#include <DockMCMCycle.hh>

Inheritance diagram for protocols::docking::DockMCMCycle:

Public Member Functions
	DockMCMCycle ()
	Default constructor. More...

	DockMCMCycle (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
	Constructor with two arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking and packing. More...

	DockMCMCycle (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing. More...

	DockMCMCycle (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
	Constructor with arguments: The first argument is a DockJumps vector. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing. More...

	~DockMCMCycle () override

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

void	set_default ()
	Sets the default values for all members. More...

void	set_move_map (core::kinematics::MoveMapOP movemap)

void	set_min_type (std::string min_type)

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

moves::MonteCarloOP	get_mc ()

void	apply (core::pose::Pose &pose) override

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

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

void	reset_cycle_index ()

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

void	set_scmin (bool setting)

void	set_rtmin (bool setting)

void	set_rot_magnitude (core::Real value)

DockJumps const &	movable_jumps () const

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...

Private Types
typedef core::Real	Real

Private Member Functions
void	setup_protocol (core::pose::Pose &pose)
	main entrance to do monte carlo minimization More...

Private Attributes
core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	scorefxn_pack_

core::kinematics::MoveMapOP	movemap_

moves::CycleMoverOP	dock_mcm_cycle_

moves::MonteCarloOP	mc_

DockJumps	movable_jumps_

core::Real	trans_magnitude_

core::Real	rot_magnitude_

bool	rtmin_

bool	scmin_

core::pack::task::TaskFactoryOP	tf_
	tf_ will be used internally by dockinghires. It will be initialized through the init_task_factory_ below More...

core::Size	repack_period_
	task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF! init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory More...

core::Real	min_tolerance_

bool	nb_list_

std::string	min_type_

Friends
std::ostream &	operator<< (std::ostream &out, const DockMCMCycle &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...

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::docking::DockMCMCycle::Real

private

Constructor & Destructor Documentation

protocols::docking::DockMCMCycle::DockMCMCycle ( )

Default constructor.

References movable_jumps_, set_default(), and protocols::moves::Mover::type().

protocols::docking::DockMCMCycle::DockMCMCycle	(	core::Size const	rb_jump,
		core::scoring::ScoreFunctionOP	scorefxn
	)

Constructor with two arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking and packing.

References movable_jumps_, set_default(), and protocols::moves::Mover::type().

protocols::docking::DockMCMCycle::DockMCMCycle	(	core::Size const	rb_jump,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::scoring::ScoreFunctionOP	scorefxn_pack
	)

Constructor with arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing.

References movable_jumps_, set_default(), and protocols::moves::Mover::type().

protocols::docking::DockMCMCycle::DockMCMCycle	(	DockJumps const	movable_jumps,
		core::scoring::ScoreFunctionOP	scorefxn,
		core::scoring::ScoreFunctionOP	scorefxn_pack
	)

Constructor with arguments: The first argument is a DockJumps vector. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing.

References movable_jumps(), movable_jumps_, set_default(), and protocols::moves::Mover::type().

protocols::docking::DockMCMCycle::~DockMCMCycle ( )

overridedefault

Member Function Documentation

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

overridevirtual

decides what to call according to options

Implements protocols::moves::Mover.

References dock_mcm_cycle_, init_mc(), and protocols::docking::TR().

protocols::moves::MoverOP protocols::docking::DockMCMCycle::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::docking::DockMCMCycle::get_mc ( )

inline

References mc_.

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

overridevirtual

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

Implements protocols::moves::Mover.

void protocols::docking::DockMCMCycle::init_mc ( core::pose::Pose & pose )

References mc_, setup_protocol(), show(), and protocols::docking::TR().

Referenced by apply().

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

References movable_jumps_.

Referenced by DockMCMCycle().

void protocols::docking::DockMCMCycle::reset_cycle_index ( )

References dock_mcm_cycle_.

void protocols::docking::DockMCMCycle::set_default ( )

Sets the default values for all members.

References core::scoring::get_score_function(), mc_, min_tolerance_, min_type_, movable_jumps_, movemap_, nb_list_, repack_period_, rot_magnitude_, rtmin_, scmin_, scorefxn_, scorefxn_pack_, tf_, and trans_magnitude_.

Referenced by DockMCMCycle().

void protocols::docking::DockMCMCycle::set_min_type ( std::string min_type )

inline

References min_type_.

void protocols::docking::DockMCMCycle::set_move_map ( core::kinematics::MoveMapOP movemap )

References movemap_.

void protocols::docking::DockMCMCycle::set_rot_magnitude ( core::Real value )

inline

References rot_magnitude_.

void protocols::docking::DockMCMCycle::set_rtmin ( bool setting )

inline

References rtmin_.

void protocols::docking::DockMCMCycle::set_scmin ( bool setting )

inline

References scmin_.

void protocols::docking::DockMCMCycle::set_task_factory ( core::pack::task::TaskFactoryCOP tf )

References tf_.

void protocols::docking::DockMCMCycle::setup_protocol ( core::pose::Pose & pose )

private

main entrance to do monte carlo minimization

single cycle of mcm minimization. Then it is rigid-body minimized to a stringent tolerance.

Remarks

References: docking_mcm_protocol from docking_minimize.cc: pose_docking_monte_carlo_minimize from pose_docking.cc

Author: Monica Berrondo

References dock_mcm_cycle_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, core::pack::pack_rotamers(), protocols::rigid::partner_downstream, repack_period_, rot_magnitude_, rtmin_, scmin_, scorefxn_, scorefxn_pack_, tf_, and trans_magnitude_.

Referenced by init_mc().

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

overridevirtual

Show the complete setup of the docking protocol

Reimplemented from protocols::moves::Mover.

Referenced by init_mc().

Friends And Related Function Documentation

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

friend

Member Data Documentation

moves::CycleMoverOP protocols::docking::DockMCMCycle::dock_mcm_cycle_

private

Referenced by apply(), reset_cycle_index(), and setup_protocol().

moves::MonteCarloOP protocols::docking::DockMCMCycle::mc_

private

Referenced by get_mc(), init_mc(), set_default(), and setup_protocol().

core::Real protocols::docking::DockMCMCycle::min_tolerance_

private

Referenced by set_default(), and setup_protocol().

std::string protocols::docking::DockMCMCycle::min_type_

private

Referenced by set_default(), set_min_type(), and setup_protocol().

DockJumps protocols::docking::DockMCMCycle::movable_jumps_

private

Referenced by DockMCMCycle(), movable_jumps(), protocols::docking::operator<<(), and set_default().

core::kinematics::MoveMapOP protocols::docking::DockMCMCycle::movemap_

private

Referenced by set_default(), set_move_map(), and setup_protocol().

bool protocols::docking::DockMCMCycle::nb_list_

private

Referenced by set_default(), and setup_protocol().

core::Size protocols::docking::DockMCMCycle::repack_period_

private

task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF! init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory

Referenced by set_default(), and setup_protocol().

core::Real protocols::docking::DockMCMCycle::rot_magnitude_

private

Referenced by protocols::docking::operator<<(), set_default(), set_rot_magnitude(), and setup_protocol().