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protocols::splice::AlignEndsMover Class Reference

#include <AlignEndsMover.hh>

Inheritance diagram for protocols::splice::AlignEndsMover:
Inheritance graph
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Public Member Functions

 AlignEndsMover ()
 
 ~AlignEndsMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
core::Real distance_threshold () const
 
void distance_threshold (core::Real const r)
 
core::Size neighbors () const
 
void neighbors (core::Size n)
 
core::Size N_terminal_count () const
 
void N_terminal_count (core::Size n)
 
bool odd () const
 
void odd (bool const b)
 
bool even () const
 
void even (bool const b)
 
core::pose::PoseOP template_pose () const
 
void template_pose (core::pose::PoseOP p)
 
core::Size stagger () const
 
void stagger (core::Size const s)
 
core::Size strand_length () const
 
void strand_length (core::Size const s)
 
core::Size max_strands () const
 
void max_strands (core::Size const m)
 
bool parallel () const
 
void parallel (bool const p)
 
void chain (core::Size const c)
 
core::Size chain () const
 
void sequence_separation (core::Size const c)
 
core::Size sequence_separation () const
 
void residues_to_align_on_pose (utility::vector1< core::Size > r)
 
void residues_to_align_on_template (utility::vector1< core::Size > r)
 
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_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
 
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 Member Functions

utility::vector1< core::Sizereference_positions (core::pose::Pose const &p) const
 

Private Attributes

core::Real distance_threshold_
 
core::Size strand_length_
 
core::Size neighbors_
 
core::Size N_terminal_count_
 
core::Size max_strands_
 
bool odd_
 
bool even_
 
core::pose::PoseOP template_pose_
 
core::Size stagger_
 
bool parallel_
 
core::Size chain_
 
core::Size sequence_separation_
 
utility::vector1< core::Sizeresidues_to_align_on_pose_
 
utility::vector1< core::Sizeresidues_to_align_on_template_
 

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
 
- 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::splice::AlignEndsMover::AlignEndsMover ( )
protocols::splice::AlignEndsMover::~AlignEndsMover ( )
overridedefault

Member Function Documentation

void protocols::splice::AlignEndsMover::apply ( core::pose::Pose )
overridevirtual
void protocols::splice::AlignEndsMover::chain ( core::Size const  c)
inline

References core::pack::dunbrack::c, and chain_.

core::Size protocols::splice::AlignEndsMover::chain ( ) const
inline

References chain_.

Referenced by parse_my_tag(), and reference_positions().

moves::MoverOP protocols::splice::AlignEndsMover::clone ( ) const
overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

core::Real protocols::splice::AlignEndsMover::distance_threshold ( ) const
inline

References distance_threshold_.

Referenced by parse_my_tag(), and reference_positions().

void protocols::splice::AlignEndsMover::distance_threshold ( core::Real const  r)
inline

References distance_threshold_.

bool protocols::splice::AlignEndsMover::even ( ) const
inline

References even_.

Referenced by parse_my_tag(), and reference_positions().

void protocols::splice::AlignEndsMover::even ( bool const  b)
inline
moves::MoverOP protocols::splice::AlignEndsMover::fresh_instance ( ) const
overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

std::string protocols::splice::AlignEndsMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

core::Size protocols::splice::AlignEndsMover::max_strands ( ) const
inline

References max_strands_.

Referenced by parse_my_tag(), and reference_positions().

void protocols::splice::AlignEndsMover::max_strands ( core::Size const  m)
inline

References max_strands_.

std::string protocols::splice::AlignEndsMover::mover_name ( )
static
core::Size protocols::splice::AlignEndsMover::N_terminal_count ( ) const
inline
void protocols::splice::AlignEndsMover::N_terminal_count ( core::Size  n)
inline

References N_terminal_count_.

core::Size protocols::splice::AlignEndsMover::neighbors ( ) const
inline

References neighbors_.

Referenced by parse_my_tag(), and reference_positions().

void protocols::splice::AlignEndsMover::neighbors ( core::Size  n)
inline

References neighbors_.

bool protocols::splice::AlignEndsMover::odd ( ) const
inline

References odd_.

Referenced by parse_my_tag(), and reference_positions().

void protocols::splice::AlignEndsMover::odd ( bool const  b)
inline
bool protocols::splice::AlignEndsMover::parallel ( ) const
inline

References parallel_.

Referenced by parse_my_tag(), and reference_positions().

void protocols::splice::AlignEndsMover::parallel ( bool const  p)
inline

References parallel_.

void protocols::splice::AlignEndsMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References chain(), distance_threshold(), even(), max_strands(), N_terminal_count(), neighbors(), odd(), parallel(), core::import_pose::pose_from_file(), residues_to_align_on_pose_, residues_to_align_on_template_, sequence_separation(), stagger(), strand_length(), template_pose(), and protocols::splice::TR().

void protocols::splice::AlignEndsMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
utility::vector1< core::Size > protocols::splice::AlignEndsMover::reference_positions ( core::pose::Pose const &  p) const
private
void protocols::splice::AlignEndsMover::residues_to_align_on_pose ( utility::vector1< core::Size r)
inline
void protocols::splice::AlignEndsMover::residues_to_align_on_template ( utility::vector1< core::Size r)
inline
void protocols::splice::AlignEndsMover::sequence_separation ( core::Size const  c)
inline
core::Size protocols::splice::AlignEndsMover::sequence_separation ( ) const
inline
core::Size protocols::splice::AlignEndsMover::stagger ( ) const
inline

References stagger_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::AlignEndsMover::stagger ( core::Size const  s)
inline

References stagger_.

core::Size protocols::splice::AlignEndsMover::strand_length ( ) const
inline

References strand_length_.

Referenced by parse_my_tag(), and reference_positions().

void protocols::splice::AlignEndsMover::strand_length ( core::Size const  s)
inline

References strand_length_.

core::pose::PoseOP protocols::splice::AlignEndsMover::template_pose ( ) const

References template_pose_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::AlignEndsMover::template_pose ( core::pose::PoseOP  p)

References template_pose_.

Member Data Documentation

core::Size protocols::splice::AlignEndsMover::chain_
private

Referenced by chain().

core::Real protocols::splice::AlignEndsMover::distance_threshold_
private

Referenced by distance_threshold().

bool protocols::splice::AlignEndsMover::even_
private

Referenced by even().

core::Size protocols::splice::AlignEndsMover::max_strands_
private

Referenced by max_strands().

core::Size protocols::splice::AlignEndsMover::N_terminal_count_
private

Referenced by N_terminal_count().

core::Size protocols::splice::AlignEndsMover::neighbors_
private

Referenced by neighbors().

bool protocols::splice::AlignEndsMover::odd_
private

Referenced by odd().

bool protocols::splice::AlignEndsMover::parallel_
private

Referenced by parallel().

utility::vector1< core::Size > protocols::splice::AlignEndsMover::residues_to_align_on_pose_
private
utility::vector1< core::Size > protocols::splice::AlignEndsMover::residues_to_align_on_template_
private
core::Size protocols::splice::AlignEndsMover::sequence_separation_
private

Referenced by sequence_separation().

core::Size protocols::splice::AlignEndsMover::stagger_
private

Referenced by stagger().

core::Size protocols::splice::AlignEndsMover::strand_length_
private

Referenced by strand_length().

core::pose::PoseOP protocols::splice::AlignEndsMover::template_pose_
private

Referenced by template_pose().


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