allows docking using simulated or parallel tempering More...

#include <TemperedDocking.hh>

Inheritance diagram for protocols::docking::TemperedDocking:

[legend]

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

protocols::moves::MoverOP	clone () const override
	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)

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

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

std::string	partners () const

std::string	get_name () const override
	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) const override
	-------------------------— diagnostic output ---------------------------------------— More...

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...

virtual bool	reinitialize_for_new_input () const
	Inform 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
	Generates a new Mover object freshly created with the default ctor. 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 Strings &	info ()
	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...

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. 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::TemperatureControllerOP	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::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Detailed Description

allows docking using simulated or parallel tempering

Constructor & Destructor Documentation

◆ TemperedDocking() [1/2]

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

default constructor fills values with the expected defaults

References init().

◆ TemperedDocking() [2/2]

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

copy ctor

References copy().

Member Function Documentation

◆ add_jump()

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

inline

References movable_jumps_.

◆ apply()

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

overridevirtual

main docking protocol

Implements protocols::moves::Mover.

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().

◆ clone()

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

overridevirtual

clone

clone operator, calls the copy constructor

Reimplemented from protocols::moves::Mover.

Referenced by parse_my_tag().

◆ copy()

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

protected

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().

◆ finalize_setup()

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.. )

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().

◆ get_name()

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

inlineoverridevirtual

returns the docking partners chain identifiers

Implements protocols::moves::Mover.

◆ init()

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.

References docking_scorefxn_high_, docking_scorefxn_low_, init_from_options(), movable_jumps(), movable_jumps_, set_defaults(), and setup_objects().

Referenced by TemperedDocking().

◆ init_from_options()

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

protected

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

References core::scoring::ScoreFunctionFactory::create_score_function(), docking_scorefxn_high_, docking_scorefxn_low_, docking_scorefxn_output_, docking_scorefxn_pack_, core::scoring::get_score_function_legacy(), n_cycles_, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, rigid_rot_mag_, rigid_trans_mag_, sc_min_, set_movable_jumps(), set_partners(), set_use_constraints(), and tempering_.

Referenced by init().

◆ movable_jumps() [1/2]

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

inline

References movable_jumps_.

Referenced by init().

◆ movable_jumps() [2/2]

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

inline

returns ref to the jumps vector for docking

References movable_jumps_.

◆ operator=()

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

assignment operator

References copy().

◆ parse_my_tag()

void protocols::docking::TemperedDocking::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References clone(), partners(), set_highres_scorefxn(), set_lowres_scorefxn(), and set_partners().

◆ partners()

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

inline

References partners_.

Referenced by parse_my_tag().

◆ register_options()

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

static

Associates relevant options with the TemperedDocking class.

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

◆ set_autofoldtree()

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

inline

@ return const ref to the jumps vector for docking

References autofoldtree_.

◆ set_defaults()

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

Assigns default values to primitive members.

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

References autofoldtree_, n_cycles_, partners_, and sc_min_.

Referenced by init().

◆ set_highres_scorefxn() [1/3]

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.

References set_highres_scorefxn().

◆ set_highres_scorefxn() [2/3]

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.

References docking_scorefxn_high_, docking_scorefxn_output_, and docking_scorefxn_pack_.

◆ set_highres_scorefxn() [3/3]

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.

Referenced by parse_my_tag(), and set_highres_scorefxn().

◆ set_lowres_scorefxn()

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.

References docking_scorefxn_low_.

Referenced by parse_my_tag().

◆ set_movable_jumps()

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

inline

References movable_jumps_.

Referenced by init_from_options().

◆ set_partners()

void protocols::docking::TemperedDocking::set_partners ( std::string const & setting )

inline

References partners_.

Referenced by init_from_options(), and parse_my_tag().

◆ set_sc_min()

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

◆ set_use_constraints()

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

References flags_and_objects_are_in_sync_, and use_csts_.

Referenced by init_from_options().

◆ setup_objects()

void protocols::docking::TemperedDocking::setup_objects ( )

protected

References core::chemical::CENTROID, docking_constraint_, docking_scorefxn_low_, fold_tree_, n_cycles_, previous_sequence_, rb_mover_, rigid_rot_mag_, rigid_trans_mag_, sampler_, sync_objects_with_flags(), tempering_, and to_centroid_.

Referenced by init().

◆ show()

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

overridevirtual

-------------------------— diagnostic output ---------------------------------------—

Show the complete setup of the docking protocol

Reimplemented from protocols::moves::Mover.

References core::conformation::membrane::out.

Referenced by apply().

◆ sync_objects_with_flags()

void protocols::docking::TemperedDocking::sync_objects_with_flags ( )

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

References docking_constraint_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, and use_csts_.

Referenced by apply(), and setup_objects().

◆ to_centroid()

protocols::moves::MoverCOP protocols::docking::TemperedDocking::to_centroid ( ) const

--------------------------------------— Getters ---------------------------------------—

References to_centroid_.

Friends And Related Function Documentation

◆ operator<<

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

friend

Member Data Documentation

◆ autofoldtree_

bool protocols::docking::TemperedDocking::autofoldtree_

private

information about the mode

Referenced by copy(), finalize_setup(), set_autofoldtree(), and set_defaults().

◆ docking_constraint_

protocols::moves::MoverOP protocols::docking::TemperedDocking::docking_constraint_

private

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

◆ docking_scorefxn_high_

core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_high_

private

Referenced by copy(), init(), init_from_options(), and set_highres_scorefxn().

◆ docking_scorefxn_low_

core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_low_

private

Referenced by copy(), init(), init_from_options(), set_lowres_scorefxn(), and setup_objects().

◆ docking_scorefxn_output_

core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_output_

private

Referenced by init_from_options(), and set_highres_scorefxn().

◆ docking_scorefxn_pack_

core::scoring::ScoreFunctionCOP protocols::docking::TemperedDocking::docking_scorefxn_pack_

private

Referenced by init_from_options(), and set_highres_scorefxn().

◆ first_apply_with_current_setup_

bool protocols::docking::TemperedDocking::first_apply_with_current_setup_

private

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

◆ flags_and_objects_are_in_sync_

bool protocols::docking::TemperedDocking::flags_and_objects_are_in_sync_

private

Referenced by apply(), copy(), set_use_constraints(), and sync_objects_with_flags().

◆ fold_tree_

core::kinematics::FoldTree protocols::docking::TemperedDocking::fold_tree_

private

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

◆ movable_jumps_

DockJumps protocols::docking::TemperedDocking::movable_jumps_

private

jumps that rigid_body transformations can occur over

Referenced by add_jump(), copy(), finalize_setup(), init(), movable_jumps(), and set_movable_jumps().

◆ n_cycles_

core::Size protocols::docking::TemperedDocking::n_cycles_

private

how many cycles of monte-carlo per trajectory in the sampler ?

Referenced by init_from_options(), set_defaults(), and setup_objects().

◆ options_registered_

bool protocols::docking::TemperedDocking::options_registered_

staticprivate

Referenced by register_options().

◆ partners_

std::string protocols::docking::TemperedDocking::partners_

private

Referenced by copy(), finalize_setup(), partners(), set_defaults(), and set_partners().

◆ previous_sequence_

std::string protocols::docking::TemperedDocking::previous_sequence_

private

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

◆ rb_mover_

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::TemperedDocking::rb_mover_

private

Referenced by finalize_setup(), and setup_objects().

◆ recover_sidechains_filename_

std::string protocols::docking::TemperedDocking::recover_sidechains_filename_

private

◆ rigid_rot_mag_

core::Real protocols::docking::TemperedDocking::rigid_rot_mag_

private

Referenced by init_from_options(), and setup_objects().

◆ rigid_trans_mag_

core::Real protocols::docking::TemperedDocking::rigid_trans_mag_

private

Referenced by init_from_options(), and setup_objects().

◆ sampler_

protocols::canonical_sampling::MetropolisHastingsMoverOP protocols::docking::TemperedDocking::sampler_

private

Referenced by apply(), and setup_objects().

◆ sc_min_

bool protocols::docking::TemperedDocking::sc_min_

private

Referenced by copy(), init_from_options(), and set_defaults().

◆ tempering_

protocols::canonical_sampling::TemperatureControllerOP protocols::docking::TemperedDocking::tempering_

private

Referenced by init_from_options(), and setup_objects().

◆ to_centroid_

protocols::moves::MoverOP protocols::docking::TemperedDocking::to_centroid_

private

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

◆ use_csts_

bool protocols::docking::TemperedDocking::use_csts_

private

Referenced by copy(), set_use_constraints(), and sync_objects_with_flags().

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

src/protocols/docking/TemperedDocking.hh
src/protocols/docking/TemperedDocking.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Static Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TemperedDocking() [1/2]

◆ TemperedDocking() [2/2]

Member Function Documentation

◆ add_jump()

◆ apply()

◆ clone()

◆ copy()

◆ finalize_setup()

◆ get_name()

◆ init()

◆ init_from_options()

◆ movable_jumps() [1/2]

◆ movable_jumps() [2/2]

◆ operator=()

◆ parse_my_tag()

◆ partners()

◆ register_options()

◆ set_autofoldtree()

◆ set_defaults()

◆ set_highres_scorefxn() [1/3]

◆ set_highres_scorefxn() [2/3]

◆ set_highres_scorefxn() [3/3]

◆ set_lowres_scorefxn()

◆ set_movable_jumps()

◆ set_partners()

◆ set_sc_min()

◆ set_use_constraints()

◆ setup_objects()

◆ show()

◆ sync_objects_with_flags()

◆ to_centroid()

Friends And Related Function Documentation

◆ operator<<

Member Data Documentation

◆ autofoldtree_

◆ docking_constraint_

◆ docking_scorefxn_high_

◆ docking_scorefxn_low_

◆ docking_scorefxn_output_

◆ docking_scorefxn_pack_

◆ first_apply_with_current_setup_

◆ flags_and_objects_are_in_sync_

◆ fold_tree_

◆ movable_jumps_

◆ n_cycles_

◆ options_registered_

◆ partners_

◆ previous_sequence_

◆ rb_mover_

◆ recover_sidechains_filename_

◆ rigid_rot_mag_

◆ rigid_trans_mag_

◆ sampler_

◆ sc_min_

◆ tempering_

◆ to_centroid_

◆ use_csts_