protocols::docking::DockingLowResEnsemble Class Reference

#include <DockingLowResEnsemble.hh>

Inheritance diagram for protocols::docking::DockingLowResEnsemble:

Public Member Functions
	DockingLowResEnsemble ()
	Default constructor. More...
	~DockingLowResEnsemble () override
	DockingLowResEnsemble (core::scoring::ScoreFunctionCOP scorefxn, DockJumps const movable_jumps)
	Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps. More...
void	ensemble_defaults ()
protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...
core::Size	get_current_conformer_ensemble1 () override
core::Size	get_current_conformer_ensemble2 () override
void	show (std::ostream &out=std::cout) const override
void	set_ensemble1 (DockingEnsembleOP ensemble1)
void	set_ensemble2 (DockingEnsembleOP ensemble2)
void	lowres_inner_cycle (core::pose::Pose &pose) override
void	adaptive_inner_cycle (core::pose::Pose &pose)
void	try_all_conformers (core::pose::Pose &pose)
void	initialize_movers ()
void	calc_ensemble_accept_rate_ ()
void	reset_ensemble_trial_counters ()
Public Member Functions inherited from protocols::docking::DockingLowRes
	DockingLowRes ()
	Default constructor. More...
	~DockingLowRes () override
	DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, core::Size const rb_jump=1)
	Constructor with two arguments. The first is scorefunction to be used for docking, the second is the jump to dock over. More...
	DockingLowRes (core::scoring::ScoreFunctionCOP scorefxn, DockJumps const movable_jumps)
	Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps. More...
void	set_default ()
	Assigns default values to primitive members. More...
void	set_scorefxn (core::scoring::ScoreFunctionCOP scorefxn)
void	sync_magnitudes_with_flags ()
void	sync_objects_with_flags ()
	Instantiates non-primitive members based on the value of the primitive members. More...
moves::MonteCarloOP	get_mc ()
void	apply (core::pose::Pose &pose) override
	Perform several cycles of rigid-body Monte Carlo moves and adapt the step size. More...
std::string	get_name () const override
	Each derived class must specify its name. The class name. More...
void	rigid_body_trial (core::pose::Pose &pose)
	Perform a cycle of rigid-body Monte Carlo moves. More...
core::Real	get_trans_magnitude ()
	Option getters - added by SSRB. More...
core::Real	get_rot_magnitude ()
core::Real	get_accept_rate ()
core::Size	get_inner_cycles ()
core::Size	get_outer_cycles ()
core::Real	get_temperature ()
protocols::moves::TrialMoverOP	get_rb_trial ()
protocols::moves::SequenceMoverOP	get_rb_seq ()
protocols::rigid::RigidBodyPerturbNoCenterMoverOP	get_rb_mover ()
DockJumps	get_movable_jumps ()
core::scoring::ScoreFunctionCOP	get_scorefxn ()
protocols::moves::PyMOLMoverOP	get_pymol_mover ()
bool	get_view_in_pymol ()
void	set_inner_cycles (core::Size inner_cycles)
void	set_outer_cycles (core::Size outer_cycles)
void	set_trans_magnitude (core::Real trans_magnitude)
void	set_rot_magnitude (core::Real rot_magnitude)
void	set_rb_trial (protocols::moves::TrialMoverOP rb_trial_in)
void	reset_rb_trial_counters ()
void	calc_accept_rate ()
void	pymol_color_change (core::pose::Pose &pose)
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
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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...

Protected Member Functions
void	finalize_setup (core::pose::Pose &pose) override
	Performs the portion of setup of non-primitive members that requires a pose - called on apply. More...
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Private Member Functions
void	ensemble1_trial (core::pose::Pose &pose)
void	ensemble2_trial (core::pose::Pose &pose)

Private Attributes
protocols::docking::ConformerSwitchMoverOP	ensemble1_mover_
protocols::docking::ConformerSwitchMoverOP	ensemble2_mover_
core::Size	current_outer_cycle_
core::Real	accept_rate_ens1_
core::Real	num_trials_ens1_
core::Real	num_accepted_ens1_
core::Real	accept_rate_ens2_
core::Real	num_trials_ens2_
core::Real	num_accepted_ens2_
core::Real	rb_trial_wt_
core::Real	ens1_trial_wt_
core::Real	ens2_trial_wt_
protocols::moves::SequenceMoverOP	ensemble1_seq_
protocols::moves::SequenceMoverOP	ensemble2_seq_
protocols::moves::TrialMoverOP	ensemble1_trial_
protocols::moves::TrialMoverOP	ensemble2_trial_
core::Size	current_conformer_ensemble1_
core::Size	current_conformer_ensemble2_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef std::list< std::string >	Strings
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	Overload this static method if you access options within the mover. More...
Public Attributes inherited from protocols::docking::DockingLowRes
bool	flags_and_objects_are_in_sync_
bool	first_apply_with_current_setup_

Constructor & Destructor Documentation

protocols::docking::DockingLowResEnsemble::DockingLowResEnsemble

(

)

Default constructor.

References protocols::moves::Mover::type().

protocols::docking::DockingLowResEnsemble::~DockingLowResEnsemble ( )

overridedefault

protocols::docking::DockingLowResEnsemble::DockingLowResEnsemble	(	core::scoring::ScoreFunctionCOP	scorefxn,
		DockJumps const	movable_jumps
	)

Constructor with two arguments. The first is scorefunction to be used for docking, the second is the DockJumps.

References protocols::moves::Mover::type().

Member Function Documentation

void protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle

(

core::pose::Pose &

pose

)

References accept_rate_ens1_, accept_rate_ens2_, protocols::docking::DockingLowRes::calc_accept_rate(), calc_ensemble_accept_rate_(), ens1_trial_wt_, ens2_trial_wt_, ensemble1_trial(), ensemble2_trial(), protocols::docking::DockingLowRes::get_accept_rate(), protocols::docking::DockingLowRes::get_inner_cycles(), protocols::docking::DockingLowRes::get_mc(), initialize_movers(), rb_trial_wt_, reset_ensemble_trial_counters(), protocols::docking::DockingLowRes::reset_rb_trial_counters(), core::scoring::rg, protocols::docking::DockingLowRes::rigid_body_trial(), and protocols::docking::TR().

Referenced by lowres_inner_cycle().

void protocols::docking::DockingLowResEnsemble::calc_ensemble_accept_rate_

(

)

References accept_rate_ens1_, accept_rate_ens2_, num_accepted_ens1_, num_accepted_ens2_, num_trials_ens1_, and num_trials_ens2_.

Referenced by adaptive_inner_cycle().

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

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::docking::DockingLowRes.

void protocols::docking::DockingLowResEnsemble::ensemble1_trial ( core::pose::Pose &  pose )

private

References current_conformer_ensemble1_, ensemble1_mover_, ensemble1_trial_, protocols::docking::DockingLowRes::get_view_in_pymol(), num_accepted_ens1_, num_trials_ens1_, protocols::docking::DockingLowRes::pymol_color_change(), and protocols::docking::TR().

Referenced by adaptive_inner_cycle(), and try_all_conformers().

void protocols::docking::DockingLowResEnsemble::ensemble2_trial ( core::pose::Pose &  pose )

private

References current_conformer_ensemble2_, ensemble2_mover_, ensemble2_trial_, protocols::docking::DockingLowRes::get_view_in_pymol(), num_accepted_ens2_, num_trials_ens2_, protocols::docking::DockingLowRes::pymol_color_change(), and protocols::docking::TR().

Referenced by adaptive_inner_cycle(), and try_all_conformers().

void protocols::docking::DockingLowResEnsemble::ensemble_defaults

(

)

References current_conformer_ensemble1_, current_conformer_ensemble2_, current_outer_cycle_, ens1_trial_wt_, ens2_trial_wt_, rb_trial_wt_, reset_ensemble_trial_counters(), protocols::docking::DockingLowRes::set_inner_cycles(), and protocols::docking::DockingLowRes::set_outer_cycles().

Referenced by finalize_setup().

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

overrideprotectedvirtual

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

Reimplemented from protocols::docking::DockingLowRes.

References ensemble1_mover_, ensemble1_seq_, ensemble2_mover_, ensemble2_seq_, ensemble_defaults(), protocols::docking::DockingLowRes::finalize_setup(), protocols::docking::DockingLowRes::get_pymol_mover(), and protocols::docking::DockingLowRes::get_view_in_pymol().

core::Size protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble1 ( )

overridevirtual

Reimplemented from protocols::docking::DockingLowRes.

References current_conformer_ensemble1_.

Referenced by lowres_inner_cycle().

core::Size protocols::docking::DockingLowResEnsemble::get_current_conformer_ensemble2 ( )

overridevirtual

Reimplemented from protocols::docking::DockingLowRes.

References current_conformer_ensemble2_.

Referenced by lowres_inner_cycle().

void protocols::docking::DockingLowResEnsemble::initialize_movers

(

)

References protocols::moves::accept_reject, ensemble1_seq_, ensemble1_trial_, ensemble2_seq_, ensemble2_trial_, protocols::docking::DockingLowRes::get_mc(), protocols::docking::DockingLowRes::get_rb_mover(), protocols::docking::DockingLowRes::get_rb_seq(), protocols::docking::DockingLowRes::get_rot_magnitude(), protocols::docking::DockingLowRes::get_trans_magnitude(), and protocols::docking::DockingLowRes::set_rb_trial().

Referenced by adaptive_inner_cycle(), and try_all_conformers().

void protocols::docking::DockingLowResEnsemble::lowres_inner_cycle ( core::pose::Pose &  pose )

overridevirtual

Reimplemented from protocols::docking::DockingLowRes.

References accept_rate_ens1_, accept_rate_ens2_, adaptive_inner_cycle(), current_outer_cycle_, ens1_trial_wt_, ens2_trial_wt_, ensemble1_mover_, ensemble2_mover_, get_current_conformer_ensemble1(), get_current_conformer_ensemble2(), and try_all_conformers().

void protocols::docking::DockingLowResEnsemble::reset_ensemble_trial_counters

(

)

References accept_rate_ens1_, accept_rate_ens2_, num_accepted_ens1_, num_accepted_ens2_, num_trials_ens1_, and num_trials_ens2_.

Referenced by adaptive_inner_cycle(), and ensemble_defaults().

void protocols::docking::DockingLowResEnsemble::set_ensemble1

(

DockingEnsembleOP

ensemble1

)

References ensemble1_mover_.

Referenced by protocols::docking::DockingProtocol::finalize_setup().

void protocols::docking::DockingLowResEnsemble::set_ensemble2

(

DockingEnsembleOP

ensemble2

)

References ensemble2_mover_.

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

overridevirtual

Show the complete setup of the docking protocol

Reimplemented from protocols::docking::DockingLowRes.

References ensemble1_mover_, ensemble2_mover_, and protocols::docking::DockingLowRes::show().

void protocols::docking::DockingLowResEnsemble::try_all_conformers

(

core::pose::Pose &

pose

)

References ensemble1_mover_, ensemble1_trial(), ensemble2_mover_, ensemble2_trial(), protocols::docking::DockingLowRes::get_mc(), and initialize_movers().

Referenced by lowres_inner_cycle().

Member Data Documentation

core::Real protocols::docking::DockingLowResEnsemble::accept_rate_ens1_

private

Referenced by adaptive_inner_cycle(), calc_ensemble_accept_rate_(), lowres_inner_cycle(), and reset_ensemble_trial_counters().

core::Real protocols::docking::DockingLowResEnsemble::accept_rate_ens2_

private

Referenced by adaptive_inner_cycle(), calc_ensemble_accept_rate_(), lowres_inner_cycle(), and reset_ensemble_trial_counters().

core::Size protocols::docking::DockingLowResEnsemble::current_conformer_ensemble1_

private

Referenced by ensemble1_trial(), ensemble_defaults(), and get_current_conformer_ensemble1().

core::Size protocols::docking::DockingLowResEnsemble::current_conformer_ensemble2_

private

Referenced by ensemble2_trial(), ensemble_defaults(), and get_current_conformer_ensemble2().

core::Size protocols::docking::DockingLowResEnsemble::current_outer_cycle_

private

Referenced by ensemble_defaults(), and lowres_inner_cycle().

core::Real protocols::docking::DockingLowResEnsemble::ens1_trial_wt_

private

Referenced by adaptive_inner_cycle(), ensemble_defaults(), and lowres_inner_cycle().

core::Real protocols::docking::DockingLowResEnsemble::ens2_trial_wt_

private

Referenced by adaptive_inner_cycle(), ensemble_defaults(), and lowres_inner_cycle().

protocols::docking::ConformerSwitchMoverOP protocols::docking::DockingLowResEnsemble::ensemble1_mover_

private

Referenced by ensemble1_trial(), finalize_setup(), lowres_inner_cycle(), set_ensemble1(), show(), and try_all_conformers().

protocols::moves::SequenceMoverOP protocols::docking::DockingLowResEnsemble::ensemble1_seq_

private

Referenced by finalize_setup(), and initialize_movers().

protocols::moves::TrialMoverOP protocols::docking::DockingLowResEnsemble::ensemble1_trial_

private

Referenced by ensemble1_trial(), and initialize_movers().

protocols::docking::ConformerSwitchMoverOP protocols::docking::DockingLowResEnsemble::ensemble2_mover_

private

Referenced by ensemble2_trial(), finalize_setup(), lowres_inner_cycle(), set_ensemble2(), show(), and try_all_conformers().

protocols::moves::SequenceMoverOP protocols::docking::DockingLowResEnsemble::ensemble2_seq_

private

Referenced by finalize_setup(), and initialize_movers().

protocols::moves::TrialMoverOP protocols::docking::DockingLowResEnsemble::ensemble2_trial_

private

Referenced by ensemble2_trial(), and initialize_movers().

core::Real protocols::docking::DockingLowResEnsemble::num_accepted_ens1_

private

Referenced by calc_ensemble_accept_rate_(), ensemble1_trial(), and reset_ensemble_trial_counters().

core::Real protocols::docking::DockingLowResEnsemble::num_accepted_ens2_

private

Referenced by calc_ensemble_accept_rate_(), ensemble2_trial(), and reset_ensemble_trial_counters().

core::Real protocols::docking::DockingLowResEnsemble::num_trials_ens1_

private

Referenced by calc_ensemble_accept_rate_(), ensemble1_trial(), and reset_ensemble_trial_counters().

core::Real protocols::docking::DockingLowResEnsemble::num_trials_ens2_

private

Referenced by calc_ensemble_accept_rate_(), ensemble2_trial(), and reset_ensemble_trial_counters().

core::Real protocols::docking::DockingLowResEnsemble::rb_trial_wt_

private

Referenced by adaptive_inner_cycle(), and ensemble_defaults().

---

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

• src/protocols/docking/DockingLowResEnsemble.hh
• src/protocols/docking/DockingLowResEnsemble.cc