#include <DockingHighRes.hh>

Inheritance diagram for protocols::docking::DockingHighRes:

Collaboration diagram for protocols::docking::DockingHighRes:

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

	DockingHighRes (core::Size const rb_jump)
	Constructor with one argument - the jump number to dock over. More...

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

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

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

	DockingHighRes (DockingHighRes const &old_instance)

virtual	~DockingHighRes ()

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

void	set_ignore_default_task (bool ignore_default_task)

bool	ignore_default_task ()

void	set_scorefxn (core::scoring::ScoreFunctionOP scorefxn)

void	set_scorefxn_pack (core::scoring::ScoreFunctionOP scorefxn_pack)

DockJumps &	movable_jumps ()

DockJumps const &	movable_jumps () const

core::pack::task::TaskFactoryCOP	task_factory ()

virtual void	apply (core::pose::Pose &pose)=0

virtual std::string	get_name () const =0
	Each derived class must specify its name. The class name. More...

void	set_sc_min (bool sc_min)

void	set_rt_min (bool rt_min)

void	set_partners (std::string partners)

void	set_interface_definition_task_operation (protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition)

void	set_additional_task_operarations (utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)

void	add_additional_task_operaration (core::pack::task::operation::TaskOperationOP task_operation)

utility::vector1 < core::pack::task::operation::TaskOperationOP >	get_additional_task_operarations ()

bool	sc_min ()

bool	rt_min ()

std::string	partners ()

core::scoring::ScoreFunctionOP	scorefxn () const

core::scoring::ScoreFunctionOP	scorefxn_pack () const

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Protected Member Functions
protocols::docking::DockTaskFactoryOP	tf2 ()

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 Types
typedef core::Real	Real

Private Member Functions
void	init (DockJumps const movable_jumps)

Private Attributes
bool	sc_min_

bool	rt_min_

std::string	partners_

core::scoring::ScoreFunctionOP	scorefxn_

core::scoring::ScoreFunctionOP	scorefxn_pack_

DockJumps	movable_jumps_

core::pack::task::TaskFactoryOP	tf_

protocols::docking::DockTaskFactoryOP	tf2_

bool	ignore_default_task_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Detailed Description

Definition at line 48 of file DockingHighRes.hh.

Member Typedef Documentation

typedef core::Real protocols::docking::DockingHighRes::Real

private

Definition at line 50 of file DockingHighRes.hh.

Constructor & Destructor Documentation

protocols::docking::DockingHighRes::DockingHighRes ( )

Default constructor.

Definition at line 65 of file DockingHighRes.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), init(), scorefxn_, and scorefxn_pack_.

protocols::docking::DockingHighRes::DockingHighRes ( core::Size const rb_jump)

Constructor with one argument - the jump number to dock over.

Definition at line 72 of file DockingHighRes.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), init(), scorefxn_, and scorefxn_pack_.

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

Constructor with two arguments. The first is thejump number, the second is a scorefunction that will be used for docking and packing.

Definition at line 83 of file DockingHighRes.cc.

References init().

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

Constructor with three arguments. The first is the jump number, the second is a scorefunction that will be used for docking and the third is a scorefunction that will be used for packing.

Definition at line 93 of file DockingHighRes.cc.

References init().

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

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

Definition at line 104 of file DockingHighRes.cc.

References init().

protocols::docking::DockingHighRes::DockingHighRes ( DockingHighRes const & old_instance)

Definition at line 113 of file DockingHighRes.cc.

References movable_jumps_, partners_, rt_min_, sc_min_, scorefxn_, scorefxn_pack_, tf2_, and tf_.

protocols::docking::DockingHighRes::~DockingHighRes ( )

virtual

Definition at line 145 of file DockingHighRes.cc.

Member Function Documentation

void protocols::docking::DockingHighRes::add_additional_task_operaration ( core::pack::task::operation::TaskOperationOP task_operation)

Definition at line 188 of file DockingHighRes.cc.

References tf2_.

virtual void protocols::docking::DockingHighRes::apply ( core::pose::Pose & pose)

pure virtual

Implements protocols::moves::Mover.

Implemented in protocols::docking::InterfaceSidechainMinMover, protocols::docking::DockingHighResLegacy, protocols::docking::DockMCMProtocol, protocols::docking::DockMinMover, protocols::docking::SidechainMinMover, protocols::antibody2::SnugDock, protocols::docking::DockingPrepackProtocol, and protocols::docking::DockingEnsemblePrepackProtocol.

utility::vector1< core::pack::task::operation::TaskOperationOP > protocols::docking::DockingHighRes::get_additional_task_operarations ( )

Definition at line 193 of file DockingHighRes.cc.

References tf2_.

virtual std::string protocols::docking::DockingHighRes::get_name ( ) const

pure virtual

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

Implements protocols::moves::Mover.

Implemented in protocols::docking::InterfaceSidechainMinMover, protocols::docking::DockingHighResLegacy, protocols::docking::DockMCMProtocol, protocols::docking::DockMinMover, protocols::docking::SidechainMinMover, protocols::docking::DockingPrepackProtocol, protocols::antibody2::SnugDock, and protocols::docking::DockingEnsemblePrepackProtocol.

bool protocols::docking::DockingHighRes::ignore_default_task ( )

Definition at line 158 of file DockingHighRes.cc.

References ignore_default_task_.

Referenced by protocols::docking::DockMCMProtocol::apply(), and set_ignore_default_task().

void protocols::docking::DockingHighRes::init ( DockJumps const movable_jumps)

private

Definition at line 131 of file DockingHighRes.cc.

References ignore_default_task_, movable_jumps(), movable_jumps_, partners_, rt_min_, sc_min_, tf2_, tf_, and protocols::moves::Mover::type().

Referenced by DockingHighRes().

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

inline

Definition at line 100 of file DockingHighRes.hh.

References movable_jumps_.

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

inline

Definition at line 101 of file DockingHighRes.hh.

References movable_jumps_.

std::string protocols::docking::DockingHighRes::partners ( )

inline

Definition at line 119 of file DockingHighRes.hh.

References partners_.

Referenced by protocols::docking::DockingPrepackProtocol::finalize_setup(), protocols::docking::DockingEnsemblePrepackProtocol::finalize_setup(), and set_partners().

bool protocols::docking::DockingHighRes::rt_min ( )

inline

Definition at line 118 of file DockingHighRes.hh.

References rt_min_.

Referenced by protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), set_rt_min(), protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers(), and protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers().

bool protocols::docking::DockingHighRes::sc_min ( )

inline

Definition at line 117 of file DockingHighRes.hh.

References sc_min_.

Referenced by protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), set_sc_min(), protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers(), and protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers().

core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn ( ) const

Definition at line 198 of file DockingHighRes.cc.

References scorefxn_.

core::scoring::ScoreFunctionOP protocols::docking::DockingHighRes::scorefxn_pack ( ) const

Definition at line 203 of file DockingHighRes.cc.

References scorefxn_pack_.

Referenced by protocols::docking::DockMCMProtocol::apply(), protocols::docking::DockMCMProtocol::scorefxn_packing(), protocols::docking::DockingHighResLegacy::set_dock_mcm_protocol(), protocols::docking::DockingHighResLegacy::set_dock_ppk_protocol(), set_scorefxn_pack(), protocols::antibody2::SnugDock::setup_objects(), protocols::docking::DockingEnsemblePrepackProtocol::setup_pack_operation_movers(), and protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers().

void protocols::docking::DockingHighRes::set_additional_task_operarations ( utility::vector1< core::pack::task::operation::TaskOperationOP > additional_task_operations)

Definition at line 183 of file DockingHighRes.cc.

References tf2_.

void protocols::docking::DockingHighRes::set_ignore_default_task ( bool ignore_default_task)

Definition at line 153 of file DockingHighRes.cc.

References ignore_default_task(), and ignore_default_task_.

void protocols::docking::DockingHighRes::set_interface_definition_task_operation ( protocols::toolbox::task_operations::InterfaceTaskOperationOP interface_definition)

Definition at line 178 of file DockingHighRes.cc.

References tf2_.

void protocols::docking::DockingHighRes::set_partners ( std::string partners)

inline

Definition at line 110 of file DockingHighRes.hh.

References partners(), and partners_.

Referenced by protocols::docking::DockingPrepackProtocol::init_from_options(), and protocols::docking::DockingEnsemblePrepackProtocol::init_from_options().

void protocols::docking::DockingHighRes::set_rt_min ( bool rt_min)

inline

Definition at line 109 of file DockingHighRes.hh.

References rt_min(), and rt_min_.

Referenced by protocols::docking::DockingPrepackProtocol::init_from_options(), and protocols::docking::DockingEnsemblePrepackProtocol::init_from_options().