#include <DockingLowRes.hh>

Inheritance diagram for protocols::docking::DockingLowRes:

Public Member Functions
	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...

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. 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 ()

virtual core::Size	get_current_conformer_ensemble1 ()

virtual core::Size	get_current_conformer_ensemble2 ()

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	show (std::ostream &out=std::cout) const override

virtual void	lowres_inner_cycle (core::pose::Pose &pose)

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...

Public Attributes
bool	flags_and_objects_are_in_sync_

bool	first_apply_with_current_setup_

Protected Member Functions
virtual void	finalize_setup (core::pose::Pose &pose)
	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	init (DockJumps const movable_jumps, core::scoring::ScoreFunctionCOP scorefxn)
	Sets up the instance of DockingLowRes and initializes all members based on values passed in at construction or via the command line. More...

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

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...

Constructor & Destructor Documentation

protocols::docking::DockingLowRes::DockingLowRes ( )

Default constructor.

References init().

protocols::docking::DockingLowRes::~DockingLowRes ( )

overridedefault

protocols::docking::DockingLowRes::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.

References init().

protocols::docking::DockingLowRes::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.

References init().

Member Function Documentation

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

overridevirtual

Perform several cycles of rigid-body Monte Carlo moves and adapt the step size.

Remarks: currently used only in the low-resolution step (centroid mode)

References: pose_docking_centroid_rigid_body_adaptive from pose_docking.cc and: rigid_body_MC_cycle_adaptive from dock_structure.cc

Author: Monica Berrondo October 22 2007

Implements protocols::moves::Mover.

References accept_rate_, finalize_setup(), first_apply_with_current_setup_, flags_and_objects_are_in_sync_, lowres_inner_cycle(), mc_, outer_cycles_, rot_magnitude_, show(), sync_magnitudes_with_flags(), sync_objects_with_flags(), protocols::docking::TR(), and trans_magnitude_.

void protocols::docking::DockingLowRes::calc_accept_rate ( )

References accept_rate_, num_rb_accepted_, and num_rb_trials_.

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(), and lowres_inner_cycle().

protocols::moves::MoverOP protocols::docking::DockingLowRes::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::moves::Mover.

Reimplemented in protocols::docking::DockingLowResEnsemble.

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

protectedvirtual

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

Reimplemented in protocols::docking::DockingLowResEnsemble.

References core::pose::Pose::data(), core::pose::datacache::CacheableDataType::INTERFACE_INFO, movable_jumps_, movemap_, protocols::rigid::n2c, pymol_mover_, rb_mover_, rb_seq_, rot_magnitude_, trans_magnitude_, and view_in_pymol_.

Referenced by apply(), and protocols::docking::DockingLowResEnsemble::finalize_setup().

core::Real protocols::docking::DockingLowRes::get_accept_rate ( )

References accept_rate_.

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle().

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

virtual

Reimplemented in protocols::docking::DockingLowResEnsemble.

References protocols::docking::TR().

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

virtual

Reimplemented in protocols::docking::DockingLowResEnsemble.

References protocols::docking::TR().

core::Size protocols::docking::DockingLowRes::get_inner_cycles ( )

References inner_cycles_.

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle().

moves::MonteCarloOP protocols::docking::DockingLowRes::get_mc ( )

References mc_.

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(), protocols::docking::DockingLowResEnsemble::initialize_movers(), and protocols::docking::DockingLowResEnsemble::try_all_conformers().

DockJumps protocols::docking::DockingLowRes::get_movable_jumps ( )

References movable_jumps_.

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

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

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

core::Size protocols::docking::DockingLowRes::get_outer_cycles ( )

References outer_cycles_.

protocols::moves::PyMOLMoverOP protocols::docking::DockingLowRes::get_pymol_mover ( )

References pymol_mover_.

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

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::DockingLowRes::get_rb_mover ( )

References rb_mover_.

Referenced by protocols::docking::DockingLowResEnsemble::initialize_movers().

protocols::moves::SequenceMoverOP protocols::docking::DockingLowRes::get_rb_seq ( )

References rb_seq_.

Referenced by protocols::docking::DockingLowResEnsemble::initialize_movers().

protocols::moves::TrialMoverOP protocols::docking::DockingLowRes::get_rb_trial ( )

References rb_trial_.

core::Real protocols::docking::DockingLowRes::get_rot_magnitude ( )

References rot_magnitude_.

Referenced by protocols::docking::DockingLowResEnsemble::initialize_movers().

core::scoring::ScoreFunctionCOP protocols::docking::DockingLowRes::get_scorefxn ( )

References scorefxn_.

core::Real protocols::docking::DockingLowRes::get_temperature ( )

References temperature_.

core::Real protocols::docking::DockingLowRes::get_trans_magnitude ( )

Option getters - added by SSRB.

References trans_magnitude_.

Referenced by protocols::docking::DockingLowResEnsemble::initialize_movers().

bool protocols::docking::DockingLowRes::get_view_in_pymol ( )

References view_in_pymol_.

Referenced by protocols::docking::DockingLowResEnsemble::ensemble1_trial(), protocols::docking::DockingLowResEnsemble::ensemble2_trial(), and protocols::docking::DockingLowResEnsemble::finalize_setup().

void protocols::docking::DockingLowRes::init	(	DockJumps const	movable_jumps,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

private

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

References core::scoring::ScoreFunctionFactory::create_score_function(), movable_jumps_, scorefxn_, set_default(), sync_objects_with_flags(), and protocols::moves::Mover::type().

Referenced by DockingLowRes().

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

virtual

Reimplemented in protocols::docking::DockingLowResEnsemble.

References accept_rate_, calc_accept_rate(), inner_cycles_, mc_, rb_mover_, rb_seq_, rb_trial_, reset_rb_trial_counters(), rigid_body_trial(), rot_magnitude_, protocols::docking::TR(), and trans_magnitude_.

Referenced by apply().

void protocols::docking::DockingLowRes::pymol_color_change ( core::pose::Pose & pose )

References pymol_mover_, and protocols::moves::XC_last_color.

Referenced by protocols::docking::DockingLowResEnsemble::ensemble1_trial(), protocols::docking::DockingLowResEnsemble::ensemble2_trial(), and rigid_body_trial().

void protocols::docking::DockingLowRes::reset_rb_trial_counters ( )

References accept_rate_, num_rb_accepted_, and num_rb_trials_.

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(), and lowres_inner_cycle().

void protocols::docking::DockingLowRes::rigid_body_trial ( core::pose::Pose & pose )

Perform a cycle of rigid-body Monte Carlo moves.

Performs a number (nattempts) of MC rigid-body moves (of size trans_magnitude, rot_magnitude). The number of successful attempts is stored in accept_rate_ and used in adaptive trials.

Remarks: the success_rate defines whether the translation/rotation size is increased or decreased for the next cycle. currently used only in the low-resolution step (centroid mode)

References: pose_docking_rigid_body_trial from pose_docking.cc and: rigid_body_MC_cycle from dock_structure.cc

Author: Monica Berrondo October 22 2007

References num_rb_accepted_, num_rb_trials_, pymol_color_change(), rb_trial_, protocols::docking::TR(), and view_in_pymol_.

Referenced by protocols::docking::DockingLowResEnsemble::adaptive_inner_cycle(), and lowres_inner_cycle().

void protocols::docking::DockingLowRes::set_default ( )

Assigns default values to primitive members.

References accept_rate_, bb_, chi_, inner_cycles_, nb_list_, num_rb_accepted_, num_rb_trials_, outer_cycles_, sync_magnitudes_with_flags(), temperature_, and view_in_pymol_.

Referenced by init().

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

inline

References inner_cycles_.

Referenced by protocols::docking::DockingLowResEnsemble::ensemble_defaults().

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

inline

References outer_cycles_.

Referenced by protocols::docking::DockingLowResEnsemble::ensemble_defaults().

void protocols::docking::DockingLowRes::set_rb_trial ( protocols::moves::TrialMoverOP rb_trial_in )

References rb_trial_.

Referenced by protocols::docking::DockingLowResEnsemble::initialize_movers().

void protocols::docking::DockingLowRes::set_rot_magnitude ( core::Real rot_magnitude )

References rot_magnitude_.

Referenced by sync_magnitudes_with_flags().

void protocols::docking::DockingLowRes::set_scorefxn ( core::scoring::ScoreFunctionCOP scorefxn )

References flags_and_objects_are_in_sync_, and scorefxn_.

void protocols::docking::DockingLowRes::set_trans_magnitude ( core::Real trans_magnitude )

References trans_magnitude_.

Referenced by sync_magnitudes_with_flags().

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

overridevirtual

Show the complete setup of the docking protocol

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::docking::DockingLowResEnsemble.

References protocols::comparative_modeling::features::A, inner_cycles_, outer_cycles_, and scorefxn_.

Referenced by apply(), protocols::docking::operator<<(), and protocols::docking::DockingLowResEnsemble::show().

void protocols::docking::DockingLowRes::sync_magnitudes_with_flags ( )

References set_rot_magnitude(), and set_trans_magnitude().

Referenced by apply(), and set_default().

void protocols::docking::DockingLowRes::sync_objects_with_flags ( )

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

References bb_, chi_, first_apply_with_current_setup_, flags_and_objects_are_in_sync_, mc_, movable_jumps_, movemap_, rb_mover_, rb_seq_, rb_trial_, scorefxn_, and temperature_.

Referenced by apply(), and init().

Friends And Related Function Documentation

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

friend

Member Data Documentation

core::Real protocols::docking::DockingLowRes::accept_rate_

private

Referenced by apply(), calc_accept_rate(), get_accept_rate(), lowres_inner_cycle(), reset_rb_trial_counters(), and set_default().

bool protocols::docking::DockingLowRes::bb_

private

Referenced by set_default(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::chi_

private

Referenced by set_default(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::first_apply_with_current_setup_

Referenced by apply(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::flags_and_objects_are_in_sync_

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

core::Size protocols::docking::DockingLowRes::inner_cycles_

private

Referenced by get_inner_cycles(), lowres_inner_cycle(), set_default(), set_inner_cycles(), and show().

protocols::moves::MonteCarloOP protocols::docking::DockingLowRes::mc_

private

Referenced by apply(), get_mc(), lowres_inner_cycle(), and sync_objects_with_flags().

DockJumps protocols::docking::DockingLowRes::movable_jumps_

private

Referenced by finalize_setup(), get_movable_jumps(), init(), and sync_objects_with_flags().

core::kinematics::MoveMapOP protocols::docking::DockingLowRes::movemap_

private

Referenced by finalize_setup(), and sync_objects_with_flags().

bool protocols::docking::DockingLowRes::nb_list_

private

Referenced by set_default().

core::Real protocols::docking::DockingLowRes::num_rb_accepted_

private

Referenced by calc_accept_rate(), reset_rb_trial_counters(), rigid_body_trial(), and set_default().

core::Real protocols::docking::DockingLowRes::num_rb_trials_

private

Referenced by calc_accept_rate(), reset_rb_trial_counters(), rigid_body_trial(), and set_default().

core::Size protocols::docking::DockingLowRes::outer_cycles_

private

Referenced by apply(), get_outer_cycles(), set_default(), set_outer_cycles(), and show().

protocols::moves::PyMOLMoverOP protocols::docking::DockingLowRes::pymol_mover_

private

Referenced by finalize_setup(), get_pymol_mover(), and pymol_color_change().

protocols::rigid::RigidBodyPerturbNoCenterMoverOP protocols::docking::DockingLowRes::rb_mover_

private

Referenced by finalize_setup(), get_rb_mover(), lowres_inner_cycle(), and sync_objects_with_flags().

protocols::moves::SequenceMoverOP protocols::docking::DockingLowRes::rb_seq_

private

Referenced by finalize_setup(), get_rb_seq(), lowres_inner_cycle(), and sync_objects_with_flags().

protocols::moves::TrialMoverOP protocols::docking::DockingLowRes::rb_trial_

private

Referenced by get_rb_trial(), lowres_inner_cycle(), rigid_body_trial(), set_rb_trial(), and sync_objects_with_flags().

core::Real protocols::docking::DockingLowRes::rot_magnitude_

private

Referenced by apply(), finalize_setup(), get_rot_magnitude(), lowres_inner_cycle(), and set_rot_magnitude().

core::scoring::ScoreFunctionCOP protocols::docking::DockingLowRes::scorefxn_

private

Referenced by get_scorefxn(), init(), set_scorefxn(), show(), and sync_objects_with_flags().

core::Real protocols::docking::DockingLowRes::temperature_

private

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

core::Real protocols::docking::DockingLowRes::trans_magnitude_

private

Referenced by apply(), finalize_setup(), get_trans_magnitude(), lowres_inner_cycle(), and set_trans_magnitude().

bool protocols::docking::DockingLowRes::view_in_pymol_

private

Referenced by finalize_setup(), get_view_in_pymol(), rigid_body_trial(), and set_default().

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

src/protocols/docking/DockingLowRes.hh
src/protocols/docking/DockingLowRes.cc

Private Attributes
core::kinematics::MoveMapOP	movemap_

protocols::rigid::RigidBodyPerturbNoCenterMoverOP	rb_mover_

protocols::moves::SequenceMoverOP	rb_seq_

protocols::moves::TrialMoverOP	rb_trial_

protocols::moves::MonteCarloOP	mc_

core::Real	trans_magnitude_

core::Real	rot_magnitude_

core::Real	accept_rate_

core::Real	num_rb_trials_

core::Real	num_rb_accepted_

core::Size	inner_cycles_

core::Size	outer_cycles_

bool	chi_

bool	bb_

bool	nb_list_

core::Real	temperature_

DockJumps	movable_jumps_

core::scoring::ScoreFunctionCOP	scorefxn_

protocols::moves::PyMOLMoverOP	pymol_mover_

bool	view_in_pymol_

Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation