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protocols::nonlocal::HelixRotate Class Reference

#include <HelixRotate.hh>

Inheritance diagram for protocols::nonlocal::HelixRotate:
Inheritance graph
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Public Member Functions

 HelixRotate ()
 
 HelixRotate (const protocols::loops::Loop &helix, core::Real degrees)
 
void apply (core::pose::Pose &pose) override
 Rotates the helix by the specified number of degrees. More...
 
std::string get_name () const override
 Returns the protocol's name. More...
 
moves::MoverOP clone () const override
 Creates a new instance with the copy constructor. More...
 
moves::MoverOP fresh_instance () const override
 Creates a new instance with the default constructor. More...
 
const protocols::loops::Loopget_helix () const
 Returns the helix to be modified. More...
 
core::Real get_degrees () const
 Returns the number of degrees to rotate the helix. More...
 
void set_helix (const protocols::loops::Loop &helix)
 Updates the helix to be modified. More...
 
void set_degrees (core::Real degrees)
 Updates the number of degrees to rotate the helix. 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_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...
 

Private Member Functions

void initialize (const protocols::loops::Loop &helix, core::Real degrees)
 Shared initialization routine. More...
 
bool is_valid () const
 Returns true if this instance is valid and fully configured. More...
 
void decompose_structure (unsigned num_residues, protocols::loops::Loops *chunks) const
 Partitions the structure such that the helix to be rotated belongs to its own chunk, which will be subsequently connected to the star fold tree by its own jump. More...
 
unsigned jump_containing_helix (const protocols::loops::Loops &chunks) const
 Searches chunks for the member representing the helix, returning its index. More...
 
void get_rotation_parameters (const core::pose::Pose &pose, numeric::xyzVector< core::Real > *axis, numeric::xyzVector< core::Real > *point) const
 Computes rotational parameters– axis and point. More...
 

Private Attributes

protocols::loops::Loop helix_
 Stretch of contiguous residues representing the helix to be rotated. More...
 
core::Real degrees_
 Number of degrees to rotate the helix. More...
 

Additional Inherited Members

- 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
 
- 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...
 
- 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...
 

Constructor & Destructor Documentation

protocols::nonlocal::HelixRotate::HelixRotate ( )

References initialize().

protocols::nonlocal::HelixRotate::HelixRotate ( const protocols::loops::Loop helix,
core::Real  degrees 
)

References initialize().

Member Function Documentation

void protocols::nonlocal::HelixRotate::apply ( core::pose::Pose pose)
overridevirtual
moves::MoverOP protocols::nonlocal::HelixRotate::clone ( ) const
overridevirtual

Creates a new instance with the copy constructor.

Reimplemented from protocols::moves::Mover.

void protocols::nonlocal::HelixRotate::decompose_structure ( unsigned  num_residues,
protocols::loops::Loops chunks 
) const
private

Partitions the structure such that the helix to be rotated belongs to its own chunk, which will be subsequently connected to the star fold tree by its own jump.

References protocols::loops::Loops::add_loop(), get_helix(), protocols::loops::Loops::sequential_order(), protocols::loops::Loop::start(), protocols::loops::start, protocols::loops::Loop::stop(), and protocols::loops::stop.

Referenced by apply().

moves::MoverOP protocols::nonlocal::HelixRotate::fresh_instance ( ) const
overridevirtual

Creates a new instance with the default constructor.

Reimplemented from protocols::moves::Mover.

core::Real protocols::nonlocal::HelixRotate::get_degrees ( ) const

Returns the number of degrees to rotate the helix.

References degrees_.

Referenced by apply().

const protocols::loops::Loop & protocols::nonlocal::HelixRotate::get_helix ( ) const

Returns the helix to be modified.

References helix_.

Referenced by apply(), and decompose_structure().

std::string protocols::nonlocal::HelixRotate::get_name ( ) const
overridevirtual

Returns the protocol's name.

Implements protocols::moves::Mover.

void protocols::nonlocal::HelixRotate::get_rotation_parameters ( const core::pose::Pose pose,
numeric::xyzVector< core::Real > *  axis,
numeric::xyzVector< core::Real > *  point 
) const
private
void protocols::nonlocal::HelixRotate::initialize ( const protocols::loops::Loop helix,
core::Real  degrees 
)
private

Shared initialization routine.

References degrees_, protocols::loops::loop_closure::ccd::helix, and helix_.

Referenced by HelixRotate().

bool protocols::nonlocal::HelixRotate::is_valid ( ) const
private

Returns true if this instance is valid and fully configured.

References helix_, protocols::loops::Loop::start(), and protocols::loops::Loop::stop().

Referenced by apply().

unsigned protocols::nonlocal::HelixRotate::jump_containing_helix ( const protocols::loops::Loops chunks) const
private

Searches chunks for the member representing the helix, returning its index.

References helix_, protocols::loops::Loops::num_loop(), protocols::loops::Loop::start(), and protocols::loops::start.

Referenced by apply().

void protocols::nonlocal::HelixRotate::set_degrees ( core::Real  degrees)

Updates the number of degrees to rotate the helix.

References degrees_.

void protocols::nonlocal::HelixRotate::set_helix ( const protocols::loops::Loop helix)

Updates the helix to be modified.

References protocols::loops::loop_closure::ccd::helix, and helix_.

Member Data Documentation

core::Real protocols::nonlocal::HelixRotate::degrees_
private

Number of degrees to rotate the helix.

Referenced by get_degrees(), initialize(), and set_degrees().

protocols::loops::Loop protocols::nonlocal::HelixRotate::helix_
private

Stretch of contiguous residues representing the helix to be rotated.

Referenced by get_helix(), get_rotation_parameters(), initialize(), is_valid(), jump_containing_helix(), and set_helix().


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