This is the standard RosettaDock protocol. More...

#include <DockingProtocol.hh>

Inheritance diagram for protocols::docking::DockingProtocol:

Collaboration diagram for protocols::docking::DockingProtocol:

Public Member Functions
	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 ()

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

std::string	partners () const

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

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

Static Public Member Functions
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. 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...

Private Member Functions
void	init_from_options ()
	Assigns user specified values to primitive members using command line options. More...

void	finalize_setup (core::pose::Pose &pose)
	Performs the portion of setup of non-primitive members that requires a pose - called on apply. More...

void	init (DockJumps const movable_jumps, bool const low_res_protocol_only_, bool const docking_local_refine, bool const autofoldtree, core::scoring::ScoreFunctionOP docking_score_low, core::scoring::ScoreFunctionOP docking_score_high)
	Sets up the instance of DockingProtocol and initializes all members based on values passed in at construction or via the command line. More...

void	initForEqualOperatorAndCopyConstructor (DockingProtocol &lhs, DockingProtocol const &rhs)

void	setup_objects ()

void	setup_constraints (core::pose::Pose &pose)
	setup the constrainta for each application of the docking protocol More...

void	add_constraints_to_scorefunction ()
	add distance constraint to the docking score functions More...

void	check_high_res_protocol ()

Private Attributes
bool	user_defined_
	information about the mode More...

bool	low_res_protocol_only_

bool	reporting_

bool	autofoldtree_

bool	flags_and_objects_are_in_sync_

bool	first_apply_with_current_setup_

bool	sc_min_

bool	rt_min_

bool	dock_min_

bool	if_ensemble_

bool	no_filters_

bool	use_legacy_protocol_

bool	docking_local_refine_

bool	use_csts_

core::Real	cst_weight_

core::Real	score_cutoff_

core::kinematics::FoldTree	fold_tree_

std::string	partners_

std::string	previous_sequence_

core::SSize	lowres_inner_cycles_

core::SSize	lowres_outer_cycles_

DockJumps	movable_jumps_
	jumps that rigid_body transformations can occur over More...

core::scoring::ScoreFunctionOP	docking_scorefxn_low_

core::scoring::ScoreFunctionOP	docking_scorefxn_high_

core::scoring::ScoreFunctionOP	docking_scorefxn_pack_

core::scoring::ScoreFunctionOP	docking_scorefxn_output_

protocols::moves::MonteCarloOP	mc_

protocols::docking::DockingLowResFilterOP	lowres_filter_

protocols::docking::DockingHighResFilterOP	highres_filter_

protocols::docking::DockingLowResOP	docking_lowres_mover_

protocols::docking::DockingHighResOP	docking_highres_mover_

protocols::docking::DockingInitialPerturbationOP	perturber_

protocols::simple_moves::SwitchResidueTypeSetMoverOP	to_centroid_

protocols::moves::MoverOP	to_all_atom_

protocols::docking::DockingEnsembleOP	ensemble1_

protocols::docking::DockingEnsembleOP	ensemble2_

std::string	ensemble1_filename_

std::string	ensemble2_filename_

protocols::simple_moves::ConstraintSetMoverOP	docking_constraint_

protocols::simple_moves::ReturnSidechainMoverOP	recover_sidechains_

protocols::moves::SequenceMoverOP	additional_low_resolution_steps_

std::string	recover_sidechains_filename_

core::pack::task::TaskFactoryOP	init_task_factory_

bool	design_

bool	ignore_default_docking_task_

Friends
std::ostream &	operator<< (std::ostream &out, const DockingProtocol &dp)

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

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...

Detailed Description

This is the standard RosettaDock protocol.

Detailed: RosettaDock protocol based on [refs...Gray2003, Wang2005, Chaudhury 2007 ... ]

Definition at line 63 of file DockingProtocol.hh.

Constructor & Destructor Documentation

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

Definition at line 131 of file DockingProtocol.cc.

References core::init().

Referenced by clone(), protocols::docking::DockingProtocolCreator::create_mover(), and fresh_instance().

protocols::docking::DockingProtocol::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)`
	)

Definition at line 137 of file DockingProtocol.cc.

References init(), and user_defined_.

protocols::docking::DockingProtocol::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)`
	)

Definition at line 150 of file DockingProtocol.cc.

References init(), and user_defined_.

protocols::docking::DockingProtocol::~DockingProtocol ( )

Definition at line 607 of file DockingProtocol.cc.

protocols::docking::DockingProtocol::DockingProtocol ( DockingProtocol const & rhs)

copy ctor

Definition at line 628 of file DockingProtocol.cc.

References initForEqualOperatorAndCopyConstructor().

Member Function Documentation

void protocols::docking::DockingProtocol::add_additional_low_resolution_step ( protocols::moves::MoverOP additional_low_resolution_mover)

Definition at line 1078 of file DockingProtocol.cc.

References additional_low_resolution_steps_.

void protocols::docking::DockingProtocol::add_additional_task_operaration ( core::pack::task::operation::TaskOperationOP task_operation)

Definition at line 815 of file DockingProtocol.cc.

References check_high_res_protocol(), and docking_highres_mover_.

void protocols::docking::DockingProtocol::add_constraints_to_scorefunction ( )

private

add distance constraint to the docking score functions

Definition at line 854 of file DockingProtocol.cc.

References core::scoring::atom_pair_constraint, cst_weight_, docking_highres_mover_, docking_lowres_mover_, docking_scorefxn_high_, docking_scorefxn_low_, docking_scorefxn_output_, docking_scorefxn_pack_, set_highres_scorefxn(), and set_lowres_scorefxn().

Referenced by setup_constraints().

void protocols::docking::DockingProtocol::add_jump ( core::Size const jump_number)

inline

Definition at line 197 of file DockingProtocol.hh.

References movable_jumps_.

void protocols::docking::DockingProtocol::apply ( core::pose::Pose & pose)

virtual

main docking protocol

Docking apply

Detailed:: 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

Implements protocols::moves::Mover.

Reimplemented in protocols::docking::stateless::SaneDockingProtocol.

Definition at line 891 of file DockingProtocol.cc.

References additional_low_resolution_steps_, protocols::docking::calc_Fnat(), protocols::docking::calc_interaction_energy(), protocols::docking::calc_Irmsd(), protocols::docking::calc_Lrmsd(), cst_weight_, protocols::nonlocal::current_job(), docking_constraint_, docking_highres_mover_, docking_lowres_mover_, docking_scorefxn_output_, core::pose::Pose::energies(), ensemble1_, ensemble2_, protocols::moves::FAIL_RETRY, finalize_setup(), first_apply_with_current_setup_, flags_and_objects_are_in_sync_, core::pose::Pose::fold_tree(), fold_tree_, protocols::jd2::JobDistributor::get_instance(), protocols::moves::Mover::get_native_pose(), highres_filter_, core::pose::Pose::is_fullatom(), lowres_filter_, movable_jumps_, protocols::moves::MS_SUCCESS, core::scoring::pair, perturber_, previous_sequence_, recover_sidechains_, reporting_, protocols::jd2::ScoreMap::score_map_from_scored_pose(), core::pose::Pose::sequence(), protocols::moves::Mover::set_last_move_status(), protocols::moves::Mover::set_native_pose(), setup_constraints(), show(), sync_objects_with_flags(), to_all_atom_, to_centroid_, core::scoring::Energies::total_energies(), core::scoring::total_score, protocols::TR(), and protocols::jd2::write_score_tracer().

Referenced by protocols::docking::stateless::SaneDockingProtocol::apply().

void protocols::docking::DockingProtocol::check_high_res_protocol ( )

private

Definition at line 828 of file DockingProtocol.cc.

References docking_highres_mover_, low_res_protocol_only_, and sync_objects_with_flags().

Referenced by add_additional_task_operaration(), get_additional_task_operarations(), set_additional_task_operarations(), set_interface_definition_task_operation(), set_rt_min(), and set_sc_min().

protocols::moves::MoverOP protocols::docking::DockingProtocol::clone ( ) const

virtual

clone operator, calls the copy constructor

Reimplemented from protocols::moves::Mover.

Definition at line 611 of file DockingProtocol.cc.

References DockingProtocol().

protocols::docking::DockingHighResCOP protocols::docking::DockingProtocol::docking_highres_mover ( ) const

Definition at line 1055 of file DockingProtocol.cc.

References docking_highres_mover_.

Referenced by set_docking_highres_mover().

protocols::docking::DockingLowResCOP protocols::docking::DockingProtocol::docking_lowres_mover ( ) const

Definition at line 1052 of file DockingProtocol.cc.

References docking_lowres_mover_.

void protocols::docking::DockingProtocol::finalize_setup ( core::pose::Pose & pose)

private

Performs the portion of setup of non-primitive members that requires a pose - called on apply.

Definition at line 497 of file DockingProtocol.cc.

References autofoldtree_, cst_weight_, core::kinematics::FoldTree::cutpoint_by_jump(), design_, core::scoring::dock_ens_conf, docking_constraint_, docking_highres_mover_, docking_lowres_mover_, docking_scorefxn_high_, docking_scorefxn_low_, ensemble1_, ensemble1_filename_, ensemble2_, ensemble2_filename_, core::pose::Pose::fold_tree(), fold_tree_, protocols::moves::Mover::get_input_pose(), highres_filter_, if_ensemble_, ignore_default_docking_task_, init_task_factory_, lowres_inner_cycles_, lowres_outer_cycles_, movable_jumps_, partners_, core::import_pose::pose_from_pdb(), recover_sidechains_, recover_sidechains_filename_, score_cutoff_, protocols::docking::DockingLowResEnsemble::set_ensemble1(), protocols::docking::DockingLowResEnsemble::set_ensemble2(), protocols::moves::Mover::set_input_pose(), set_lowres_scorefxn(), setup_constraints(), protocols::docking::setup_foldtree(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply().

protocols::moves::MoverOP protocols::docking::DockingProtocol::fresh_instance ( ) const

virtual

fresh_instance returns a default-constructed object for the JD2

Reimplemented from protocols::moves::Mover.

Definition at line 618 of file DockingProtocol.cc.

References DockingProtocol().

utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::docking::DockingProtocol::get_additional_task_operarations ( )

Definition at line 821 of file DockingProtocol.cc.

References check_high_res_protocol(), and docking_highres_mover_.

virtual std::string protocols::docking::DockingProtocol::get_name ( ) const

inlinevirtual

returns the docking partners chain identifiers

Implements protocols::moves::Mover.

Reimplemented in protocols::docking::stateless::SaneDockingProtocol.

Definition at line 163 of file DockingProtocol.hh.

void protocols::docking::DockingProtocol::init	(	DockJumps const	movable_jumps,
		bool const	low_res_protocol_only_,
		bool const	docking_local_refine,
		bool const	autofoldtree,
		core::scoring::ScoreFunctionOP	docking_score_low,
		core::scoring::ScoreFunctionOP	docking_score_high
	)

private

Sets up the instance of DockingProtocol and initializes all members based on values passed in at construction or via the command line.

Definition at line 165 of file DockingProtocol.cc.

References autofoldtree_, core::scoring::ScoreFunctionFactory::create_score_function(), docking_local_refine_, docking_scorefxn_high_, docking_scorefxn_low_, docking_scorefxn_output_, docking_scorefxn_pack_, init_from_options(), low_res_protocol_only_, movable_jumps(), movable_jumps_, set_default(), setup_objects(), protocols::moves::Mover::type(), and user_defined_.

Referenced by DockingProtocol().

void protocols::docking::DockingProtocol::init_from_options ( )

private

Assigns user specified values to primitive members using command line options.

Definition at line 374 of file DockingProtocol.cc.

References core::import_pose::pose_from_pdb(), rt_min_, sc_min_, score_cutoff_, set_cst_weight(), set_dock_min(), set_docking_local_refine(), set_ensemble1(), set_ensemble2(), set_ignore_default_docking_task(), set_inner_cycles(), set_low_res_protocol_only(), set_movable_jumps(), protocols::moves::Mover::set_native_pose(), set_no_filters(), set_outer_cycles(), set_partners(), set_recover_sidechains_filename(), set_use_constraints(), and set_use_legacy_protocol().

Referenced by init().

void protocols::docking::DockingProtocol::initForEqualOperatorAndCopyConstructor	(	DockingProtocol &	lhs,
		DockingProtocol const &	rhs
	)

private

Definition at line 643 of file DockingProtocol.cc.

References autofoldtree_, cst_weight_, design_, dock_min_, docking_constraint_, docking_highres_mover_, docking_local_refine_, docking_lowres_mover_, docking_scorefxn_high_, docking_scorefxn_low_, docking_scorefxn_output_, docking_scorefxn_pack_, ensemble1_, ensemble1_filename_, ensemble2_, ensemble2_filename_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, fold_tree_, highres_filter_, ignore_default_docking_task_, init_task_factory_, low_res_protocol_only_, lowres_filter_, lowres_inner_cycles_, lowres_outer_cycles_, mc_, movable_jumps_, no_filters_, partners_, previous_sequence_, recover_sidechains_, reporting_, rt_min_, sc_min_, score_cutoff_, to_all_atom_, to_centroid_, use_csts_, use_legacy_protocol_, and user_defined_.

Referenced by DockingProtocol(), and operator=().

DockJumps& protocols::docking::DockingProtocol::movable_jumps ( )

inline

Definition at line 164 of file DockingProtocol.hh.

References movable_jumps_.

Referenced by init().

DockJumps const& protocols::docking::DockingProtocol::movable_jumps ( ) const

inline

returns ref to the jumps vector for docking

Definition at line 165 of file DockingProtocol.hh.

References movable_jumps_.

DockingProtocol & protocols::docking::DockingProtocol::operator= ( DockingProtocol const & rhs)

assignment operator

Definition at line 635 of file DockingProtocol.cc.

References initForEqualOperatorAndCopyConstructor(), and protocols::moves::Mover::operator=().

void protocols::docking::DockingProtocol::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::Pose const &	pose
	)

virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

Definition at line 1144 of file DockingProtocol.cc.

References protocols::moves::DataMap::get(), protocols::rosetta_scripts::parse_task_operations(), partners(), set_dock_min(), set_docking_local_refine(), set_highres_scorefxn(), set_ignore_default_docking_task(), set_low_res_protocol_only(), set_lowres_scorefxn(), set_partners(), and set_task_factory().

std::string protocols::docking::DockingProtocol::partners ( ) const

inline

Definition at line 162 of file DockingProtocol.hh.

References partners_.

Referenced by parse_my_tag(), and set_partners().

protocols::docking::DockingInitialPerturbationCOP protocols::docking::DockingProtocol::perturber ( ) const

Definition at line 1058 of file DockingProtocol.cc.

References perturber_.

void protocols::docking::DockingProtocol::register_options ( )

static

Associates relevant options with the DockingProtocol class.

Definition at line 470 of file DockingProtocol.cc.

Referenced by protocols::antibody2::SnugDockProtocol::register_options().

bool protocols::docking::DockingProtocol::reinitialize_for_new_input ( ) const

virtual

This mover retains state such that a fresh version is needed if the input Pose is about to change.

Reimplemented from protocols::moves::Mover.

Definition at line 623 of file DockingProtocol.cc.

void protocols::docking::DockingProtocol::set_additional_task_operarations ( utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)

Definition at line 809 of file DockingProtocol.cc.

References check_high_res_protocol(), and docking_highres_mover_.

void protocols::docking::DockingProtocol::set_autofoldtree ( bool const autofoldtree)

inline

Definition at line 184 of file DockingProtocol.hh.

References autofoldtree_.

void protocols::docking::DockingProtocol::set_cst_weight ( core::Real const cst_weight)

Definition at line 786 of file DockingProtocol.cc.

References cst_weight_, and flags_and_objects_are_in_sync_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_default ( )

Assigns default values to primitive members.

Definition at line 226 of file DockingProtocol.cc.

References autofoldtree_, cst_weight_, design_, dock_min_, docking_local_refine_, ensemble1_, ensemble1_filename_, ensemble2_, ensemble2_filename_, if_ensemble_, ignore_default_docking_task_, low_res_protocol_only_, lowres_inner_cycles_, lowres_outer_cycles_, no_filters_, partners_, recover_sidechains_filename_, reporting_, rt_min_, sc_min_, score_cutoff_, use_csts_, and use_legacy_protocol_.

Referenced by init().

void protocols::docking::DockingProtocol::set_design ( bool const design)

inline

Definition at line 188 of file DockingProtocol.hh.

References design_.

void protocols::docking::DockingProtocol::set_dock_min ( bool const dock_min)

Definition at line 747 of file DockingProtocol.cc.

References dock_min_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_docking_highres_mover ( protocols::docking::DockingHighResOP docking_highres_mover)

Definition at line 1063 of file DockingProtocol.cc.

References docking_highres_mover(), docking_highres_mover_, and set_highres_scorefxn().

void protocols::docking::DockingProtocol::set_docking_local_refine ( bool const docking_local_refine)

Definition at line 769 of file DockingProtocol.cc.

References docking_local_refine_, and flags_and_objects_are_in_sync_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_ensemble1 ( std::string const & ensemble1)

inline

Definition at line 193 of file DockingProtocol.hh.

References ensemble1_filename_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_ensemble2 ( std::string const & ensemble2)

inline

Definition at line 194 of file DockingProtocol.hh.

References ensemble2_filename_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::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.

Definition at line 707 of file DockingProtocol.cc.

References docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

Referenced by add_constraints_to_scorefunction(), parse_my_tag(), and set_docking_highres_mover().

void protocols::docking::DockingProtocol::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.

Definition at line 714 of file DockingProtocol.cc.

References docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

void protocols::docking::DockingProtocol::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.

Definition at line 723 of file DockingProtocol.cc.

References docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

void protocols::docking::DockingProtocol::set_ignore_default_docking_task ( bool const ignore_default_docking_task)

inline

Definition at line 190 of file DockingProtocol.hh.

References ignore_default_docking_task_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_inner_cycles ( core::Size inner_cycles)

inline

Definition at line 186 of file DockingProtocol.hh.

References lowres_inner_cycles_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_interface_definition_task_operation ( protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition)

Definition at line 803 of file DockingProtocol.cc.

References check_high_res_protocol(), and docking_highres_mover_.

void protocols::docking::DockingProtocol::set_low_res_protocol_only ( bool const low_res_protocol_only)

Definition at line 761 of file DockingProtocol.cc.

References flags_and_objects_are_in_sync_, and low_res_protocol_only_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_lowres_scorefxn ( core::scoring::ScoreFunctionOP docking_scorefxn_low)

Sets the score function that will be used in the low-resolution phase.

Definition at line 701 of file DockingProtocol.cc.

References docking_scorefxn_low_.

Referenced by add_constraints_to_scorefunction(), finalize_setup(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_movable_jumps ( DockJumps const jump_numbers)

inline

Definition at line 191 of file DockingProtocol.hh.

References movable_jumps_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_no_filters ( bool no_filters)

Definition at line 753 of file DockingProtocol.cc.

References flags_and_objects_are_in_sync_, and no_filters_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_outer_cycles ( core::Size outer_cycles)

inline

Definition at line 187 of file DockingProtocol.hh.

References lowres_outer_cycles_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_partners ( std::string const & partners)

inline

Definition at line 185 of file DockingProtocol.hh.

References partners(), and partners_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingProtocol::set_recover_sidechains_filename ( std::string const & file)

inline

Definition at line 195 of file DockingProtocol.hh.

References recover_sidechains_filename_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_reporting ( bool report)

inline

Definition at line 192 of file DockingProtocol.hh.

References reporting_.

void protocols::docking::DockingProtocol::set_rt_min ( bool rt_min)

Definition at line 740 of file DockingProtocol.cc.

References check_high_res_protocol(), docking_highres_mover_, and rt_min_.

void protocols::docking::DockingProtocol::set_sc_min ( bool sc_min)

Definition at line 733 of file DockingProtocol.cc.

References check_high_res_protocol(), docking_highres_mover_, and sc_min_.

void protocols::docking::DockingProtocol::set_task_factory ( core::pack::task::TaskFactoryOP task_factory)

inline

Definition at line 189 of file DockingProtocol.hh.

References init_task_factory_, and task_factory().

Referenced by parse_my_tag().

void protocols::docking::DockingProtocol::set_use_constraints ( bool const use_csts)

Definition at line 795 of file DockingProtocol.cc.

References flags_and_objects_are_in_sync_, and use_csts_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::set_use_legacy_protocol ( bool const use_legacy_protocol)

Definition at line 777 of file DockingProtocol.cc.

References flags_and_objects_are_in_sync_, and use_legacy_protocol_.

Referenced by init_from_options().

void protocols::docking::DockingProtocol::setup_constraints ( core::pose::Pose & pose)

private

setup the constrainta for each application of the docking protocol

Definition at line 837 of file DockingProtocol.cc.

References add_constraints_to_scorefunction(), core::pose::Pose::constraint_set(), cst_weight_, lowres_filter_, and protocols::TR().

Referenced by apply(), and finalize_setup().

void protocols::docking::DockingProtocol::setup_objects ( )

private

Definition at line 261 of file DockingProtocol.cc.

References core::chemical::CENTROID, docking_constraint_, docking_highres_mover_, docking_lowres_mover_, docking_scorefxn_pack_, core::chemical::FA_STANDARD, fold_tree_, highres_filter_, init_task_factory_, lowres_filter_, perturber_, previous_sequence_, sync_objects_with_flags(), to_all_atom_, and to_centroid_.

Referenced by init().

void protocols::docking::DockingProtocol::show ( std::ostream & out = std::cout)

Show the complete setup of the docking protocol

Definition at line 1089 of file DockingProtocol.cc.

References flags_and_objects_are_in_sync_, and sync_objects_with_flags().

Referenced by apply().

void protocols::docking::DockingProtocol::sync_objects_with_flags ( )

Instantiates non-primitive members based on the value of the primitive members.

Definition at line 291 of file DockingProtocol.cc.

References dock_min_, docking_constraint_, docking_highres_mover_, docking_local_refine_, docking_lowres_mover_, docking_scorefxn_high_, docking_scorefxn_low_, docking_scorefxn_pack_, ensemble2_filename_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, highres_filter_, if_ensemble_, low_res_protocol_only_, lowres_filter_, movable_jumps_, no_filters_, partners_, perturber_, rt_min_, sc_min_, use_csts_, and use_legacy_protocol_.

Referenced by apply(), check_high_res_protocol(), setup_objects(), and show().

core::pack::task::TaskFactory const& protocols::docking::DockingProtocol::task_factory ( )

inline

@ return const ref to the jumps vector for docking

Definition at line 166 of file DockingProtocol.hh.

References init_task_factory_.

Referenced by set_task_factory().

protocols::moves::MoverCOP protocols::docking::DockingProtocol::to_all_atom ( ) const

Definition at line 1049 of file DockingProtocol.cc.

References to_all_atom_.

protocols::simple_moves::SwitchResidueTypeSetMoverCOP protocols::docking::DockingProtocol::to_centroid ( ) const

Definition at line 1046 of file DockingProtocol.cc.

References to_centroid_.

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	out,
		const DockingProtocol &	dp
	)

friend

Definition at line 1096 of file DockingProtocol.cc.

Member Data Documentation

protocols::moves::SequenceMoverOP protocols::docking::DockingProtocol::additional_low_resolution_steps_

private

Definition at line 271 of file DockingProtocol.hh.

Referenced by add_additional_low_resolution_step(), and apply().

bool protocols::docking::DockingProtocol::autofoldtree_

private

Definition at line 210 of file DockingProtocol.hh.

Referenced by finalize_setup(), init(), initForEqualOperatorAndCopyConstructor(), set_autofoldtree(), and set_default().

core::Real protocols::docking::DockingProtocol::cst_weight_

private

Definition at line 226 of file DockingProtocol.hh.

Referenced by add_constraints_to_scorefunction(), apply(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_cst_weight(), set_default(), and setup_constraints().

bool protocols::docking::DockingProtocol::design_

private

Definition at line 277 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_design().

bool protocols::docking::DockingProtocol::dock_min_

private

Definition at line 217 of file DockingProtocol.hh.

Referenced by initForEqualOperatorAndCopyConstructor(), set_default(), set_dock_min(), and sync_objects_with_flags().

protocols::simple_moves::ConstraintSetMoverOP protocols::docking::DockingProtocol::docking_constraint_

private

Definition at line 267 of file DockingProtocol.hh.

Referenced by apply(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), setup_objects(), and sync_objects_with_flags().

protocols::docking::DockingHighResOP protocols::docking::DockingProtocol::docking_highres_mover_

private

Definition at line 254 of file DockingProtocol.hh.

Referenced by add_additional_task_operaration(), add_constraints_to_scorefunction(), apply(), check_high_res_protocol(), docking_highres_mover(), finalize_setup(), get_additional_task_operarations(), initForEqualOperatorAndCopyConstructor(), protocols::docking::operator<<(), set_additional_task_operarations(), set_docking_highres_mover(), set_interface_definition_task_operation(), set_rt_min(), set_sc_min(), setup_objects(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::docking_local_refine_

private

Definition at line 223 of file DockingProtocol.hh.

Referenced by init(), initForEqualOperatorAndCopyConstructor(), set_default(), set_docking_local_refine(), and sync_objects_with_flags().

protocols::docking::DockingLowResOP protocols::docking::DockingProtocol::docking_lowres_mover_

private

Definition at line 253 of file DockingProtocol.hh.

Referenced by add_constraints_to_scorefunction(), apply(), docking_lowres_mover(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), protocols::docking::operator<<(), setup_objects(), and sync_objects_with_flags().

core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_high_

private

Definition at line 242 of file DockingProtocol.hh.

Referenced by add_constraints_to_scorefunction(), finalize_setup(), init(), initForEqualOperatorAndCopyConstructor(), set_highres_scorefxn(), and sync_objects_with_flags().

core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_low_

private

Definition at line 241 of file DockingProtocol.hh.

Referenced by add_constraints_to_scorefunction(), finalize_setup(), init(), initForEqualOperatorAndCopyConstructor(), set_lowres_scorefxn(), and sync_objects_with_flags().

core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_output_

private

Definition at line 244 of file DockingProtocol.hh.

Referenced by add_constraints_to_scorefunction(), apply(), init(), initForEqualOperatorAndCopyConstructor(), and set_highres_scorefxn().

core::scoring::ScoreFunctionOP protocols::docking::DockingProtocol::docking_scorefxn_pack_

private

Definition at line 243 of file DockingProtocol.hh.

Referenced by add_constraints_to_scorefunction(), init(), initForEqualOperatorAndCopyConstructor(), set_highres_scorefxn(), setup_objects(), and sync_objects_with_flags().

protocols::docking::DockingEnsembleOP protocols::docking::DockingProtocol::ensemble1_

private

Definition at line 262 of file DockingProtocol.hh.

Referenced by apply(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), and set_default().

std::string protocols::docking::DockingProtocol::ensemble1_filename_

private

Definition at line 264 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_ensemble1().

protocols::docking::DockingEnsembleOP protocols::docking::DockingProtocol::ensemble2_

private

Definition at line 263 of file DockingProtocol.hh.

Referenced by apply(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), and set_default().

std::string protocols::docking::DockingProtocol::ensemble2_filename_

private

Definition at line 264 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_default(), set_ensemble2(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::first_apply_with_current_setup_

private

Definition at line 213 of file DockingProtocol.hh.

Referenced by apply(), initForEqualOperatorAndCopyConstructor(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::flags_and_objects_are_in_sync_

private

Definition at line 212 of file DockingProtocol.hh.

Referenced by apply(), initForEqualOperatorAndCopyConstructor(), set_cst_weight(), set_docking_local_refine(), set_low_res_protocol_only(), set_no_filters(), set_use_constraints(), set_use_legacy_protocol(), show(), and sync_objects_with_flags().

core::kinematics::FoldTree protocols::docking::DockingProtocol::fold_tree_

private

Definition at line 229 of file DockingProtocol.hh.

Referenced by apply(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), and setup_objects().

protocols::docking::DockingHighResFilterOP protocols::docking::DockingProtocol::highres_filter_

private

Definition at line 249 of file DockingProtocol.hh.

Referenced by apply(), finalize_setup(), initForEqualOperatorAndCopyConstructor(), protocols::docking::operator<<(), setup_objects(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::if_ensemble_

private

Definition at line 219 of file DockingProtocol.hh.

Referenced by finalize_setup(), set_default(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::ignore_default_docking_task_

private

Definition at line 278 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_ignore_default_docking_task().

core::pack::task::TaskFactoryOP protocols::docking::DockingProtocol::init_task_factory_

private

Definition at line 276 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_task_factory(), setup_objects(), and task_factory().

bool protocols::docking::DockingProtocol::low_res_protocol_only_

private

Definition at line 208 of file DockingProtocol.hh.

Referenced by check_high_res_protocol(), init(), initForEqualOperatorAndCopyConstructor(), set_default(), set_low_res_protocol_only(), and sync_objects_with_flags().

protocols::docking::DockingLowResFilterOP protocols::docking::DockingProtocol::lowres_filter_

private

Definition at line 248 of file DockingProtocol.hh.

Referenced by apply(), initForEqualOperatorAndCopyConstructor(), protocols::docking::operator<<(), setup_constraints(), setup_objects(), and sync_objects_with_flags().

core::SSize protocols::docking::DockingProtocol::lowres_inner_cycles_

private

Definition at line 235 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_inner_cycles().

core::SSize protocols::docking::DockingProtocol::lowres_outer_cycles_

private

Definition at line 235 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_outer_cycles().

protocols::moves::MonteCarloOP protocols::docking::DockingProtocol::mc_

private

Definition at line 247 of file DockingProtocol.hh.

Referenced by initForEqualOperatorAndCopyConstructor().

DockJumps protocols::docking::DockingProtocol::movable_jumps_

private

jumps that rigid_body transformations can occur over

Definition at line 238 of file DockingProtocol.hh.

Referenced by add_jump(), apply(), finalize_setup(), init(), initForEqualOperatorAndCopyConstructor(), movable_jumps(), protocols::docking::operator<<(), set_movable_jumps(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::no_filters_

private

Definition at line 221 of file DockingProtocol.hh.

Referenced by initForEqualOperatorAndCopyConstructor(), set_default(), set_no_filters(), and sync_objects_with_flags().

std::string protocols::docking::DockingProtocol::partners_

private

Definition at line 230 of file DockingProtocol.hh.

Referenced by finalize_setup(), initForEqualOperatorAndCopyConstructor(), partners(), set_default(), set_partners(), and sync_objects_with_flags().

protocols::docking::DockingInitialPerturbationOP protocols::docking::DockingProtocol::perturber_

private

Definition at line 255 of file DockingProtocol.hh.

Referenced by apply(), perturber(), setup_objects(), and sync_objects_with_flags().

std::string protocols::docking::DockingProtocol::previous_sequence_

private

Definition at line 232 of file DockingProtocol.hh.

Referenced by apply(), initForEqualOperatorAndCopyConstructor(), and setup_objects().

protocols::simple_moves::ReturnSidechainMoverOP protocols::docking::DockingProtocol::recover_sidechains_

private

Definition at line 269 of file DockingProtocol.hh.

Referenced by apply(), finalize_setup(), and initForEqualOperatorAndCopyConstructor().

std::string protocols::docking::DockingProtocol::recover_sidechains_filename_

private

Definition at line 274 of file DockingProtocol.hh.

Referenced by finalize_setup(), set_default(), and set_recover_sidechains_filename().

bool protocols::docking::DockingProtocol::reporting_

private

Definition at line 209 of file DockingProtocol.hh.

Referenced by apply(), initForEqualOperatorAndCopyConstructor(), set_default(), and set_reporting().

bool protocols::docking::DockingProtocol::rt_min_

private

Definition at line 216 of file DockingProtocol.hh.

Referenced by init_from_options(), initForEqualOperatorAndCopyConstructor(), set_default(), set_rt_min(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::sc_min_

private

Definition at line 215 of file DockingProtocol.hh.

Referenced by init_from_options(), initForEqualOperatorAndCopyConstructor(), set_default(), set_sc_min(), and sync_objects_with_flags().

core::Real protocols::docking::DockingProtocol::score_cutoff_

private

Definition at line 228 of file DockingProtocol.hh.

Referenced by finalize_setup(), init_from_options(), initForEqualOperatorAndCopyConstructor(), and set_default().

protocols::moves::MoverOP protocols::docking::DockingProtocol::to_all_atom_

private

Definition at line 259 of file DockingProtocol.hh.

Referenced by apply(), initForEqualOperatorAndCopyConstructor(), setup_objects(), and to_all_atom().

protocols::simple_moves::SwitchResidueTypeSetMoverOP protocols::docking::DockingProtocol::to_centroid_

private

Definition at line 258 of file DockingProtocol.hh.

Referenced by apply(), initForEqualOperatorAndCopyConstructor(), setup_objects(), and to_centroid().

bool protocols::docking::DockingProtocol::use_csts_

private

Definition at line 225 of file DockingProtocol.hh.

Referenced by initForEqualOperatorAndCopyConstructor(), set_default(), set_use_constraints(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::use_legacy_protocol_

private

Definition at line 222 of file DockingProtocol.hh.

Referenced by initForEqualOperatorAndCopyConstructor(), set_default(), set_use_legacy_protocol(), and sync_objects_with_flags().

bool protocols::docking::DockingProtocol::user_defined_

private

information about the mode

Definition at line 207 of file DockingProtocol.hh.

Referenced by DockingProtocol(), init(), and initForEqualOperatorAndCopyConstructor().

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

src/protocols/docking/DockingProtocol.hh
src/protocols/docking/DockingProtocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation