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protocols::simple_moves::PackRotamersMoverLazy Class Reference

a mover that packs the side-chains using a rotamer library in a lazy fashion. More...

#include <PackRotamersMoverLazy.hh>

Inheritance diagram for protocols::simple_moves::PackRotamersMoverLazy:
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Collaboration diagram for protocols::simple_moves::PackRotamersMoverLazy:
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Public Member Functions

 PackRotamersMoverLazy (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)
 default constructor More...
 
 PackRotamersMoverLazy ()
 
virtual ~PackRotamersMoverLazy ()
 constructor with typename More...
 
virtual void call_setup (Pose &pose)
 
virtual void apply_to_rotpack (Pose &pose, utility::vector0< int > rot_to_pack)
 
virtual void parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
 allow non-const access to the internal minimizer options object More...
 
- Public Member Functions inherited from protocols::simple_moves::PackRotamersMover
 PackRotamersMover ()
 default constructor More...
 
 PackRotamersMover (std::string const &)
 constructor with typename More...
 
 PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)
 Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn> More...
 
virtual ~PackRotamersMover ()
 
 PackRotamersMover (PackRotamersMover const &other)
 
virtual void apply (Pose &pose)
 Performs side-chain packing based on the input PackerTask using the input ScoreFunction. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
bool task_is_valid (Pose const &pose) const
 when the PackerTask was not generated locally, verify compatibility with pose More...
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, protocols::moves::MoverCacheSP cache)
 
virtual void parse_score_function (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
 parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...
 
virtual void parse_task_operations (TagPtr const, protocols::moves::DataMap const &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
 parse "task_operations" XML option (can be employed virtually by derived Packing movers) More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 required in the context of the parser/scripting scheme More...
 
virtual protocols::moves::MoverOP clone () const
 required in the context of the parser/scripting scheme More...
 
void score_function (ScoreFunctionCOP sf)
 Sets the ScoreFunction to <sf> More...
 
void task_factory (TaskFactoryCOP tf)
 Sets the TaskFactory to <tf> More...
 
void task (PackerTaskCOP t)
 Sets the PackerTask to <t> More...
 
void nloop (core::Size nloop_in)
 
ScoreFunctionCOP score_function () const
 Returns the ScoreFunction. More...
 
PackerTaskCOP task () const
 Returns the PackerTask. More...
 
core::Size nloop () const
 
TaskFactoryCOP task_factory () const
 Returns the TaskFactory. More...
 
RotamerSetsCOP rotamer_sets () const
 
InteractionGraphBaseCOP ig () 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 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)
 
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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Additional Inherited Members

- Public Types inherited from protocols::simple_moves::PackRotamersMover
typedef
core::pack::interaction_graph::InteractionGraphBaseOP 
InteractionGraphBaseOP
 please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here! More...
 
typedef
core::pack::interaction_graph::InteractionGraphBaseCOP 
InteractionGraphBaseCOP
 
typedef
core::pack::rotamer_set::RotamerSetsOP 
RotamerSetsOP
 
typedef
core::pack::rotamer_set::RotamerSetsCOP 
RotamerSetsCOP
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryCOP 
TaskFactoryCOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
- 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...
 
- Protected Member Functions inherited from protocols::simple_moves::PackRotamersMover
virtual void setup (Pose &pose)
 get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask. More...
 
virtual core::PackerEnergy run (Pose &pose, utility::vector0< int > rot_to_pack=utility::vector0< int >()) const
 
virtual void note_packertask_settings (Pose const &)
 note PackerTask's packable and designable residues as string info More...
 

Detailed Description

a mover that packs the side-chains using a rotamer library in a lazy fashion.

Constructor & Destructor Documentation

protocols::simple_moves::PackRotamersMoverLazy::PackRotamersMoverLazy ( ScoreFunctionCOP  scorefxn,
PackerTaskCOP  task = 0,
core::Size  nloop = 1 
)

default constructor

protocols::simple_moves::PackRotamersMoverLazy::PackRotamersMoverLazy ( )
protocols::simple_moves::PackRotamersMoverLazy::~PackRotamersMoverLazy ( )
virtual

constructor with typename

Member Function Documentation

void protocols::simple_moves::PackRotamersMoverLazy::apply_to_rotpack ( Pose pose,
utility::vector0< int rot_to_pack 
)
virtual
void protocols::simple_moves::PackRotamersMoverLazy::call_setup ( Pose pose)
virtual
void protocols::simple_moves::PackRotamersMoverLazy::parse_my_tag ( TagPtr const  tag,
protocols::moves::DataMap datamap,
Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
Pose const &  pose 
)
virtual

allow non-const access to the internal minimizer options object

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::simple_moves::PackRotamersMover.

References protocols::simple_moves::PackRotamersMover::nloop(), protocols::simple_moves::PackRotamersMover::parse_score_function(), protocols::simple_moves::PackRotamersMover::parse_task_operations(), and protocols::simple_moves::TR().


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