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protocols::simple_moves::WobbleMover Class Reference

A protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: -—lfff bbb-— f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl— the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment(). More...

#include <WobbleMover.hh>

Inheritance diagram for protocols::simple_moves::WobbleMover:
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Public Types

typedef
protocols::simple_moves::SmoothFragmentMover 
Parent
 
- Public Types inherited from protocols::simple_moves::SmoothFragmentMover
typedef ClassicFragmentMover Parent
 

Public Member Functions

 WobbleMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, protocols::simple_moves::FragmentCostOP cost)
 
 WobbleMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)
 
 ~WobbleMover ()
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_defaults ()
 set defaults More...
 
void set_buffer_length (core::Size setting)
 
- Public Member Functions inherited from protocols::simple_moves::SmoothFragmentMover
 SmoothFragmentMover (core::fragment::FragSetCOP fragset, FragmentCostOP cost)
 
 SmoothFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, FragmentCostOP cost)
 
 ~SmoothFragmentMover ()
 
- Public Member Functions inherited from protocols::simple_moves::ClassicFragmentMover
 ClassicFragmentMover (core::fragment::FragSetCOP fragset)
 
 ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)
 
 ClassicFragmentMover (core::fragment::ConstantLengthFragSet const &fragset, core::kinematics::MoveMap const &movemap)
 Temp work around for PyRosetta code, until we found a way how to handle owning pointers in this case More...
 
 ~ClassicFragmentMover ()
 
void apply (core::pose::Pose &)
 Applies classic fragment insertion based on a FragSet. 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...
 
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::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

bool apply_fragment (core::fragment::Frame const &frame, core::Size frag_num, core::kinematics::MoveMap const &movemap, core::pose::Pose &pose) const
 make a wobble move ( smooth move + ccd loop closure ) NEEDS MORE WORK IF MULTIPLE CHAINS OR JUMPS ARE USED: total_residue!=end of chain More...
 
bool ccd_closure (core::pose::Pose &pose, protocols::loops::Loops const &loops, core::kinematics::MoveMap const &mm) const
 close loop and return if successful ( deviations smaller than thresholds ) More...
 
- Protected Member Functions inherited from protocols::simple_moves::SmoothFragmentMover
 SmoothFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, FragmentCostOP cost, std::string move_type)
 
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...
 
virtual bool use_ss_length_screen () const
 
- Protected Member Functions inherited from protocols::simple_moves::ClassicFragmentMover
 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 (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

core::Size buffer_length_
 how many variable residues on opposite side of fragment More...
 
core::Real forward_threshold_
 cutoffs that ccd has to undercut to be accepted More...
 
core::Real backward_threshold_
 

Additional Inherited Members

- 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...
 
- 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 protocols::moves::Mover class for a classic-wobble analog: a smooth move followed by ccd closure a smooth fragment is chosen according to the FragmentCost Functor; a cutpoint is inserted just in front of or just after the fragment a loop is defined around the fragment and cutpoint to be closed with ccd: a cut_Cterm insertion: -—lfff bbb-— f: fragment_res b: buffer_res -: immovable residues a !cut_Cterm insertion: —bbb fffl— the number of b resiudes is controlled by buffer_length_ (default 3); the move is used by apply() (inherited from FragmentMover). the insertion and loop closure is implemented in the virtual method apply_fragment().

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::simple_moves::WobbleMover::WobbleMover ( core::fragment::FragSetCOP  fragset,
core::kinematics::MoveMapCOP  movemap,
protocols::simple_moves::FragmentCostOP  cost 
)

References set_defaults().

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

References set_defaults().

protocols::simple_moves::WobbleMover::~WobbleMover ( )

Copy constructor disabled until the virtual base class ClassicFragmentMover's construction is sorted out

Member Function Documentation

bool protocols::simple_moves::WobbleMover::apply_fragment ( core::fragment::Frame const &  frame,
core::Size  frag_num,
core::kinematics::MoveMap const &  movemap,
core::pose::Pose pose 
) const
protectedvirtual

make a wobble move ( smooth move + ccd loop closure ) NEEDS MORE WORK IF MULTIPLE CHAINS OR JUMPS ARE USED: total_residue!=end of chain

Reimplemented from protocols::simple_moves::ClassicFragmentMover.

References protocols::loops::Loops::add_loop(), buffer_length_, ccd_closure(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), protocols::simple_moves::RG(), core::pose::Pose::total_residue(), and protocols::simple_moves::TR().

bool protocols::simple_moves::WobbleMover::ccd_closure ( core::pose::Pose pose,
protocols::loops::Loops const &  loops,
core::kinematics::MoveMap const &  mm 
) const
protected

close loop and return if successful ( deviations smaller than thresholds )

References backward_threshold_, protocols::loops::Loops::begin(), protocols::loops::loop_closure::ccd::fast_ccd_loop_closure(), and forward_threshold_.

Referenced by apply_fragment().

std::string protocols::simple_moves::WobbleMover::get_name ( ) const
virtual

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

Reimplemented from protocols::simple_moves::SmoothFragmentMover.

void protocols::simple_moves::WobbleMover::set_buffer_length ( core::Size  setting)
inline

References buffer_length_.

void protocols::simple_moves::WobbleMover::set_defaults ( )
inlinevirtual

Member Data Documentation

core::Real protocols::simple_moves::WobbleMover::backward_threshold_
private

Referenced by ccd_closure(), and set_defaults().

core::Size protocols::simple_moves::WobbleMover::buffer_length_
private

how many variable residues on opposite side of fragment

Referenced by apply_fragment(), set_buffer_length(), and set_defaults().

core::Real protocols::simple_moves::WobbleMover::forward_threshold_
private

cutoffs that ccd has to undercut to be accepted

Referenced by ccd_closure(), and set_defaults().


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