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protocols::docking::stateless::SaneDockingProtocol Class Reference

#include <SaneDockingProtocol.hh>

Inheritance diagram for protocols::docking::stateless::SaneDockingProtocol:
Inheritance graph
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Public Member Functions

void apply (core::pose::Pose &pose) override
 main docking protocol More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 (core::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(nullptr), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(nullptr))
 
 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(nullptr), core::scoring::ScoreFunctionOP docking_score_high=core::scoring::ScoreFunctionOP(nullptr))
 
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 () override
 
protocols::moves::MoverOP clone () const override
 clone operator, calls the copy constructor More...
 
protocols::moves::MoverOP fresh_instance () const override
 fresh_instance returns a default-constructed object for the JD2 More...
 
bool reinitialize_for_new_input () const override
 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...
 
DockingProtocoloperator= (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...
 
core::scoring::ScoreFunctionCOP get_highres_scorefxn () const
 
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::simple_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
 returns the docking partners chain identifiers More...
 
DockJumpsmovable_jumps ()
 returns ref to the jumps vector for docking More...
 
DockJumps const & movable_jumps () const
 returns a const ref to the jumps vector for docking More...
 
core::pack::task::TaskFactory
const & 
task_factory ()
 
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) const override
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 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 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...
 
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
 
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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...
 

Additional Inherited Members

- 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
 
- Static Public Member Functions inherited from protocols::docking::DockingProtocol
static void register_options ()
 Associates relevant options with the DockingProtocol class. More...
 
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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 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...
 

Member Function Documentation

void protocols::docking::stateless::SaneDockingProtocol::apply ( core::pose::Pose pose)
overridevirtual

main docking protocol

Main function for docking. Includes the following steps: 0) prepack mode: prepare a starting structure for later runs OR: 1) perturbation of decoy (see docking_perturb_decoy): changes orientation of docking partners 2) low-resolution search: refine structure with rigid-body, centroid-mode MC cycles 3) high-resolution search: further refinement of structure in fullatom mode

Reimplemented from protocols::docking::DockingProtocol.

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().

std::string protocols::docking::stateless::SaneDockingProtocol::get_name ( ) const
overridevirtual

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

Reimplemented from protocols::docking::DockingProtocol.


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