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protocols::simple_moves::ShortBackrubMover Class Reference

#include <ShortBackrubMover.hh>

Inheritance diagram for protocols::simple_moves::ShortBackrubMover:
Inheritance graph
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Public Types

typedef protocols::moves::MoverOP MoverOP
 
- 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

 ShortBackrubMover ()
 
 ShortBackrubMover (core::pose::PoseOP pose)
 constructor that sets input pose More...
 
 ShortBackrubMover (ShortBackrubMover const &rval)
 copy constructor More...
 
 ~ShortBackrubMover () override
 destructor More...
 
protocols::moves::MoverOP clone () const override
 clone this object More...
 
protocols::moves::MoverOP fresh_instance () const override
 create this type of object More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void set_resnum (core::Size resnum)
 
void set_rotation_std_dev (core::Real rotation_std_dev)
 
void set_randomize_resnum (bool randomize_resnum)
 
void set_uniform_backrub (bool uniform_backrub)
 
void set_input_pose (core::pose::PoseCOP pose) override
 setter for poses contained for rms More...
 
core::Size get_resnum () const
 
core::Real get_rotation_std_dev () const
 
bool get_randomize_resnum () const
 
bool get_uniform_backrub () const
 
protocols::backrub::BackrubMoverOP get_backrubmover () const
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) override
 parse xml More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- 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 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...
 
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_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
 
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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Attributes

protocols::backrub::BackrubMoverOP backrubmover_
 mover used for Backrub moves More...
 
core::Size resnum_
 residue number specifying the center residue for the next Backrub move More...
 
core::Real rotation_std_dev_
 standard deviation of rotation angle (degrees) used for Backrub moves More...
 
bool randomize_resnum_
 if true, choose a random residue for the next move More...
 
bool uniform_backrub_
 if true, sample rotation angle from a uniform distribution from -20 to 20 More...
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::ShortBackrubMover::ShortBackrubMover ( )
protocols::simple_moves::ShortBackrubMover::ShortBackrubMover ( core::pose::PoseOP  pose)
protocols::simple_moves::ShortBackrubMover::ShortBackrubMover ( ShortBackrubMover const &  rval)
default

copy constructor

protocols::simple_moves::ShortBackrubMover::~ShortBackrubMover ( )
overridedefault

destructor

Member Function Documentation

void protocols::simple_moves::ShortBackrubMover::apply ( core::pose::Pose )
overridevirtual
ShortBackrubMover::MoverOP protocols::simple_moves::ShortBackrubMover::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

ShortBackrubMover::MoverOP protocols::simple_moves::ShortBackrubMover::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

protocols::backrub::BackrubMoverOP protocols::simple_moves::ShortBackrubMover::get_backrubmover ( ) const

References backrubmover_.

std::string protocols::simple_moves::ShortBackrubMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::simple_moves::ShortBackrubMover::get_randomize_resnum ( ) const

References randomize_resnum_.

core::Size protocols::simple_moves::ShortBackrubMover::get_resnum ( ) const

References resnum_.

core::Real protocols::simple_moves::ShortBackrubMover::get_rotation_std_dev ( ) const

References rotation_std_dev_.

bool protocols::simple_moves::ShortBackrubMover::get_uniform_backrub ( ) const

References uniform_backrub_.

std::string protocols::simple_moves::ShortBackrubMover::mover_name ( )
static
void protocols::simple_moves::ShortBackrubMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

parse xml

Reimplemented from protocols::moves::Mover.

References backrubmover_.

void protocols::simple_moves::ShortBackrubMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_moves::ShortBackrubMover::set_input_pose ( core::pose::PoseCOP  pose)
overridevirtual

setter for poses contained for rms

Reimplemented from protocols::moves::Mover.

References backrubmover_.

void protocols::simple_moves::ShortBackrubMover::set_randomize_resnum ( bool  randomize_resnum)

References randomize_resnum_.

void protocols::simple_moves::ShortBackrubMover::set_resnum ( core::Size  resnum)

References resnum_.

void protocols::simple_moves::ShortBackrubMover::set_rotation_std_dev ( core::Real  rotation_std_dev)

References rotation_std_dev_.

void protocols::simple_moves::ShortBackrubMover::set_uniform_backrub ( bool  uniform_backrub)

References uniform_backrub_.

Member Data Documentation

protocols::backrub::BackrubMoverOP protocols::simple_moves::ShortBackrubMover::backrubmover_
private

mover used for Backrub moves

Referenced by apply(), get_backrubmover(), parse_my_tag(), set_input_pose(), and ShortBackrubMover().

bool protocols::simple_moves::ShortBackrubMover::randomize_resnum_
private

if true, choose a random residue for the next move

Referenced by apply(), get_randomize_resnum(), set_randomize_resnum(), and ShortBackrubMover().

core::Size protocols::simple_moves::ShortBackrubMover::resnum_
private

residue number specifying the center residue for the next Backrub move

Referenced by apply(), get_resnum(), set_resnum(), and ShortBackrubMover().

core::Real protocols::simple_moves::ShortBackrubMover::rotation_std_dev_
private

standard deviation of rotation angle (degrees) used for Backrub moves

Referenced by apply(), get_rotation_std_dev(), set_rotation_std_dev(), and ShortBackrubMover().

bool protocols::simple_moves::ShortBackrubMover::uniform_backrub_
private

if true, sample rotation angle from a uniform distribution from -20 to 20

Referenced by apply(), get_uniform_backrub(), set_uniform_backrub(), and ShortBackrubMover().


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