Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
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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List of all members.

Public Types

typedef
core::pack::interaction_graph::InteractionGraphBaseOP 
InteractionGraphBaseOP
 please derive from PackRotamersMover instead of attempting to add protocol-specific stuff here!
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 Member Functions

 PackRotamersMover ()
 default constructor
 PackRotamersMover (std::string const &)
 constructor with typename
 PackRotamersMover (ScoreFunctionCOP scorefxn, PackerTaskCOP task=0, core::Size nloop=1)
 Constructs a PackRotamersMover with PackerTask <task> evaluated using <scorefxn>
virtual ~PackRotamersMover ()
 PackRotamersMover (PackRotamersMover const &other)
virtual void apply (Pose &pose)
 Performs side-chain packing based on the input PackerTask using the input ScoreFunction.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
bool task_is_valid (Pose const &pose) const
 when the PackerTask was not generated locally, verify compatibility with pose
virtual void parse_my_tag (TagPtr const, protocols::moves::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
 parse XML (specifically in the context of the parser/scripting scheme)
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)
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)
virtual protocols::moves::MoverOP fresh_instance () const
 required in the context of the parser/scripting scheme
virtual protocols::moves::MoverOP clone () const
 required in the context of the parser/scripting scheme
void score_function (ScoreFunctionCOP sf)
 Sets the ScoreFunction to <sf>
void task_factory (TaskFactoryCOP tf)
 Sets the TaskFactory to <tf>
void task (PackerTaskCOP t)
 Sets the PackerTask to <t>
void nloop (core::Size nloop_in)
ScoreFunctionCOP score_function () const
 Returns the ScoreFunction.
PackerTaskCOP task () const
 Returns the PackerTask.
core::Size nloop () const
TaskFactoryCOP task_factory () const
 Returns the TaskFactory.
RotamerSetsCOP rotamer_sets () const
InteractionGraphBaseCOP ig () const

Protected Member Functions

virtual void setup (Pose &pose)
 get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask.
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

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 clone(), and 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)

Referenced by PackRotamersMover().

core::Size protocols::simple_moves::PackRotamersMover::nloop ( ) const [inline]
void protocols::simple_moves::PackRotamersMover::note_packertask_settings ( Pose const &  pose) [protected, virtual]

note PackerTask's packable and designable residues as string info

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

Referenced by setup().

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 [protected, virtual]
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

Referenced by PackRotamersMover().

ScoreFunctionCOP protocols::simple_moves::PackRotamersMover::score_function ( ) const
void protocols::simple_moves::PackRotamersMover::setup ( Pose pose) [protected, virtual]
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(), and core::pose::Pose::total_residue().

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


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