#include <SaneDockingProtocol.hh>

Inheritance diagram for protocols::docking::stateless::SaneDockingProtocol:

Public Member Functions
virtual void	apply (core::pose::Pose &pose)
	main docking protocol More...

virtual std::string	get_name () const
	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 (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
	returns the docking partners chain identifiers More...

DockJumps &	movable_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)

virtual void	show (std::ostream &out=std::cout) const

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::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 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...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

void	set_type (std::string const &setting)

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 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
	Inform 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::TagCOP	TagCOP

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...

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 )

virtual

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

virtual

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:

src/protocols/docking/stateless/SaneDockingProtocol.hh
src/protocols/docking/stateless/SaneDockingProtocol.cc

Public Member Functions

Additional Inherited Members

Member Function Documentation