#include <SymDockingLowRes.hh>

Inheritance diagram for protocols::symmetric_docking::SymDockingLowRes:

Public Member Functions
	SymDockingLowRes (core::scoring::ScoreFunctionCOP scorefxn_in)

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

	~SymDockingLowRes () override

void	set_default (core::pose::Pose &pose)

void	set_default_mc (core::pose::Pose &pose)

void	set_default_protocol (core::pose::Pose &pose)

void	set_default_move_map (core::pose::Pose &pose)

moves::MonteCarloOP	get_mc ()

moves::PyMOLMoverOP	get_pymol_mover ()

void	apply (core::pose::Pose &pose) override
	Perform several cycles of rigid-body Monte Carlo moves and adapt the step size. More...

void	rigid_body_trial (core::pose::Pose &pose)
	Perform a cycle of rigid-body Monte Carlo moves. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. 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

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 void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. 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...

Private Types
typedef core::Real	Real

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...

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...

Member Typedef Documentation

typedef core::Real protocols::symmetric_docking::SymDockingLowRes::Real

private

Constructor & Destructor Documentation

protocols::symmetric_docking::SymDockingLowRes::SymDockingLowRes ( core::scoring::ScoreFunctionCOP scorefxn_in )

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

protocols::symmetric_docking::SymDockingLowRes::~SymDockingLowRes ( )

overridedefault

Member Function Documentation

void protocols::symmetric_docking::SymDockingLowRes::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_, mc_, outer_cycles_, rigid_body_trial(), rot_magnitude_, set_default(), protocols::symmetric_docking::TR(), and trans_magnitude_.

moves::MoverOP protocols::symmetric_docking::SymDockingLowRes::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.

moves::MonteCarloOP protocols::symmetric_docking::SymDockingLowRes::get_mc ( )

References mc_.

std::string protocols::symmetric_docking::SymDockingLowRes::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

moves::PyMOLMoverOP protocols::symmetric_docking::SymDockingLowRes::get_pymol_mover ( )

References pymol_mover_.

void protocols::symmetric_docking::SymDockingLowRes::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 accept_rate_, protocols::moves::accept_reject, docking_lowres_protocol_, inner_cycles_, mc_, rb_mover_, rot_magnitude_, and trans_magnitude_.

Referenced by apply().

void protocols::symmetric_docking::SymDockingLowRes::set_default ( core::pose::Pose & pose )

References accept_rate_, bb_, chi_, inner_cycles_, nb_list_, outer_cycles_, rot_magnitude_, set_default_mc(), set_default_move_map(), set_default_protocol(), temperature_, and trans_magnitude_.

Referenced by apply().

void protocols::symmetric_docking::SymDockingLowRes::set_default_mc ( core::pose::Pose & pose )

References mc_, scorefxn_, and temperature_.

Referenced by set_default().

void protocols::symmetric_docking::SymDockingLowRes::set_default_move_map ( core::pose::Pose & pose )

References bb_, chi_, core::pose::symmetry::make_symmetric_movemap(), and movemap_.

Referenced by set_default().

void protocols::symmetric_docking::SymDockingLowRes::set_default_protocol ( core::pose::Pose & pose )

References core::pose::Pose::conformation(), docking_lowres_protocol_, core::pose::symmetry::is_symmetric(), pymol_mover_, rb_mover_, rot_magnitude_, protocols::symmetric_docking::TR(), and trans_magnitude_.

Referenced by set_default().

Member Data Documentation

Real protocols::symmetric_docking::SymDockingLowRes::accept_rate_

private

Referenced by apply(), rigid_body_trial(), and set_default().

bool protocols::symmetric_docking::SymDockingLowRes::bb_

private

Referenced by set_default(), and set_default_move_map().

bool protocols::symmetric_docking::SymDockingLowRes::chi_

private

Referenced by set_default(), and set_default_move_map().

moves::SequenceMoverOP protocols::symmetric_docking::SymDockingLowRes::docking_lowres_protocol_

private

Referenced by rigid_body_trial(), and set_default_protocol().

int protocols::symmetric_docking::SymDockingLowRes::inner_cycles_

private

Referenced by rigid_body_trial(), and set_default().

moves::MonteCarloOP protocols::symmetric_docking::SymDockingLowRes::mc_

private

Referenced by apply(), get_mc(), rigid_body_trial(), and set_default_mc().

core::kinematics::MoveMapOP protocols::symmetric_docking::SymDockingLowRes::movemap_

private

Referenced by set_default_move_map().

bool protocols::symmetric_docking::SymDockingLowRes::nb_list_

private

Referenced by set_default().

int protocols::symmetric_docking::SymDockingLowRes::outer_cycles_

private

Referenced by apply(), and set_default().

protocols::moves::PyMOLMoverOP protocols::symmetric_docking::SymDockingLowRes::pymol_mover_

private

Referenced by get_pymol_mover(), and set_default_protocol().

rigid::RigidBodyDofSeqPerturbMoverOP protocols::symmetric_docking::SymDockingLowRes::rb_mover_

private

Referenced by rigid_body_trial(), and set_default_protocol().

Real protocols::symmetric_docking::SymDockingLowRes::rot_magnitude_

private

Referenced by apply(), rigid_body_trial(), set_default(), and set_default_protocol().

core::scoring::ScoreFunctionCOP protocols::symmetric_docking::SymDockingLowRes::scorefxn_

private

Referenced by set_default_mc().

Real protocols::symmetric_docking::SymDockingLowRes::temperature_

private

Referenced by set_default(), and set_default_mc().

Real protocols::symmetric_docking::SymDockingLowRes::trans_magnitude_

private

Referenced by apply(), rigid_body_trial(), set_default(), and set_default_protocol().

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

src/protocols/symmetric_docking/SymDockingLowRes.hh
src/protocols/symmetric_docking/SymDockingLowRes.cc

Private Attributes
core::scoring::ScoreFunctionCOP	scorefxn_

core::kinematics::MoveMapOP	movemap_

moves::MonteCarloOP	mc_

moves::SequenceMoverOP	docking_lowres_protocol_

rigid::RigidBodyDofSeqPerturbMoverOP	rb_mover_

protocols::moves::PyMOLMoverOP	pymol_mover_

int	inner_cycles_

int	outer_cycles_

Real	trans_magnitude_

Real	rot_magnitude_

Real	accept_rate_

bool	chi_

bool	bb_

bool	nb_list_

Real	temperature_

Public Member Functions

Private Types

Private Attributes

Additional Inherited Members

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation