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protocols::simple_moves::FragmentMover Class Referenceabstract

abstract base class for FragmentMovers More...

#include <FragmentMover.hh>

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

Public Member Functions

 ~FragmentMover ()
virtual void apply (core::pose::Pose &)=0
 choose and insert a fragment –> has to be overloaded More...
virtual bool apply (core::pose::Pose &, Size pos) const
 apply a fragment at pos to movemable dofs More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
virtual 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...
virtual void set_movemap (core::kinematics::MoveMapCOP movemap)
 setter for the movemap More...
core::kinematics::MoveMapCOP movemap () const
core::fragment::InsertMap const & insert_map () const
core::fragment::InsertSize const & insert_size () const
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
virtual ~Mover ()
virtual MoverSP create ()
virtual void apply (core::io::serialization::PipeMap &pmap)
virtual void parse_state (SerializableState const &state)
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
virtual void save_state (SerializableState &state)
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 Mover (Mover const &other)
Moveroperator= (Mover const &other)
 assignment operator More...
virtual core::Real last_proposal_density_ratio ()
std::string const & type () const
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...
void set_current_tag (std::string const &new_tag)
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 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...
void type (const std::string &type_in)
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string get_type () const
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...
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
void set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP get_current_job () const

Protected Member Functions

 FragmentMover (core::fragment::FragSetCOP fragset, std::string type)
 FragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string 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_

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Detailed Description

abstract base class for FragmentMovers

Constructor & Destructor Documentation

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

Member Function Documentation

virtual void protocols::simple_moves::FragmentMover::apply ( core::pose::Pose )
pure virtual

choose and insert a fragment –> has to be overloaded

Implements protocols::moves::Mover.

Implemented in protocols::simple_moves::ClassicFragmentMover.

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

apply a fragment at pos to movemable dofs

References protocols::simple_moves::ClassicFragmentMover::apply_frames(), and fragset_.

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

apply at all movemable positions — honors movemap

References apply_frames(), core::sequence::end, fragset_, and insert_map().

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

accessor to the fragment set

References fragset_.

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

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

References insert_map_.

Referenced by apply_at_all_positions().

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

References insert_size_.

core::kinematics::MoveMapCOP protocols::simple_moves::FragmentMover::movemap ( ) const
virtual void protocols::simple_moves::FragmentMover::on_new_fragments ( )
void protocols::simple_moves::FragmentMover::set_fragments ( core::fragment::FragSetCOP  new_frags_)

setter for the fragment set

References fragset_, and on_new_fragments().

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

setter for the movemap

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

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

Member Data Documentation

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

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