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protocols::fldsgn::CircularPermutation Class Reference

#include <CircularPermutation.hh>

Inheritance diagram for protocols::fldsgn::CircularPermutation:
Inheritance graph
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Public Types

typedef core::Size Size
 
typedef core::pose::Pose Pose
 
typedef core::kinematics::MoveMap MoveMap
 
typedef core::kinematics::MoveMapOP MoveMapOP
 
typedef protocols::moves::MoverOP MoverOP
 
typedef utility::tag::TagCOP TagCOP
 
typedef basic::datacache::DataMap DataMap
 
- 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

 CircularPermutation ()
 default constructor More...
 
 CircularPermutation (CircularPermutation const &rval)
 copy constructor More...
 
 ~CircularPermutation () override
 default destructor More...
 
MoverOP clone () const override
 clone this object More...
 
MoverOP fresh_instance () const override
 create this type of object More...
 
core::Size new_terminal_pos () const
 total number of cycles More...
 
void new_terminal_pos (core::Size const s)
 new N- & C- terminal position More...
 
core::Size which_chain (core::Size const s, Pose const &pose) const
 total number of cycles More...
 
void split_chains (Pose &pose, utility::vector1< core::Size > const &pos)
 
void apply (Pose &pose) override
 apply defined moves to given Pose More...
 
void parse_my_tag (TagCOP tag, basic::datacache::DataMap &) override
 parse xml file 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_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 Types

typedef protocols::moves::Mover Super
 

Private Member Functions

CircularPermutationoperator= (CircularPermutation const &rval)
 copy assignment More...
 

Private Attributes

core::Size new_terminal_pos_
 new N- & C- terminal position More...
 
bool ignore_chain_
 
core::Size split_
 

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

typedef basic::datacache::DataMap protocols::fldsgn::CircularPermutation::DataMap
typedef utility::tag::TagCOP protocols::fldsgn::CircularPermutation::TagCOP

Constructor & Destructor Documentation

protocols::fldsgn::CircularPermutation::CircularPermutation ( )

default constructor

protocols::fldsgn::CircularPermutation::CircularPermutation ( CircularPermutation const &  rval)

copy constructor

copy constructor

protocols::fldsgn::CircularPermutation::~CircularPermutation ( )
overridedefault

default destructor

Member Function Documentation

void protocols::fldsgn::CircularPermutation::apply ( Pose pose)
overridevirtual
CircularPermutation::MoverOP protocols::fldsgn::CircularPermutation::clone ( ) const
overridevirtual

clone this object

Reimplemented from protocols::moves::Mover.

CircularPermutation::MoverOP protocols::fldsgn::CircularPermutation::fresh_instance ( ) const
overridevirtual

create this type of object

Reimplemented from protocols::moves::Mover.

std::string protocols::fldsgn::CircularPermutation::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::fldsgn::CircularPermutation::mover_name ( )
static
CircularPermutation::Size protocols::fldsgn::CircularPermutation::new_terminal_pos ( ) const

total number of cycles

References new_terminal_pos_.

void protocols::fldsgn::CircularPermutation::new_terminal_pos ( core::Size const  s)

new N- & C- terminal position

References new_terminal_pos_.

CircularPermutation& protocols::fldsgn::CircularPermutation::operator= ( CircularPermutation const &  rval)
private

copy assignment

Remarks
Mover base class prevents this from working properly...
void protocols::fldsgn::CircularPermutation::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

parse xml file

parse xml

Reimplemented from protocols::moves::Mover.

References ignore_chain_, new_terminal_pos_, and split_.

void protocols::fldsgn::CircularPermutation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::fldsgn::CircularPermutation::split_chains ( Pose pose,
utility::vector1< core::Size > const &  pos 
)
CircularPermutation::Size protocols::fldsgn::CircularPermutation::which_chain ( core::Size const  s,
Pose const &  pose 
) const

Member Data Documentation

bool protocols::fldsgn::CircularPermutation::ignore_chain_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::fldsgn::CircularPermutation::new_terminal_pos_
private

new N- & C- terminal position

Referenced by apply(), new_terminal_pos(), and parse_my_tag().

core::Size protocols::fldsgn::CircularPermutation::split_
private

Referenced by apply(), and parse_my_tag().


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