- Public Member Functions inherited from protocols::loops::loop_mover::LoopMover
 LoopMover ()
 LoopMover (protocols::loops::LoopsOP loops_in)
 LoopMover (protocols::loops::LoopsFileData const &loops_from_file)
 LoopMover (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
 LoopMover (LoopMover const &rhs)
 copy ctor More...
LoopMoveroperator= (LoopMover const &rhs)
 assignment operator More...
virtual ~LoopMover ()
void set_guarded_loops_not_in_charge ()
 Inform the GuardedLoopsFromFile object that it is not in charge of updating its Loops object at the beginning of apply() More...
void set_scorefxn (const core::scoring::ScoreFunctionOP score_in)
scorefxn () const
void loops (protocols::loops::LoopsOP lptr)
 Set the loops pointer by giving the LoopMover resolved loop indices; implicity sets the GuardedLoopsFromFile object into a "not in charge" state (since something else must be controlling the the Loops object). The GuardedLoopFromFile object copies the pointer, not the data. More...
void loops (LoopsFileData const &loop_file_data)
 Set the loops by giving the LoopMover unresolved loop indices (which cannot be resolved until apply() ). More...
void loops (protocols::loops::GuardedLoopsFromFileOP guarded_loops)
 Set the guarded_loops pointer. More...
protocols::loops::LoopsCOP loops () const
 Accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...
protocols::loops::LoopsOP loops ()
 non-const accessor for the loops data. Requires that the loop indices have been resolved; do not call this before apply() has been called. More...
const utility::vector1
< core::fragment::FragSetOP > & 
frag_libs () const
std::string torsion_features_string (core::pose::Pose const &pose) const
 bin torsion angles as described in generates a string with the torsion angle bins, using uppercase letters as in the publication above for omega ~ 180, and lowercase letters for omega ~ 0; to be used in loop sampling analysis More...
virtual void set_extended_torsions (core::pose::Pose &pose, Loop const &loop)
 Extend a loop. More...
void add_fragments (core::fragment::FragSetOP fragset)
 add a fragment set More...
void clear_fragments ()
 clear the list of fragment sets More...
MoveMapOP const & false_movemap () const
 explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...
void false_movemap (MoveMapOP const &mm)
 explicit False settings in this MoveMap will override any automatically generated MoveMap settings during the loop modeling protocol More...
checkpoint::CheckPointerOPget_checkpoints ()
- 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)
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual void parse_my_tag (TagPtr const tag, 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
 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...
virtual 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 set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Protected Member Functions

virtual LoopResult model_loop (core::pose::Pose &pose, protocols::loops::Loop const &loop)=0
- Protected Member Functions inherited from protocols::loops::loop_mover::LoopMover
Size enforce_false_movemap (MoveMapOP &mm) const
 import the false_movemap's explicit False settings into the given MoveMap More...
void set_loops_from_pose_observer_cache (core::pose::Pose const &pose)
 allow the loops to be set from the segments stored in the poses observer cache. makes it possible to have LoopMovers be part of parser protocols where the loops were determined by some previous on the fly step More...
bool use_loops_from_observer_cache () const
void set_use_loops_from_observer_cache (bool const loops_from_observer_cache)
virtual basic::Tracer & tr () const =0
void resolve_loop_indices (core::pose::Pose const &p)
 Turn the unresolved loop indices read in from disk into pose-specific loop indices. Must be called by derived classes at the beginning of apply. 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 select_loops (Loops &selected_loops)
 select loops to be built More...

Private Attributes

int build_attempts_
 Try loopbuilding n times before extending. More...
int grow_attempts_
 Try extending n times. More...
bool accept_aborted_loops_
 danger - can lead to infinite loops ! More...
bool strict_loops_
 Grow loops outwards if building fails. More...
bool random_order_
 Randomise loop build order. More...
bool build_all_loops_
 Force to build all loops (i.e. ignore skiprate) More...
bool all_loops_closed_
core::Real loop_combine_rate_
 Loop combine rate. More...

Additional Inherited Members

- Public Types inherited from protocols::loops::loop_mover::LoopMover
typedef core::kinematics::MoveMapOP MoveMapOP
- 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...

Constructor & Destructor Documentation

protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover ( )

References set_defaults().

protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover ( LoopsOP  loops_in)

References set_defaults().

protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover ( LoopsFileData const &  lfd)

References set_defaults().

protocols::loops::loop_mover::IndependentLoopMover::IndependentLoopMover ( GuardedLoopsFromFileOP  guarded_loops)

References set_defaults().

protocols::loops::loop_mover::IndependentLoopMover::~IndependentLoopMover ( )

Member Function Documentation

void protocols::loops::loop_mover::IndependentLoopMover::apply ( core::pose::Pose pose)
bool protocols::loops::loop_mover::IndependentLoopMover::get_accept_aborted_loops ( ) const

References accept_aborted_loops_.

bool protocols::loops::loop_mover::IndependentLoopMover::get_all_loops_closed ( ) const

References all_loops_closed_.

bool protocols::loops::loop_mover::IndependentLoopMover::get_build_all_loops ( ) const

References build_all_loops_.

int protocols::loops::loop_mover::IndependentLoopMover::get_build_attempts ( ) const

References build_attempts_.

int protocols::loops::loop_mover::IndependentLoopMover::get_grow_attempts ( ) const

References grow_attempts_.

bool protocols::loops::loop_mover::IndependentLoopMover::get_loop_combine_rate ( ) const

References loop_combine_rate_.

std::string protocols::loops::loop_mover::IndependentLoopMover::get_name ( ) const
bool protocols::loops::loop_mover::IndependentLoopMover::get_random_order ( ) const

References random_order_.

bool protocols::loops::loop_mover::IndependentLoopMover::get_strict_loops ( ) const

References strict_loops_.

virtual LoopResult protocols::loops::loop_mover::IndependentLoopMover::model_loop ( core::pose::Pose pose,
protocols::loops::Loop const &  loop 
protectedpure virtual
void protocols::loops::loop_mover::IndependentLoopMover::select_loops ( Loops selected_loops)
void protocols::loops::loop_mover::IndependentLoopMover::set_accept_aborted_loops_ ( bool  value)
void protocols::loops::loop_mover::IndependentLoopMover::set_build_all_loops_ ( bool  value)
void protocols::loops::loop_mover::IndependentLoopMover::set_build_attempts_ ( int  value)
void protocols::loops::loop_mover::IndependentLoopMover::set_defaults ( )
void protocols::loops::loop_mover::IndependentLoopMover::set_grow_attempts_ ( int  value)
void protocols::loops::loop_mover::IndependentLoopMover::set_loop_combine_rate_ ( core::Real  value)
void protocols::loops::loop_mover::IndependentLoopMover::set_random_order_ ( bool  value)
void protocols::loops::loop_mover::IndependentLoopMover::set_strict_loops ( bool  value)

Member Data Documentation

bool protocols::loops::loop_mover::IndependentLoopMover::accept_aborted_loops_

danger - can lead to infinite loops !

Referenced by apply(), get_accept_aborted_loops(), set_accept_aborted_loops_(), and set_defaults().

bool protocols::loops::loop_mover::IndependentLoopMover::all_loops_closed_

determines if all the loops were closed in the last time mover was called.

Referenced by apply(), and get_all_loops_closed().

bool protocols::loops::loop_mover::IndependentLoopMover::build_all_loops_

Force to build all loops (i.e. ignore skiprate)

Referenced by get_build_all_loops(), select_loops(), set_build_all_loops_(), and set_defaults().

int protocols::loops::loop_mover::IndependentLoopMover::build_attempts_

Try loopbuilding n times before extending.

Referenced by apply(), get_build_attempts(), set_build_attempts_(), and set_defaults().

int protocols::loops::loop_mover::IndependentLoopMover::grow_attempts_

Try extending n times.

Referenced by apply(), get_grow_attempts(), set_defaults(), and set_grow_attempts_().

core::Real protocols::loops::loop_mover::IndependentLoopMover::loop_combine_rate_
bool protocols::loops::loop_mover::IndependentLoopMover::random_order_

Randomise loop build order.

Referenced by get_random_order(), select_loops(), set_defaults(), and set_random_order_().

bool protocols::loops::loop_mover::IndependentLoopMover::strict_loops_

Grow loops outwards if building fails.

Referenced by apply(), get_strict_loops(), set_defaults(), and set_strict_loops().

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