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protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD Class Reference

LoopMover utilizing fragment insertion, ccd loop closure, and minimization. More...

#include <LoopMover_QuickCCD.hh>

Inheritance diagram for protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD:
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Collaboration diagram for protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD:
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Public Member Functions

 LoopMover_Perturb_QuickCCD ()
 Loops constructor. More...
 
 LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in)
 Loops constructor. More...
 
 LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn)
 Loops & ScoreFunction constructor. More...
 
 LoopMover_Perturb_QuickCCD (protocols::loops::LoopsOP loops_in, core::scoring::ScoreFunctionOP scorefxn, core::fragment::FragSetOP fragset)
 Loops & ScoreFunction constructor. More...
 
 ~LoopMover_Perturb_QuickCCD ()
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual protocols::moves::MoverOP clone () const
 clone this object More...
 
bool randomize_loop () const
 randomize loops prior to loop modeling? More...
 
void randomize_loop (bool const flag)
 indicate whether loops should be randomized prior to modeling More...
 
void set_default_settings ()
 set default settings More...
 
- Public Member Functions inherited from protocols::loops::loop_mover::IndependentLoopMover
 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...
 
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)
 
const
core::scoring::ScoreFunctionOP
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 http://www.ncbi.nlm.nih.gov/pubmed/19646450 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 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)
 loop modeling protocol implementation More...
 
virtual basic::Tracer & tr () const
 

Protected Attributes

bool randomize_loop_
 randomize loops prior to performing loop modeling? 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...
 

Detailed Description

LoopMover utilizing fragment insertion, ccd loop closure, and minimization.

Constructor & Destructor Documentation

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( )
protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( protocols::loops::LoopsOP  loops_in)

Loops constructor.

Parameters
[in]loops_inthe set of loops to model
Remarks
Will be initialized with centroid level score function 'score4L'.

References protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn 
)

Loops & ScoreFunction constructor.

Parameters
[in]loops_inthe set of loops to model
[in]scorefxndesired ScoreFunction

References protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::LoopMover_Perturb_QuickCCD ( protocols::loops::LoopsOP  loops_in,
core::scoring::ScoreFunctionOP  scorefxn,
core::fragment::FragSetOP  fragset 
)

Loops & ScoreFunction constructor.

Parameters
[in]loops_inthe set of loops to model
[in]scorefxndesired ScoreFunction
[in]fragsetis the FragSet to be used line?

References protocols::loops::loop_mover::LoopMover::add_fragments(), protocols::loops::get_cen_scorefxn(), set_default_settings(), protocols::loops::loop_mover::LoopMover::set_scorefxn(), and protocols::moves::Mover::type().

protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::~LoopMover_Perturb_QuickCCD ( )

Member Function Documentation

protocols::moves::MoverOP protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::clone ( ) const
virtual
std::string protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::get_name ( ) const
virtual

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

Reimplemented from protocols::loops::loop_mover::IndependentLoopMover.

Reimplemented in protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves.

LoopResult protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::model_loop ( core::pose::Pose pose,
protocols::loops::Loop const &  loop 
)
protectedvirtual

loop modeling protocol implementation

Implements protocols::loops::loop_mover::IndependentLoopMover.

Reimplemented in protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves.

References core::pose::add_variant_type_to_pose_residue(), core::scoring::atom_pair_constraint, core::scoring::chainbreak, core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::loops::Loop::cut(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pack::interaction_graph::debug, core::pose::Pose::energies(), protocols::loops::loop_mover::ExtendFailure, protocols::loops::loop_mover::Failure, protocols::loops::loop_mover::perturb::fast_ccd_close_loops(), core::pose::Pose::fold_tree(), protocols::loops::loop_mover::LoopMover::frag_libs(), protocols::loops::idealize_loop(), protocols::loops::Loop::is_extended(), core::pose::symmetry::is_symmetric(), core::scoring::linear_chainbreak, core::pose::symmetry::make_symmetric_movemap(), protocols::rigid::random, randomize_loop_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), protocols::loops::loop_mover::LoopMover::scorefxn(), protocols::loops::loop_mover::LoopMover::set_extended_torsions(), protocols::loops::set_move_map_for_centroid_loop(), protocols::loops::set_single_loop_fold_tree(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), protocols::loops::loop_mover::Success, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::scoring::Energies::total_energies(), core::pose::Pose::total_residue(), and tr().

bool protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::randomize_loop ( ) const
inline

randomize loops prior to loop modeling?

References randomize_loop_.

void protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::randomize_loop ( bool const  flag)
inline

indicate whether loops should be randomized prior to modeling

References randomize_loop_.

void protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::set_default_settings ( )
inline

set default settings

default settings are as follows:

References randomize_loop_.

Referenced by LoopMover_Perturb_QuickCCD().

basic::Tracer & protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::tr ( ) const
protectedvirtual

Member Data Documentation

bool protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD::randomize_loop_
protected

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