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Rosetta 3.5
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Rosetta 3.5
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#include <AnchorMovers.hh>
Public Member Functions | |
| AnchoredRefineMover (protocols::anchored_design::AnchorMoversDataOP interface_in) | |
| virtual | ~AnchoredRefineMover () |
| virtual void | apply (core::pose::Pose &pose) |
| virtual std::string | get_name () const |
| Each derived class must specify its name. The class name. More... | |
| bool | get_debug () const |
| debugging mode activates a bunch of extra output More... | |
| bool | get_refine_CCD_off () const |
| do not perform CCD style closure (use KIC only) More... | |
| bool | get_refine_KIC_off () const |
| do not perform KIC style closure (use CCD only) More... | |
| bool | get_nonpivot_torsion_sampling () const |
| use nonpivot torsion sampling for KIC? More... | |
| bool | get_vicinity_sampling () const |
| KIC use vicinity sampling? More... | |
| core::Real | get_vicinity_degree () const |
| KIC vicinity sampling degrees. More... | |
| core::Real | get_refine_temp () const |
| MC temperature. More... | |
| core::Size | get_refine_cycles () const |
| number of MC cycles More... | |
| std::string const & | get_min_type () const |
| what minimizer type to use? More... | |
| core::Size | get_refine_repack_cycles () const |
| how many cycles between repack/design opportunities? More... | |
| void | set_debug (bool const debug) |
| debugging mode activates a bunch of extra output More... | |
| void | set_refine_CCD_off (bool const refine_CCD_off) |
| do not perform CCD style closure (use KIC only) More... | |
| void | set_refine_KIC_off (bool const refine_KIC_off) |
| do not perform KIC style closure (use CCD only) More... | |
| void | set_nonpivot_torsion_sampling (bool const nonpivot_torsion_sampling) |
| use nonpivot torsion sampling for KIC? More... | |
| void | set_vicinity_sampling (bool const vicinity_sampling) |
| KIC use vicinity sampling? More... | |
| void | set_vicinity_degree (core::Size const vicinity_degree) |
| KIC vicinity sampling degrees. More... | |
| void | set_refine_temp (core::Real const refine_temp) |
| MC temperature. More... | |
| void | set_refine_cycles (core::Size const refine_cycles) |
| number of MC cycles More... | |
| void | set_min_type (std::string const &min_type) |
| what minimizer type to use? More... | |
| void | set_refine_repack_cycles (core::Size const refine_repack_cycles) |
| how many cycles between repack/design opportunities? More... | |
| void | read_options () |
| read in options from the options system More... | |
 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) | |
| Mover & | operator= (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 Strings & | info () |
| 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 |
Private Attributes | |
| protocols::anchored_design::AnchorMoversDataOP | interface_ |
| bool | debug_ |
| debugging mode activates a bunch of extra output More... | |
| bool | refine_CCD_off_ |
| do not perform CCD style closure (use KIC only) More... | |
| bool | refine_KIC_off_ |
| do not perform KIC style closure (use CCD only) More... | |
| bool | nonpivot_torsion_sampling_ |
| use nonpivot torsion sampling for KIC? More... | |
| bool | vicinity_sampling_ |
| KIC use vicinity sampling? More... | |
| core::Real | vicinity_degree_ |
| KIC vicinity sampling degrees. More... | |
| core::Real | refine_temp_ |
| MC temperature. More... | |
| core::Size | refine_cycles_ |
| number of MC cycles More... | |
| std::string | min_type_ |
| what minimizer type to use? More... | |
| core::Size | refine_repack_cycles_ |
| how many cycles between repack/design opportunities? More... | |
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 protocols::filters::Filters_map | Filters_map |
| 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... | |
| 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... | |
Definition at line 261 of file AnchorMovers.hh.
| protocols::anchored_design::AnchoredRefineMover::AnchoredRefineMover | ( | protocols::anchored_design::AnchorMoversDataOP | interface_in) |
Definition at line 1239 of file AnchorMovers.cc.
References read_options(), and protocols::moves::Mover::type().
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Definition at line 1246 of file AnchorMovers.cc.
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Implements protocols::moves::Mover.
Definition at line 1250 of file AnchorMovers.cc.
References debug_, protocols::anchored_design::debug_dump_pose(), protocols::anchored_design::dump_cutpoint_info(), interface_, core::conformation::Residue::is_terminus(), min_type_, nonpivot_torsion_sampling_, refine_CCD_off_, refine_cycles_, refine_KIC_off_, refine_repack_cycles_, refine_temp_, core::pose::Pose::residue(), T_perturb(), T_refine(), protocols::simple_moves::PackRotamersMover::task_factory(), and vicinity_degree_.
Referenced by protocols::anchored_design::AnchoredDesignMover::apply().
| bool protocols::anchored_design::AnchoredRefineMover::get_debug | ( | ) | const |
debugging mode activates a bunch of extra output
Definition at line 1510 of file AnchorMovers.cc.
References debug_.
| std::string const & protocols::anchored_design::AnchoredRefineMover::get_min_type | ( | ) | const |
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Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
Definition at line 1504 of file AnchorMovers.cc.
| bool protocols::anchored_design::AnchoredRefineMover::get_nonpivot_torsion_sampling | ( | ) | const |
use nonpivot torsion sampling for KIC?
Definition at line 1516 of file AnchorMovers.cc.
References nonpivot_torsion_sampling_.
| bool protocols::anchored_design::AnchoredRefineMover::get_refine_CCD_off | ( | ) | const |
do not perform CCD style closure (use KIC only)
Definition at line 1512 of file AnchorMovers.cc.
References refine_CCD_off_.
| core::Size protocols::anchored_design::AnchoredRefineMover::get_refine_cycles | ( | ) | const |
| bool protocols::anchored_design::AnchoredRefineMover::get_refine_KIC_off | ( | ) | const |
do not perform KIC style closure (use CCD only)
Definition at line 1514 of file AnchorMovers.cc.
References refine_KIC_off_.
| core::Size protocols::anchored_design::AnchoredRefineMover::get_refine_repack_cycles | ( | ) | const |
how many cycles between repack/design opportunities?
Definition at line 1528 of file AnchorMovers.cc.
References refine_repack_cycles_.
| core::Real protocols::anchored_design::AnchoredRefineMover::get_refine_temp | ( | ) | const |
| core::Real protocols::anchored_design::AnchoredRefineMover::get_vicinity_degree | ( | ) | const |
KIC vicinity sampling degrees.
Definition at line 1520 of file AnchorMovers.cc.
References vicinity_degree_.
| bool protocols::anchored_design::AnchoredRefineMover::get_vicinity_sampling | ( | ) | const |
KIC use vicinity sampling?
Definition at line 1518 of file AnchorMovers.cc.
References vicinity_sampling_.
| void protocols::anchored_design::AnchoredRefineMover::read_options | ( | ) |
read in options from the options system
Definition at line 1551 of file AnchorMovers.cc.
References core::pack::interaction_graph::debug, debug_, min_type_, nonpivot_torsion_sampling_, refine_CCD_off_, refine_cycles_, refine_KIC_off_, refine_repack_cycles_, refine_temp_, vicinity_degree_, and vicinity_sampling_.
Referenced by AnchoredRefineMover().
| void protocols::anchored_design::AnchoredRefineMover::set_debug | ( | bool const | debug) |
debugging mode activates a bunch of extra output
Definition at line 1531 of file AnchorMovers.cc.
References core::pack::interaction_graph::debug, and debug_.
| void protocols::anchored_design::AnchoredRefineMover::set_min_type | ( | std::string const & | min_type) |
| void protocols::anchored_design::AnchoredRefineMover::set_nonpivot_torsion_sampling | ( | bool const | nonpivot_torsion_sampling) |
use nonpivot torsion sampling for KIC?
Definition at line 1537 of file AnchorMovers.cc.
References nonpivot_torsion_sampling_.
| void protocols::anchored_design::AnchoredRefineMover::set_refine_CCD_off | ( | bool const | refine_CCD_off) |
do not perform CCD style closure (use KIC only)
Definition at line 1533 of file AnchorMovers.cc.
References refine_CCD_off_.
| void protocols::anchored_design::AnchoredRefineMover::set_refine_cycles | ( | core::Size const | refine_cycles) |
| void protocols::anchored_design::AnchoredRefineMover::set_refine_KIC_off | ( | bool const | refine_KIC_off) |
do not perform KIC style closure (use CCD only)
Definition at line 1535 of file AnchorMovers.cc.
References refine_KIC_off_.
| void protocols::anchored_design::AnchoredRefineMover::set_refine_repack_cycles | ( | core::Size const | refine_repack_cycles) |
how many cycles between repack/design opportunities?
Definition at line 1549 of file AnchorMovers.cc.
References refine_repack_cycles_.
| void protocols::anchored_design::AnchoredRefineMover::set_refine_temp | ( | core::Real const | refine_temp) |
| void protocols::anchored_design::AnchoredRefineMover::set_vicinity_degree | ( | core::Size const | vicinity_degree) |
KIC vicinity sampling degrees.
Definition at line 1541 of file AnchorMovers.cc.
References vicinity_degree_.
| void protocols::anchored_design::AnchoredRefineMover::set_vicinity_sampling | ( | bool const | vicinity_sampling) |
KIC use vicinity sampling?
Definition at line 1539 of file AnchorMovers.cc.
References vicinity_sampling_.
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debugging mode activates a bunch of extra output
Definition at line 324 of file AnchorMovers.hh.
Referenced by apply(), get_debug(), read_options(), and set_debug().
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Definition at line 320 of file AnchorMovers.hh.
Referenced by apply().
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what minimizer type to use?
Definition at line 340 of file AnchorMovers.hh.
Referenced by apply(), get_min_type(), read_options(), and set_min_type().
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use nonpivot torsion sampling for KIC?
Definition at line 330 of file AnchorMovers.hh.
Referenced by apply(), get_nonpivot_torsion_sampling(), read_options(), and set_nonpivot_torsion_sampling().
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do not perform CCD style closure (use KIC only)
Definition at line 326 of file AnchorMovers.hh.
Referenced by apply(), get_refine_CCD_off(), read_options(), and set_refine_CCD_off().
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number of MC cycles
Definition at line 338 of file AnchorMovers.hh.
Referenced by apply(), get_refine_cycles(), read_options(), and set_refine_cycles().
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do not perform KIC style closure (use CCD only)
Definition at line 328 of file AnchorMovers.hh.
Referenced by apply(), get_refine_KIC_off(), read_options(), and set_refine_KIC_off().
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how many cycles between repack/design opportunities?
Definition at line 342 of file AnchorMovers.hh.
Referenced by apply(), get_refine_repack_cycles(), read_options(), and set_refine_repack_cycles().
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MC temperature.
Definition at line 336 of file AnchorMovers.hh.
Referenced by apply(), get_refine_temp(), read_options(), and set_refine_temp().
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KIC vicinity sampling degrees.
Definition at line 334 of file AnchorMovers.hh.
Referenced by apply(), get_vicinity_degree(), read_options(), and set_vicinity_degree().
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KIC use vicinity sampling?
Definition at line 332 of file AnchorMovers.hh.
Referenced by get_vicinity_sampling(), read_options(), and set_vicinity_sampling().
1.8.4