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| | SmoothFragmentMover (core::fragment::FragSetCOP fragset, FragmentCostOP cost) |
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| | SmoothFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, FragmentCostOP cost) |
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| | ~SmoothFragmentMover () |
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| virtual std::string | get_name () const |
| | Each derived class must specify its name. The class name. More...
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| | ClassicFragmentMover () |
| | Empty constructor. More...
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| | ClassicFragmentMover (core::fragment::FragSetCOP fragset) |
| | Constructor with supplied FragSet. More...
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| | ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap) |
| | Constructor with supplied FragSet and MoveMap. More...
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| | ClassicFragmentMover (core::fragment::ConstantLengthFragSet const &fragset, core::kinematics::MoveMap const &movemap) |
| | Constructor with supplied ConstantLengthFragSet and MoveMap. More...
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| | ~ClassicFragmentMover () |
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| virtual void | apply (core::pose::Pose &) |
| | Applies classic fragment insertion based on a FragSet. More...
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| virtual void | show (std::ostream &output=std::cout) const |
| | Outputs details about the Mover, including current settings. More...
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| virtual protocols::moves::MoverOP | clone () const |
| | Return a clone of the Mover object. More...
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| virtual protocols::moves::MoverOP | fresh_instance () const |
| | Generates a new Mover object freshly created with the default ctor. More...
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| void | set_check_ss (bool setting) |
| | check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2) More...
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| bool | check_ss () const |
| | accessor More...
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| core::Real | end_bias () const |
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| void | set_end_bias (core::Real setting) |
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| bool | end_bias_check_enabled () const |
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| void | enable_end_bias_check (bool setting=true) |
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| void | set_min_overlap (Size setting) |
| | min_overlap controls the behaviour fragset->region() More...
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| void | set_min_frag_length (Size setting) |
| | min_frag_length controls the behaviour fragset->region() More...
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| 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, this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards More...
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| virtual void | set_defaults () |
| | set defaults More...
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| void | define_start_window (Size window_start) |
| | apply fragment at predefined position More...
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| 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...
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| 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...
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| void | on_new_fragments () |
| | is called from set_fragments() More...
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| virtual bool | end_bias_check (core::pose::Pose const &, Size window_start) const |
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| virtual bool | valid_ss (std::string const &new_ss) const |
| | returns true if the ss string is acceptable More...
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| | ~FragmentMover () |
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| virtual bool | apply (core::pose::Pose &, Size pos) const |
| | apply a fragment at pos to movemable dofs More...
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| virtual Size | apply_at_all_positions (core::pose::Pose &) const |
| | apply at all movemable positions — honors movemap More...
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| core::fragment::FragSetCOP | fragments () const |
| | accessor to the fragment set More...
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| virtual void | set_fragments (core::fragment::FragSetCOP new_frags_) |
| | setter for the fragment set More...
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| virtual void | set_movemap (core::kinematics::MoveMapCOP movemap) |
| | setter for the movemap More...
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| core::kinematics::MoveMapCOP | movemap () const |
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| core::fragment::InsertMap const & | insert_map () const |
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| core::fragment::InsertSize const & | insert_size () const |
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| | MoveMapMover () |
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| | MoveMapMover (std::string const &name) |
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| | MoveMapMover (MoveMapMover const &other) |
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| virtual | ~MoveMapMover () |
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| virtual void | initialize (core::pose::Pose &) |
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| | Mover () |
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| virtual | ~Mover () |
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| virtual MoverOP | create () |
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| MoverCOP | get_self_ptr () const |
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| MoverOP | get_self_ptr () |
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| MoverCAP | get_self_weak_ptr () const |
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| MoverAP | get_self_weak_ptr () |
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| | Mover (std::string const &type_name) |
| | sets the type for a mover; name_ has been removed (2010/05/14) More...
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| | Mover (Mover const &other) |
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| Mover & | operator= (Mover const &other) |
| | assignment operator More...
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| virtual core::Real | last_proposal_density_ratio () |
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| std::string const & | type () const |
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| void | set_type (std::string const &setting) |
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| 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...
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| virtual void | set_current_tag (std::string const &new_tag) |
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| virtual void | set_input_pose (PoseCOP pose) |
| | setter for poses contained for rms More...
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| 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...
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| PoseCOP | get_input_pose () const |
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| PoseCOP | get_native_pose () const |
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| 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...
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| void | type (const std::string &type_in) |
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| 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...
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| std::string | get_type () const |
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| MoverStatus | get_last_move_status () const |
| | end parser interface, start Job Distributor interface///////////// More...
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| 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...
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| virtual core::pose::PoseOP | get_additional_output () |
| | Mechanism by which a mover may return multiple output poses from a single input pose. More...
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| 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...
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| virtual Strings & | info () |
| | non-const accessor More...
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| virtual Strings const & | info () const |
| | const accessor More...
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| 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...
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| 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...
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| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
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| jobdist::BasicJobCOP | get_current_job () const |
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Public Types inherited from protocols::moves::Mover
1.8.7