Public Member Functions | Protected Member Functions | Protected Attributes | Private Types | List of all members
protocols::simple_moves::FragmentMover Class Referenceabstract

abstract base class for FragmentMovers More...

#include <FragmentMover.hh>

Inheritance diagram for protocols::simple_moves::FragmentMover:
Inheritance graph

Public Member Functions

 ~FragmentMover () override
virtual bool apply (core::pose::Pose &, core::Size pos) const
 apply a fragment at pos to movemable dofs More...
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
virtual core::Size apply_at_all_positions (core::pose::Pose &) const
 apply at all movemable positions — honors movemap More...
core::fragment::FragSetCOP fragments () const
 accessor to the fragment set More...
virtual void set_fragments (core::fragment::FragSetCOP new_frags_)
 setter for the fragment set More...
void set_movemap (core::kinematics::MoveMapCOP movemap) override
 setter for the movemap More...
core::kinematics::MoveMapCOP movemap (core::pose::Pose const &) const override
 Get a movemap for the given pose (As the movemap may vary based on the Pose (e.g. MoveMapFactory), we need the Pose information) More...
core::kinematics::MoveMapCOP movemap () const
core::fragment::InsertMap const & insert_map () const
core::fragment::InsertSize const & insert_size () const
virtual void apply (Pose &)=0
 Main Method. More...
- Public Member Functions inherited from protocols::moves::MoveMapMover
 MoveMapMover ()
 MoveMapMover (std::string const &name)
 MoveMapMover (MoveMapMover const &)=default
 ~MoveMapMover () override=default
virtual void initialize (core::pose::Pose &)
- 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 apply (Pose &)=0
 Main Method. 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Protected Member Functions

 FragmentMover (std::string const &type)
 Empty constructor. More...
 FragmentMover (core::fragment::FragSetCOP fragset, std::string const &type)
 FragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string const &type)
 constructor More...
virtual void on_new_fragments ()
void update_insert_map ()
virtual bool apply_frames (core::pose::Pose &, core::fragment::FrameList const &) const =0
- 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...

Protected Attributes

core::fragment::FragSetCOP fragset_
core::kinematics::MoveMapCOP movemap_
core::fragment::InsertMap insert_map_
core::fragment::InsertSize insert_size_

Private Types

typedef moves::MoveMapMover Parent

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...

Detailed Description

abstract base class for FragmentMovers

Member Typedef Documentation

◆ Parent

Constructor & Destructor Documentation

◆ ~FragmentMover()

protocols::simple_moves::FragmentMover::~FragmentMover ( )

◆ FragmentMover() [1/3]

protocols::simple_moves::FragmentMover::FragmentMover ( std::string const &  type)

Empty constructor.

References set_movemap(), and protocols::moves::Mover::type().

◆ FragmentMover() [2/3]

protocols::simple_moves::FragmentMover::FragmentMover ( core::fragment::FragSetCOP  fragset,
std::string const &  type 

◆ FragmentMover() [3/3]

protocols::simple_moves::FragmentMover::FragmentMover ( core::fragment::FragSetCOP  fragset,
core::kinematics::MoveMapCOP  movemap,
std::string const &  type 

Member Function Documentation

◆ apply() [1/2]

bool protocols::simple_moves::FragmentMover::apply ( core::pose::Pose pose,
core::Size  pos 
) const

apply a fragment at pos to movemable dofs

References apply_frames(), and fragset_.

◆ apply() [2/2]

virtual void protocols::moves::Mover::apply

Main Method.

◆ apply_at_all_positions()

Size protocols::simple_moves::FragmentMover::apply_at_all_positions ( core::pose::Pose pose) const

apply at all movemable positions — honors movemap

References apply_frames(), fragset_, and insert_map().

◆ apply_frames()

virtual bool protocols::simple_moves::FragmentMover::apply_frames ( core::pose::Pose ,
core::fragment::FrameList const &   
) const
protectedpure virtual

◆ fragments()

core::fragment::FragSetCOP protocols::simple_moves::FragmentMover::fragments ( ) const

accessor to the fragment set

References fragset_.

Referenced by protocols::topology_broker::LoopFragmentClaimer::loop_frags().

◆ get_name()

std::string protocols::simple_moves::FragmentMover::get_name ( ) const

◆ insert_map()

core::fragment::InsertMap const& protocols::simple_moves::FragmentMover::insert_map ( ) const

References insert_map_.

Referenced by apply_at_all_positions().

◆ insert_size()

core::fragment::InsertSize const& protocols::simple_moves::FragmentMover::insert_size ( ) const

References insert_size_.

◆ movemap() [1/2]

core::kinematics::MoveMapCOP protocols::simple_moves::FragmentMover::movemap ( ) const

◆ movemap() [2/2]

core::kinematics::MoveMapCOP protocols::simple_moves::FragmentMover::movemap ( core::pose::Pose const &  ) const

Get a movemap for the given pose (As the movemap may vary based on the Pose (e.g. MoveMapFactory), we need the Pose information)

Implements protocols::moves::MoveMapMover.

References movemap_.

Referenced by protocols::topology_broker::LoopFragmentClaimer::loop_frags().

◆ on_new_fragments()

virtual void protocols::simple_moves::FragmentMover::on_new_fragments ( )

◆ set_fragments()

void protocols::simple_moves::FragmentMover::set_fragments ( core::fragment::FragSetCOP  new_frags_)

setter for the fragment set

References fragset_, on_new_fragments(), and protocols::simple_moves::tr().

◆ set_movemap()

void protocols::simple_moves::FragmentMover::set_movemap ( core::kinematics::MoveMapCOP  movemap)

setter for the movemap

Implements protocols::moves::MoveMapMover.

References movemap(), movemap_, and update_insert_map().

Referenced by FragmentMover().

◆ update_insert_map()

void protocols::simple_moves::FragmentMover::update_insert_map ( )

Member Data Documentation

◆ fragset_

core::fragment::FragSetCOP protocols::simple_moves::FragmentMover::fragset_

◆ insert_map_

core::fragment::InsertMap protocols::simple_moves::FragmentMover::insert_map_

◆ insert_size_

core::fragment::InsertSize protocols::simple_moves::FragmentMover::insert_size_

◆ movemap_

core::kinematics::MoveMapCOP protocols::simple_moves::FragmentMover::movemap_

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