#include <DockingPrepackProtocol.hh>

Inheritance diagram for protocols::docking::DockingPrepackProtocol:

Collaboration diagram for protocols::docking::DockingPrepackProtocol:

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

	~DockingPrepackProtocol ()

void	setup_defaults ()
	Assigns default values to members. More...

void	setup_pack_operation_movers ()
	Instantiates and configures movers used by DockingPrepackProtocol More...

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

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

void	score_and_output (std::string filename, core::pose::Pose &)
	Scores and outputs the pose - jd2 compatible. More...

void	set_dock_ppk (bool dock_ppk)

Public Member Functions inherited from protocols::docking::DockingHighRes
	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 ()

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

Private Member Functions
void	finalize_setup (core::pose::Pose &)
	Performs setup that requires a pose. More...

void	register_options ()

void	init_from_options ()

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...

Protected Member Functions inherited from protocols::docking::DockingHighRes
protocols::docking::DockTaskFactoryOP	tf2 ()

Detailed Description

Definition at line 46 of file DockingPrepackProtocol.hh.

Constructor & Destructor Documentation

protocols::docking::DockingPrepackProtocol::DockingPrepackProtocol ( )

Default constructor.

Definition at line 66 of file DockingPrepackProtocol.cc.

References init_from_options(), register_options(), setup_defaults(), and protocols::moves::Mover::type().

protocols::docking::DockingPrepackProtocol::~DockingPrepackProtocol ( )

Definition at line 82 of file DockingPrepackProtocol.cc.

Member Function Documentation

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

virtual

Implements protocols::docking::DockingHighRes.

Definition at line 165 of file DockingPrepackProtocol.cc.

References dock_ppk_, fa_dock_slide_into_contact_, finalize_setup(), protocols::docking::DockingHighRes::movable_jumps(), pack_operations_, score_and_output(), and trans_magnitude_.

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

private

Performs setup that requires a pose.

Definition at line 151 of file DockingPrepackProtocol.cc.

References protocols::docking::DockingHighRes::movable_jumps(), protocols::docking::DockingHighRes::partners(), protocols::docking::setup_foldtree(), setup_pack_operation_movers(), and protocols::docking::DockingHighRes::tf2().

Referenced by apply().

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

virtual

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

Implements protocols::docking::DockingHighRes.

Definition at line 199 of file DockingPrepackProtocol.cc.

void protocols::docking::DockingPrepackProtocol::init_from_options ( )

private

Definition at line 85 of file DockingPrepackProtocol.cc.

References set_dock_ppk(), protocols::docking::DockingHighRes::set_partners(), protocols::docking::DockingHighRes::set_rt_min(), and protocols::docking::DockingHighRes::set_sc_min().

Referenced by DockingPrepackProtocol().

void protocols::docking::DockingPrepackProtocol::register_options ( )

private

Definition at line 106 of file DockingPrepackProtocol.cc.

Referenced by DockingPrepackProtocol().

void protocols::docking::DockingPrepackProtocol::score_and_output	(	std::string	filename,
		core::pose::Pose &	pose
	)

Scores and outputs the pose - jd2 compatible.

Definition at line 115 of file DockingPrepackProtocol.cc.

References protocols::jd2::JobDistributor::current_job(), protocols::jd2::JobDistributor::get_instance(), and protocols::docking::DockingHighRes::scorefxn().

Referenced by apply().

void protocols::docking::DockingPrepackProtocol::set_dock_ppk ( bool dock_ppk)

Definition at line 101 of file DockingPrepackProtocol.cc.

References dock_ppk_.

Referenced by init_from_options().

void protocols::docking::DockingPrepackProtocol::setup_defaults ( )

Assigns default values to members.

Definition at line 75 of file DockingPrepackProtocol.cc.

References dock_ppk_, pack_operations_, and trans_magnitude_.

Referenced by DockingPrepackProtocol().

void protocols::docking::DockingPrepackProtocol::setup_pack_operation_movers ( )

Instantiates and configures movers used by DockingPrepackProtocol

Definition at line 129 of file DockingPrepackProtocol.cc.

References pack_operations_, prepack_full_repack_, protocols::docking::DockingHighRes::rt_min(), rtmin_mover_, protocols::docking::DockingHighRes::sc_min(), scmin_mover_, protocols::docking::DockingHighRes::scorefxn_pack(), and protocols::docking::DockingHighRes::task_factory().

Referenced by finalize_setup().

Member Data Documentation

bool protocols::docking::DockingPrepackProtocol::dock_ppk_

private

Definition at line 79 of file DockingPrepackProtocol.hh.

Referenced by apply(), set_dock_ppk(), and setup_defaults().

FaDockingSlideIntoContactOP protocols::docking::DockingPrepackProtocol::fa_dock_slide_into_contact_

private

Definition at line 80 of file DockingPrepackProtocol.hh.

Referenced by apply().

SequenceMoverOP protocols::docking::DockingPrepackProtocol::pack_operations_

private

Definition at line 78 of file DockingPrepackProtocol.hh.

Referenced by apply(), setup_defaults(), and setup_pack_operation_movers().

protocols::simple_moves::PackRotamersMoverOP protocols::docking::DockingPrepackProtocol::prepack_full_repack_

private

Definition at line 76 of file DockingPrepackProtocol.hh.

Referenced by setup_pack_operation_movers().

protocols::simple_moves::RotamerTrialsMinMoverOP protocols::docking::DockingPrepackProtocol::rtmin_mover_

private

Definition at line 75 of file DockingPrepackProtocol.hh.

Referenced by setup_pack_operation_movers().

SidechainMinMoverOP protocols::docking::DockingPrepackProtocol::scmin_mover_

private

Definition at line 77 of file DockingPrepackProtocol.hh.

Referenced by setup_pack_operation_movers().

utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingPrepackProtocol::trans_away_vec_

private

Definition at line 70 of file DockingPrepackProtocol.hh.

utility::vector1< rigid::RigidBodyTransMoverOP > protocols::docking::DockingPrepackProtocol::trans_back_vec_

private

Definition at line 71 of file DockingPrepackProtocol.hh.

core::Real protocols::docking::DockingPrepackProtocol::trans_magnitude_

private

Definition at line 73 of file DockingPrepackProtocol.hh.

Referenced by apply(), and setup_defaults().

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

src/protocols/docking/DockingPrepackProtocol.hh
src/protocols/docking/DockingPrepackProtocol.cc

Private Attributes
utility::vector1 < rigid::RigidBodyTransMoverOP >	trans_away_vec_

utility::vector1 < rigid::RigidBodyTransMoverOP >	trans_back_vec_

core::Real	trans_magnitude_

protocols::simple_moves::RotamerTrialsMinMoverOP	rtmin_mover_

protocols::simple_moves::PackRotamersMoverOP	prepack_full_repack_

SidechainMinMoverOP	scmin_mover_

SequenceMoverOP	pack_operations_

bool	dock_ppk_

FaDockingSlideIntoContactOP	fa_dock_slide_into_contact_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation