Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::simple_moves::ClassicFragmentMover Class Reference

A FragmentMover that applies uniform sampling of fragments. More...

#include <FragmentMover.hh>

Public Member Functions

 ClassicFragmentMover ()
 Empty constructor. More...
 
 ClassicFragmentMover (core::fragment::FragSetCOP fragset)
 Constructor with supplied FragSet. More...
 
 ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)
 Constructor with supplied FragSet and MoveMap. More...
 
 ClassicFragmentMover (core::fragment::ConstantLengthFragSet const &fragset, core::kinematics::MoveMap const &movemap)
 Constructor with supplied ConstantLengthFragSet and MoveMap. More...
 
 ~ClassicFragmentMover ()
 
void apply (core::pose::Pose &)
 Applies classic fragment insertion based on a FragSet. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
void set_check_ss (bool setting)
 check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2) More...
 
bool check_ss () const
 accessor More...
 
core::Real end_bias () const
 
void set_end_bias (core::Real setting)
 
bool end_bias_check_enabled () const
 
void enable_end_bias_check (bool setting=true)
 
void set_min_overlap (Size setting)
 min_overlap controls the behaviour fragset->region() More...
 
void set_min_frag_length (Size setting)
 min_frag_length controls the behaviour fragset->region() More...
 
virtual bool apply_fragment (core::fragment::Frame const &frame, Size frag_num, core::kinematics::MoveMap const &movemap, core::pose::Pose &pose) const
 apply the chosen fragment, More...
 
virtual void set_defaults ()
 set defaults More...
 
virtual bool choose_fragment (core::fragment::FrameList const &, core::pose::Pose const &, Size &frame_num, Size &frag_num) const
 given FrameList and pose, this method yields a fragment ( frame_num/ frag_num); return false if nothing suitable is found More...
 
void define_start_window (Size window_start)
 apply fragment at predefined position More...
 
virtual bool choose_window_start (core::pose::Pose const &, Size window_length, Size &window_start) const
 yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found ) More...
 
virtual bool choose_window_length (core::pose::Pose const &, Size &window_length) const
 yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found ) More...
 
void on_new_fragments ()
 is called from set_fragments() More...
 
virtual bool end_bias_check (core::pose::Pose const &, Size window_start) const
 
virtual bool valid_ss (std::string const &new_ss) const
 returns true if the ss string is acceptable More...
 
- Public Member Functions inherited from protocols::simple_moves::FragmentMover
 ~FragmentMover ()
 
virtual bool apply (core::pose::Pose &, Size pos) const
 apply a fragment at pos to movemable dofs 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::MoveMapMover
 MoveMapMover ()
 
 MoveMapMover (std::string const &name)
 
 MoveMapMover (MoveMapMover const &other)
 
virtual ~MoveMapMover ()
 
virtual void initialize (core::pose::Pose &)
 
- 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
 
void set_type (std::string const &setting)
 
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 void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Protected Member Functions

 ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type)
 alternative Constructor to be used by derived classes More...
 
 ClassicFragmentMover (core::fragment::FragSetCOP fragset, std::string type)
 alternative Constructor to be used by derived classes More...
 
virtual bool apply_frames (core::pose::Pose &, core::fragment::FrameList const &) const
 
- Protected Member Functions inherited from protocols::simple_moves::FragmentMover
 FragmentMover (std::string type)
 Empty constructor. More...
 
 FragmentMover (core::fragment::FragSetCOP fragset, std::string type)
 
 FragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type)
 constructor More...
 
void update_insert_map ()
 
- 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...
 

Private Attributes

Size min_overlap_
 
Size min_frag_length_
 
bool check_ss_
 
core::Real end_bias_
 
bool bApplyEndBias_
 
bool use_predefined_window_start_
 
Size predefined_window_start_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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 Attributes inherited from protocols::simple_moves::FragmentMover
core::fragment::FragSetCOP fragset_
 
core::kinematics::MoveMapCOP movemap_
 
core::fragment::InsertMap insert_map_
 
core::fragment::InsertSize insert_size_
 

Detailed Description

A FragmentMover that applies uniform sampling of fragments.

Constructor & Destructor Documentation

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( )

Empty constructor.

References set_defaults().

Referenced by clone(), and fresh_instance().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP  fragset)

Constructor with supplied FragSet.

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP  fragset,
core::kinematics::MoveMapCOP  movemap 
)

Constructor with supplied FragSet and MoveMap.

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::ConstantLengthFragSet const &  fragset,
core::kinematics::MoveMap const &  movemap 
)

Constructor with supplied ConstantLengthFragSet and MoveMap.

Note
Temp workaround for PyRosetta code, until we find a way to handle owning pointers in this case

References clone(), and set_defaults().

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

alternative Constructor to be used by derived classes

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP  fragset,
std::string  type 
)
protected

alternative Constructor to be used by derived classes

References set_defaults().

Member Function Documentation

void protocols::simple_moves::ClassicFragmentMover::apply ( core::pose::Pose pose)
virtual
bool protocols::simple_moves::ClassicFragmentMover::apply_fragment ( core::fragment::Frame const &  frame,
Size  frag_num,
core::kinematics::MoveMap const &  movemap,
core::pose::Pose pose 
) const
virtual
bool protocols::simple_moves::ClassicFragmentMover::apply_frames ( core::pose::Pose ,
core::fragment::FrameList const &   
) const
protectedvirtual
bool protocols::simple_moves::ClassicFragmentMover::check_ss ( ) const
inline
bool protocols::simple_moves::ClassicFragmentMover::choose_fragment ( core::fragment::FrameList const &  ,
core::pose::Pose const &  ,
Size frame_num,
Size frag_num 
) const
virtual

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num); return false if nothing suitable is found

Reimplemented in protocols::simple_moves::SmoothSymmetricFragmentMover, and protocols::simple_moves::SmoothFragmentMover.

References N, protocols::simple_moves::RG, runtime_assert, and numeric::random::RandomGenerator::uniform().

Referenced by protocols::simple_moves::ResTypeFragmentMover::apply_frames(), and apply_frames().

virtual bool protocols::simple_moves::ClassicFragmentMover::choose_window_length ( core::pose::Pose const &  ,
Size window_length 
) const
inlinevirtual

yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found )

Referenced by apply().

bool protocols::simple_moves::ClassicFragmentMover::choose_window_start ( core::pose::Pose const &  pose,
Size  window_length,
Size window_start 
) const
virtual

yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found )

References bApplyEndBias_, end_bias_check(), protocols::simple_moves::FragmentMover::insert_map_, protocols::simple_moves::FragmentMover::insert_size_, protocols::simple_moves::RG, protocols::simple_moves::tr, and numeric::random::RandomGenerator::uniform().

Referenced by apply().

protocols::moves::MoverOP protocols::simple_moves::ClassicFragmentMover::clone ( ) const
virtual

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.

References ClassicFragmentMover().

void protocols::simple_moves::ClassicFragmentMover::define_start_window ( Size  window_start)
void protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check ( bool  setting = true)
inline
core::Real protocols::simple_moves::ClassicFragmentMover::end_bias ( ) const
inline

References end_bias_.

Referenced by end_bias_check().

bool protocols::simple_moves::ClassicFragmentMover::end_bias_check ( core::pose::Pose const &  pose,
Size  window_start 
) const
virtual
bool protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled ( ) const
inline

References bApplyEndBias_.

protocols::moves::MoverOP protocols::simple_moves::ClassicFragmentMover::fresh_instance ( ) const
virtual

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.

References ClassicFragmentMover().

std::string protocols::simple_moves::ClassicFragmentMover::get_name ( ) const
virtual
void protocols::simple_moves::ClassicFragmentMover::on_new_fragments ( )
inlinevirtual

is called from set_fragments()

Reimplemented from protocols::simple_moves::FragmentMover.

void protocols::simple_moves::ClassicFragmentMover::set_check_ss ( bool  setting)
inline
void protocols::simple_moves::ClassicFragmentMover::set_defaults ( )
virtual
void protocols::simple_moves::ClassicFragmentMover::set_end_bias ( core::Real  setting)
inline

References end_bias_.

void protocols::simple_moves::ClassicFragmentMover::set_min_frag_length ( Size  setting)
inline

min_frag_length controls the behaviour fragset->region()

References min_frag_length_.

void protocols::simple_moves::ClassicFragmentMover::set_min_overlap ( Size  setting)
inline

min_overlap controls the behaviour fragset->region()

References min_overlap_.

void protocols::simple_moves::ClassicFragmentMover::show ( std::ostream &  output = std::cout) const
virtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::simple_moves::LoggedFragmentMover.

References bApplyEndBias_, check_ss_, end_bias_, min_frag_length_, min_overlap_, protocols::simple_moves::FragmentMover::movemap(), predefined_window_start_, protocols::moves::Mover::show(), and use_predefined_window_start_.

Referenced by protocols::simple_moves::operator<<().

bool protocols::simple_moves::ClassicFragmentMover::valid_ss ( std::string const &  new_ss) const
virtual

returns true if the ss string is acceptable

DONT ALLOW HELICES OF LESS THAN 3 OR STRANDS OF LESS THAN 2 Fix this: inserting length two helices at the chain end is allowed as is inserting length 1 strands... For the moment, preserving r++'s incorrect behavior.

References protocols::simple_moves::tr.

Referenced by protocols::simple_moves::ResTypeFragmentMover::apply_frames(), and apply_frames().

Member Data Documentation

bool protocols::simple_moves::ClassicFragmentMover::bApplyEndBias_
private
bool protocols::simple_moves::ClassicFragmentMover::check_ss_
private
core::Real protocols::simple_moves::ClassicFragmentMover::end_bias_
private
Size protocols::simple_moves::ClassicFragmentMover::min_frag_length_
private
Size protocols::simple_moves::ClassicFragmentMover::min_overlap_
private
Size protocols::simple_moves::ClassicFragmentMover::predefined_window_start_
private

Referenced by apply(), define_start_window(), and show().

bool protocols::simple_moves::ClassicFragmentMover::use_predefined_window_start_
private

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