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protocols::minimization_packing::RotamerizeMover Class Reference

a mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set. More...

#include <RotamerizeMover.hh>

Inheritance diagram for protocols::minimization_packing::RotamerizeMover:
Inheritance graph
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Public Types

typedef
core::pack::rotamer_set::RotamerSetsOP 
RotamerSetsOP
 
typedef
core::pack::rotamer_set::RotamerSetsCOP 
RotamerSetsCOP
 
typedef
core::pack::task::PackerTaskOP 
PackerTaskOP
 
typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryCOP 
TaskFactoryCOP
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef std::list< std::string > Strings
 

Public Member Functions

 RotamerizeMover ()
 default constructor More...
 
 RotamerizeMover (std::string const &)
 constructor with typename More...
 
 RotamerizeMover (PackerTaskOP task)
 
 ~RotamerizeMover () override
 
 RotamerizeMover (RotamerizeMover const &other)
 
void apply (Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 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...
 
void task_factory (TaskFactoryCOP tf)
 
void task (PackerTaskOP t)
 
PackerTaskOP task () const
 
TaskFactoryCOP task_factory () const
 
RotamerSetsCOP rotamer_sets () const
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual bool reinitialize_for_each_job () const
 Inform 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
 Inform 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
 Generates a new Mover object freshly created with the default ctor. More...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Protected Member Functions

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

PackerTaskOP task_
 
TaskFactoryCOP task_factory_
 
RotamerSetsOP rotamer_sets_
 

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. More...
 

Detailed Description

a mover that replaces the repackable parts - sidechains, bases, etc. - based purely on geometric similarity to the starting structure. The purpose is to generate the best case output of a repacking calculation as a positive control for benchmarking and parameter fitting. Thus, the soft rep potential was originally derived as the score function that gave the best fit between repacked and rotamerized structures for a large test set.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::minimization_packing::RotamerizeMover::RotamerizeMover ( )

default constructor

RotamerizeMover.

protocols::minimization_packing::RotamerizeMover::RotamerizeMover ( std::string const &  type_name)

constructor with typename

protocols::minimization_packing::RotamerizeMover::RotamerizeMover ( PackerTaskOP  task)
protocols::minimization_packing::RotamerizeMover::~RotamerizeMover ( )
overridedefault
protocols::minimization_packing::RotamerizeMover::RotamerizeMover ( RotamerizeMover const &  other)

Member Function Documentation

void protocols::minimization_packing::RotamerizeMover::apply ( Pose )
overridevirtual
std::string protocols::minimization_packing::RotamerizeMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

rotamer_set::RotamerSetsCOP protocols::minimization_packing::RotamerizeMover::rotamer_sets ( ) const

References rotamer_sets_.

void protocols::minimization_packing::RotamerizeMover::setup ( Pose pose)
protectedvirtual

get rotamers, energies. Also performs lazy initialization of ScoreFunction, PackerTask.

References core::pack::pack_rotamers_setup(), rotamer_sets_, task_, task_factory_, task_is_valid(), protocols::minimization_packing::TR(), and core::pose::Pose::update_residue_neighbors().

Referenced by apply().

void protocols::minimization_packing::RotamerizeMover::task ( PackerTaskOP  t)

Referenced by RotamerizeMover().

PackerTaskOP protocols::minimization_packing::RotamerizeMover::task ( ) const

References task_.

void protocols::minimization_packing::RotamerizeMover::task_factory ( TaskFactoryCOP  tf)

References task_factory_.

Referenced by RotamerizeMover().

TaskFactoryCOP protocols::minimization_packing::RotamerizeMover::task_factory ( ) const

References task_factory_.

bool protocols::minimization_packing::RotamerizeMover::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_ptr(), core::pose::Pose::size(), and task_.

Referenced by setup().

Member Data Documentation

RotamerSetsOP protocols::minimization_packing::RotamerizeMover::rotamer_sets_
private
PackerTaskOP protocols::minimization_packing::RotamerizeMover::task_
private
TaskFactoryCOP protocols::minimization_packing::RotamerizeMover::task_factory_
private

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