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protocols::simple_moves::PackRotamersMover Class Reference

A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing. More...

#include <PackRotamersMover.hh>

Inheritance diagram for protocols::simple_moves::PackRotamersMover:
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Collaboration diagram for protocols::simple_moves::PackRotamersMover:
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Public Types

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
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 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_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...
 
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
 

Protected Member Functions

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...
 
- 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 Attributes

ScoreFunctionCOP scorefxn_
 
PackerTaskCOP task_
 
core::Size nloop_
 
TaskFactoryCOP task_factory_
 
RotamerSetsOP rotamer_sets_
 
InteractionGraphBaseOP ig_
 

Friends

std::ostream & operator<< (std::ostream &os, PackRotamersMover const &mover)
 

Additional Inherited Members

- 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

A protocols::moves::Mover that packs the side-chains using a rotamer library It uses a ScoreFunction for packing and a PackerTask, or a TaskFactory that generates a PackerTask, for instructions on what rotamer sets are allowed at each residue position during packing.

Common Methods: PackRotamersMover.apply

Member Typedef Documentation

please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!

Author
ashworth (current form)

Constructor & Destructor Documentation

protocols::simple_moves::PackRotamersMover::PackRotamersMover ( )

default constructor

Referenced by fresh_instance().

protocols::simple_moves::PackRotamersMover::PackRotamersMover ( std::string const &  type_name)

constructor with typename

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

Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn>

ScoreFunction scorefxn /function to minimize while changine rotamers PackerTask task /object specifying what to design/pack Size (int) nloop /number of loops in the Pose (???)

protocols::simple_moves::PackRotamersMover::~PackRotamersMover ( )
virtual
protocols::simple_moves::PackRotamersMover::PackRotamersMover ( PackRotamersMover const &  other)

Member Function Documentation

void protocols::simple_moves::PackRotamersMover::apply ( Pose pose)
virtual
protocols::moves::MoverOP protocols::simple_moves::PackRotamersMover::clone ( ) const
virtual
protocols::moves::MoverOP protocols::simple_moves::PackRotamersMover::fresh_instance ( ) const
virtual
std::string protocols::simple_moves::PackRotamersMover::get_name ( ) const
virtual
interaction_graph::InteractionGraphBaseCOP protocols::simple_moves::PackRotamersMover::ig ( ) const
void protocols::simple_moves::PackRotamersMover::nloop ( core::Size  nloop_in)

References nloop_.

Referenced by PackRotamersMover().

core::Size protocols::simple_moves::PackRotamersMover::nloop ( ) const
inline
void protocols::simple_moves::PackRotamersMover::note_packertask_settings ( Pose const &  pose)
protectedvirtual

note PackerTask's packable and designable residues as string info

References core::sequence::end, protocols::moves::Mover::info(), core::pose::Pose::pdb_info(), and task_.

Referenced by setup().

void protocols::simple_moves::PackRotamersMover::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks,
protocols::moves::MoverCacheSP  cache 
)
virtual
void protocols::simple_moves::PackRotamersMover::parse_my_tag ( TagPtr const  tag,
protocols::moves::DataMap datamap,
Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
Pose const &  pose 
)
virtual
void protocols::simple_moves::PackRotamersMover::parse_score_function ( TagPtr const  tag,
protocols::moves::DataMap const &  datamap,
Filters_map const &  ,
protocols::moves::Movers_map const &  ,
Pose const &   
)
virtual
void protocols::simple_moves::PackRotamersMover::parse_task_operations ( TagPtr const  tag,
protocols::moves::DataMap const &  datamap,
Filters_map const &  ,
protocols::moves::Movers_map const &  ,
Pose const &   
)
virtual
rotamer_set::RotamerSetsCOP protocols::simple_moves::PackRotamersMover::rotamer_sets ( ) const
core::PackerEnergy protocols::simple_moves::PackRotamersMover::run ( Pose pose,
utility::vector0< int rot_to_pack = utility::vector0int >() 
) const
protectedvirtual
void protocols::simple_moves::PackRotamersMover::score_function ( ScoreFunctionCOP  sf)

Sets the ScoreFunction to <sf>

example(s): packmover.score_function(scorefxn) See Also: PackRotamersMover PackRotamersMover.task

References scorefxn_.

Referenced by protocols::simple_moves::operator<<(), and PackRotamersMover().

ScoreFunctionCOP protocols::simple_moves::PackRotamersMover::score_function ( ) const
void protocols::simple_moves::PackRotamersMover::setup ( Pose pose)
protectedvirtual
void protocols::simple_moves::PackRotamersMover::task ( PackerTaskCOP  t)
PackerTaskCOP protocols::simple_moves::PackRotamersMover::task ( ) const
void protocols::simple_moves::PackRotamersMover::task_factory ( TaskFactoryCOP  tf)
TaskFactoryCOP protocols::simple_moves::PackRotamersMover::task_factory ( ) const
bool protocols::simple_moves::PackRotamersMover::task_is_valid ( Pose const &  pose) const

when the PackerTask was not generated locally, verify compatibility with pose

the pose residue types must be equivalent to the ones used to generate the ResidueLevelTasks, because of the way that prevent_repacking and its associated flags work

References core::pose::Pose::residue_type(), task_, and core::pose::Pose::total_residue().

Referenced by protocols::simple_moves::SetReturningPackRotamersMover::apply(), and setup().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
PackRotamersMover const &  mover 
)
friend

Member Data Documentation

InteractionGraphBaseOP protocols::simple_moves::PackRotamersMover::ig_
private

Referenced by ig(), PackRotamersMover(), run(), and setup().

core::Size protocols::simple_moves::PackRotamersMover::nloop_
private
RotamerSetsOP protocols::simple_moves::PackRotamersMover::rotamer_sets_
private
ScoreFunctionCOP protocols::simple_moves::PackRotamersMover::scorefxn_
private
PackerTaskCOP protocols::simple_moves::PackRotamersMover::task_
private
TaskFactoryCOP protocols::simple_moves::PackRotamersMover::task_factory_
private

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