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Rosetta 3.5
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Rosetta 3.5
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#include <SaneDockingProtocol.hh>
Public Member Functions | |
| virtual void | apply (core::pose::Pose &pose) |
| main docking protocol More... | |
| virtual std::string | get_name () const |
| returns the docking partners chain identifiers More... | |
 Public Member Functions inherited from protocols::docking::DockingProtocol | |
| DockingProtocol () | |
| empty constructor fills values with the expected defaults rb_jump will be assigned as 1 (meaning the first jump will be used as the jump across which all rigid-body perturbations will occur More... | |
| DockingProtocol (Size const rb_jump_in, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(NULL), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(NULL)) | |
| DockingProtocol (DockJumps const movable_jumps, bool const low_res_protocol_only=false, bool const docking_local_refine=false, bool const autofoldtree=true, core::scoring::ScoreFunctionOP docking_score_low=core::scoring::ScoreFunctionOP(NULL), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(NULL)) | |
| void | set_default () |
| Assigns default values to primitive members. More... | |
| void | sync_objects_with_flags () |
| Instantiates non-primitive members based on the value of the primitive members. More... | |
| ~DockingProtocol () | |
| virtual protocols::moves::MoverOP | clone () const |
| clone operator, calls the copy constructor More... | |
| virtual protocols::moves::MoverOP | fresh_instance () const |
| fresh_instance returns a default-constructed object for the JD2 More... | |
| virtual bool | reinitialize_for_new_input () const |
| This mover retains state such that a fresh version is needed if the input Pose is about to change. More... | |
| DockingProtocol (DockingProtocol const &rhs) | |
| copy ctor More... | |
| DockingProtocol & | operator= (DockingProtocol const &rhs) |
| assignment operator More... | |
| void | set_lowres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_low) |
| Sets the score function that will be used in the low-resolution phase. More... | |
| void | set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_high) |
| Sets the score function that will be used in the high-resolution phase. The same score function will be used for evaluating moves, packing and discriminating. More... | |
| void | set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack) |
| Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves and discriminating, the second will be used for packing. More... | |
| void | set_highres_scorefxn (core::scoring::ScoreFunctionOP docking_scorefxn_high, core::scoring::ScoreFunctionOP docking_scorefxn_pack, core::scoring::ScoreFunctionOP docking_scorefxn_output) |
| Sets the score function that will be used in the high-resolution phase. The first scorefunction will be used for evaluating moves, the second will be used for packing and the third for discriminating. More... | |
| void | set_sc_min (bool sc_min) |
| void | set_rt_min (bool rt_min) |
| void | set_dock_min (bool const dock_min) |
| void | set_no_filters (bool no_filters) |
| void | set_low_res_protocol_only (bool const low_res_protocol_only) |
| void | set_docking_local_refine (bool const docking_local_refine) |
| void | set_use_legacy_protocol (bool const use_legacy_protocol) |
| void | set_cst_weight (core::Real const cst_weight) |
| void | set_use_constraints (bool const use_csts) |
| void | set_interface_definition_task_operation (protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition) |
| void | set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations) |
| void | add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation) |
| utility::vector1 < core::pack::task::operation::TaskOperationOP > | get_additional_task_operarations () |
| std::string | partners () const |
| DockJumps & | movable_jumps () |
| DockJumps const & | movable_jumps () const |
| returns ref to the jumps vector for docking More... | |
| core::pack::task::TaskFactory const & | task_factory () |
| @ return const ref to the jumps vector for docking More... | |
| protocols::simple_moves::SwitchResidueTypeSetMoverCOP | to_centroid () const |
| protocols::moves::MoverCOP | to_all_atom () const |
| protocols::docking::DockingLowResCOP | docking_lowres_mover () const |
| protocols::docking::DockingHighResCOP | docking_highres_mover () const |
| protocols::docking::DockingInitialPerturbationCOP | perturber () const |
| void | set_docking_highres_mover (protocols::docking::DockingHighResOP docking_highres_mover) |
| void | add_additional_low_resolution_step (protocols::moves::MoverOP additional_low_resolution_mover) |
| void | set_autofoldtree (bool const autofoldtree) |
| void | set_partners (std::string const &partners) |
| void | set_inner_cycles (core::Size inner_cycles) |
| void | set_outer_cycles (core::Size outer_cycles) |
| void | set_design (bool const design) |
| void | set_task_factory (core::pack::task::TaskFactoryOP task_factory) |
| void | set_ignore_default_docking_task (bool const ignore_default_docking_task) |
| void | set_movable_jumps (DockJumps const jump_numbers) |
| void | set_reporting (bool report) |
| void | set_ensemble1 (std::string const &ensemble1) |
| void | set_ensemble2 (std::string const &ensemble2) |
| void | set_recover_sidechains_filename (std::string const &file) |
| void | add_jump (core::Size const jump_number) |
| void | show (std::ostream &out=std::cout) |
| void | parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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) |
| 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... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
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::docking::DockingProtocol | |
| static void | register_options () |
| Associates relevant options with the DockingProtocol class. 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 29 of file SaneDockingProtocol.hh.
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virtual |
main docking protocol
Docking apply
Reimplemented from protocols::docking::DockingProtocol.
Definition at line 29 of file SaneDockingProtocol.cc.
References protocols::docking::DockingProtocol::apply(), protocols::moves::Mover::get_input_pose(), protocols::moves::Mover::get_native_pose(), protocols::moves::Mover::set_input_pose(), and protocols::moves::Mover::set_native_pose().
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virtual |
returns the docking partners chain identifiers
Reimplemented from protocols::docking::DockingProtocol.
Definition at line 43 of file SaneDockingProtocol.cc.
1.8.4