allows docking using simulated or parallel tempering More...

#include <TemperedDocking.hh>

Inheritance diagram for protocols::docking::TemperedDocking:

Collaboration diagram for protocols::docking::TemperedDocking:

Public Member Functions
	TemperedDocking ()
	default constructor fills values with the expected defaults More...

virtual protocols::moves::MoverOP	clone () const
	clone More...

	TemperedDocking (TemperedDocking const &rhs)
	copy ctor More...

TemperedDocking &	operator= (TemperedDocking const &rhs)
	assignment operator More...

void	set_defaults ()
	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...

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::ScoreFunctionCOP docking_scorefxn_high, core::scoring::ScoreFunctionCOP 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::ScoreFunctionCOP docking_scorefxn_high, core::scoring::ScoreFunctionCOP docking_scorefxn_pack, core::scoring::ScoreFunctionCOP 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)

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

protocols::moves::MoverCOP	to_centroid () const
	--------------------------------------— Getters ---------------------------------------— 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...

void	set_autofoldtree (bool setting)
	@ return const ref to the jumps vector for docking More...

void	set_partners (std::string const &setting)

void	set_movable_jumps (DockJumps const &setting)

void	set_use_constraints (bool setting)

void	add_jump (core::SSize const jump_number)

void	show (std::ostream &out=std::cout)
	----------------------—— diagnostic output ------------------------------------—— More...

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...

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

Static Public Member Functions
static void	register_options ()
	Associates relevant options with the TemperedDocking 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...

Protected 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, core::scoring::ScoreFunctionCOP docking_score_low, core::scoring::ScoreFunctionCOP docking_score_high)
	Sets up the instance of TemperedDocking and initializes all members based on values passed in at construction or via the command line. More...

void	copy (TemperedDocking &lhs, TemperedDocking const &rhs)

void	setup_objects ()

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...

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

bool	flags_and_objects_are_in_sync_

bool	first_apply_with_current_setup_

bool	sc_min_

core::Size	n_cycles_
	how many cycles of monte-carlo per trajectory in the sampler ? More...

core::kinematics::FoldTree	fold_tree_

std::string	partners_

std::string	previous_sequence_

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

core::scoring::ScoreFunctionCOP	docking_scorefxn_low_

core::scoring::ScoreFunctionCOP	docking_scorefxn_high_

core::scoring::ScoreFunctionCOP	docking_scorefxn_pack_

core::scoring::ScoreFunctionCOP	docking_scorefxn_output_

protocols::moves::MoverOP	docking_constraint_

protocols::rigid::RigidBodyPerturbNoCenterMoverOP	rb_mover_

protocols::canonical_sampling::TemperingBaseOP	tempering_

protocols::canonical_sampling::MetropolisHastingsMoverOP	sampler_

std::string	recover_sidechains_filename_

protocols::moves::MoverOP	to_centroid_

bool	use_csts_

core::Real	rigid_rot_mag_

core::Real	rigid_trans_mag_

Static Private Attributes
static bool	options_registered_

Friends
std::ostream &	operator<< (std::ostream &out, const TemperedDocking &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

Detailed Description

allows docking using simulated or parallel tempering

Detailed:

Definition at line 52 of file TemperedDocking.hh.

Constructor & Destructor Documentation

protocols::docking::TemperedDocking::TemperedDocking ( )

default constructor fills values with the expected defaults

Definition at line 103 of file TemperedDocking.cc.

References init().

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

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

copy ctor

Definition at line 133 of file TemperedDocking.cc.

References copy().

Member Function Documentation

void protocols::docking::TemperedDocking::add_jump ( core::SSize const jump_number)

inline

Definition at line 123 of file TemperedDocking.hh.

References movable_jumps_.

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

virtual

main docking protocol

Docking apply

Detailed:

Implements protocols::moves::Mover.

Definition at line 199 of file TemperedDocking.cc.

References docking_constraint_, finalize_setup(), first_apply_with_current_setup_, flags_and_objects_are_in_sync_, core::pose::Pose::fold_tree(), fold_tree_, previous_sequence_, sampler_, core::pose::Pose::sequence(), show(), sync_objects_with_flags(), to_centroid_, and tr().

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

virtual

clone

clone operator, calls the copy constructor

Reimplemented from protocols::moves::Mover.

Definition at line 128 of file TemperedDocking.cc.

References TemperedDocking().

void protocols::docking::TemperedDocking::copy	(	TemperedDocking &	lhs,
		TemperedDocking const &	rhs
	)

protected

Definition at line 148 of file TemperedDocking.cc.

References autofoldtree_, docking_constraint_, docking_scorefxn_high_, docking_scorefxn_low_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, fold_tree_, movable_jumps_, partners_, previous_sequence_, sc_min_, to_centroid_, and use_csts_.

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

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

protected

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

setup steps when new pose comes in (this is not repeated for every reply, ... only when new sequence.. )

Definition at line 174 of file TemperedDocking.cc.

References autofoldtree_, core::pose::Pose::fold_tree(), fold_tree_, movable_jumps_, core::pose::Pose::num_jump(), partners_, rb_mover_, protocols::docking::setup_foldtree(), and tr().

Referenced by apply().

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

inlinevirtual

returns the docking partners chain identifiers

Implements protocols::moves::Mover.

Definition at line 106 of file TemperedDocking.hh.

void protocols::docking::TemperedDocking::init	(	DockJumps const	movable_jumps,
		core::scoring::ScoreFunctionCOP	docking_score_low,
		core::scoring::ScoreFunctionCOP	docking_score_high
	)

protected

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

Definition at line 107 of file TemperedDocking.cc.

References docking_scorefxn_high_, docking_scorefxn_low_, init_from_options(), movable_jumps(), movable_jumps_, set_defaults(), setup_objects(), and protocols::moves::Mover::type().

Referenced by TemperedDocking().

void protocols::docking::TemperedDocking::init_from_options ( )

protected

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

Definition at line 389 of file TemperedDocking.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), docking_scorefxn_high_, docking_scorefxn_low_, docking_scorefxn_output_, docking_scorefxn_pack_, n_cycles_, rigid_rot_mag_, rigid_trans_mag_, sc_min_, set_movable_jumps(), set_partners(), set_use_constraints(), and tempering_.

Referenced by init().

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

inline

Definition at line 108 of file TemperedDocking.hh.

References movable_jumps_.

Referenced by init().

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

inline

returns ref to the jumps vector for docking

Definition at line 110 of file TemperedDocking.hh.

References movable_jumps_.

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

assignment operator

Definition at line 140 of file TemperedDocking.cc.

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

void protocols::docking::TemperedDocking::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 442 of file TemperedDocking.cc.

References protocols::moves::DataMap::get(), partners(), set_highres_scorefxn(), set_lowres_scorefxn(), and set_partners().

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

inline

Definition at line 104 of file TemperedDocking.hh.

References partners_.

Referenced by parse_my_tag().

void protocols::docking::TemperedDocking::register_options ( )

static

Associates relevant options with the TemperedDocking class.

Definition at line 77 of file TemperedDocking.cc.

References options_registered_, protocols::canonical_sampling::SilentTrajectoryRecorder::register_options(), protocols::canonical_sampling::SimulatedTempering::register_options(), and protocols::canonical_sampling::ParallelTempering::register_options().

void protocols::docking::TemperedDocking::set_autofoldtree ( bool setting)

inline

@ return const ref to the jumps vector for docking

Definition at line 114 of file TemperedDocking.hh.

References autofoldtree_.

void protocols::docking::TemperedDocking::set_defaults ( )

Assigns default values to primitive members.

---------------— initializing helpers ------------------------------—

Definition at line 328 of file TemperedDocking.cc.

References autofoldtree_, n_cycles_, partners_, and sc_min_.

Referenced by init().

void protocols::docking::TemperedDocking::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 242 of file TemperedDocking.cc.

Referenced by parse_my_tag(), and set_highres_scorefxn().

void protocols::docking::TemperedDocking::set_highres_scorefxn	(	core::scoring::ScoreFunctionCOP	docking_scorefxn_high,
		core::scoring::ScoreFunctionCOP	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 247 of file TemperedDocking.cc.

References set_highres_scorefxn().

void protocols::docking::TemperedDocking::set_highres_scorefxn	(	core::scoring::ScoreFunctionCOP	docking_scorefxn_high,
		core::scoring::ScoreFunctionCOP	docking_scorefxn_pack,
		core::scoring::ScoreFunctionCOP	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 254 of file TemperedDocking.cc.

References docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

void protocols::docking::TemperedDocking::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 237 of file TemperedDocking.cc.

References docking_scorefxn_low_.

Referenced by parse_my_tag().

void protocols::docking::TemperedDocking::set_movable_jumps ( DockJumps const & setting)

inline

Definition at line 118 of file TemperedDocking.hh.

References movable_jumps_.

Referenced by init_from_options().