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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:
Inheritance graph
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Public Types

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

 WobbleMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, protocols::simple_moves::FragmentCostOP cost)
 
 WobbleMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)
 
 ~WobbleMover () override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 () override
 
SmoothFragmentMoverOP shared_from_this ()
 
- Public Member Functions inherited from protocols::simple_moves::ClassicFragmentMover
 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 () override
 
void apply (core::pose::Pose &) override
 Applies classic fragment insertion based on a FragSet. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 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 (core::Size setting)
 min_overlap controls the behaviour fragset->region() More...
 
void set_min_frag_length (core::Size setting)
 min_frag_length controls the behaviour fragset->region() More...
 
void define_start_window (core::Size window_start)
 apply fragment at predefined position More...
 
virtual bool choose_window_start (core::pose::Pose const &, core::Size window_length, core::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 &, core::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 () override
 is called from set_fragments() More...
 
virtual bool end_bias_check (core::pose::Pose const &, core::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 () override
 
virtual bool apply (core::pose::Pose &, core::Size pos) const
 apply a fragment at pos to movemable dofs 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
 
- 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 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
 
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 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...
 

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 override
 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)
 
bool choose_fragment (core::fragment::FrameList const &, core::pose::Pose const &, core::Size &frame_num, core::Size &frag_num) const override
 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...
 
bool apply_frames (core::pose::Pose &, core::fragment::FrameList const &) const override
 
- Protected Member Functions inherited from protocols::simple_moves::FragmentMover
 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...
 
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_ = 3
 how many variable residues on opposite side of fragment More...
 
core::Real forward_threshold_ = 0.3
 cutoffs that ccd has to undercut to be accepted More...
 

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

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

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_.

Member Data Documentation

core::Size protocols::simple_moves::WobbleMover::buffer_length_ = 3
private

how many variable residues on opposite side of fragment

Referenced by apply_fragment(), and set_buffer_length().

core::Real protocols::simple_moves::WobbleMover::forward_threshold_ = 0.3
private

cutoffs that ccd has to undercut to be accepted

Referenced by ccd_closure().


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