this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options More...

#include <DockingInitialPerturbation.hh>

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

	DockingInitialPerturbation (core::Size const rb_jump, bool const slide=true)
	Constructor with two arguments. The first is the jump number to dock over, the second is a boolean (true will use slide into contact, false will not). More...

	DockingInitialPerturbation (DockJumps const movable_jumps, bool const slide=true)
	Constructor with two arguments. The first is the DockJumps, the second is a boolean (true will use slide into contact, false will not). More...

	~DockingInitialPerturbation ()

virtual void	apply (core::pose::Pose &pose)
	Make starting perturbations for rigid body moves. More...

void	apply_body (core::pose::Pose &pose, core::Size jump_number)

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

void	init ()
	Calls set_dault, register_from_options and init_from_options. More...

void	set_default ()
	Sets members to default values. More...

void	init_from_options ()
	Assigns user specified values to primitive members using command line options. More...

void	set_randomize1 (bool randomize1)
	set functions More...

void	set_randomize2 (bool randomize2)

void	set_use_ellipsoidal_randomization (bool use_ellipsoidal_randomization)

void	set_dock_pert (utility::vector1< core::Real > dock_pert)

void	set_uniform_trans (core::Real uniform_trans)

void	set_spin (bool spin)

void	set_center (bool center)

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	zhe for rosetta_scripts More...

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

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

void	set_type (std::string const &setting)

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)

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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

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

Static Public Member Functions
static void	register_options ()
	Associates relevant options with the DockingInitialPerturbation class. More...

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...

Private Attributes
bool	slide_
	do slide into context? More...

DockJumps	movable_jumps_

bool	randomize1_

bool	randomize2_

bool	use_ellipsoidal_randomization_

bool	spin_

bool	if_dock_pert_

bool	if_uniform_trans_

bool	multiple_jumps_

bool	center_at_interface_

utility::vector1< core::Real >	dock_pert_

core::Real	uniform_trans_

core::Vector	slide_axis_

core::Vector	spin_center_

protocols::docking::RigidBodyInfoOP	rigid_body_info_

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 protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

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...

Detailed Description

this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options

Constructor & Destructor Documentation

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation ( )

Default constructor.

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

Referenced by clone().

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation	(	core::Size const	rb_jump,
		bool const	slide = `true`
	)

Constructor with two arguments. The first is the jump number to dock over, the second is a boolean (true will use slide into contact, false will not).

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

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation	(	DockJumps const	movable_jumps,
		bool const	slide = `true`
	)

Constructor with two arguments. The first is the DockJumps, the second is a boolean (true will use slide into contact, false will not).

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

protocols::docking::DockingInitialPerturbation::~DockingInitialPerturbation ( )

Member Function Documentation

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

virtual

Make starting perturbations for rigid body moves.

initial_perturbation

Detailed: There are several ways to perturb the structure before beginning: the search; they are controlled through command-line flags At the end, partners are slid into contact and scored (including mc_reset). Also, they are tested for passing the FAB filter.

References: see dock_structure or pose_docking from rosetta++

Authors: Monica Berrondo June 14 2007

Last Modified: October 17 2007

Implements protocols::moves::Mover.

References apply_body(), movable_jumps_, rigid_body_info_, runtime_assert, protocols::TR, and utility_exit_with_message.

Referenced by protocols::docking::DockingProtocol::apply(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), and protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation().

void protocols::docking::DockingInitialPerturbation::apply_body	(	core::pose::Pose &	pose,
		core::Size	jump_number
	)

References protocols::docking::EllipsoidalRandomizationMover::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::docking::FaDockingSlideIntoContact::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::UniformSphereTransMover::apply(), center_at_interface_, dock_pert_, protocols::docking::EllipsoidalRandomizationMover::get_slide_axis(), protocols::docking::EllipsoidalRandomizationMover::get_spin_center(), if_dock_pert_, if_uniform_trans_, core::pose::Pose::is_fullatom(), numeric::xyzVector< class >::length(), protocols::rigid::partner_downstream, protocols::rigid::partner_upstream, randomize1_, randomize2_, rot(), protocols::rigid::RigidBodySpinMover::rot_center(), slide_, slide_axis_, spin_, protocols::rigid::RigidBodySpinMover::spin_axis(), spin_center_, protocols::TR, trans(), uniform_trans_, and use_ellipsoidal_randomization_.

Referenced by apply().

protocols::moves::MoverOP protocols::docking::DockingInitialPerturbation::clone ( ) const

virtual

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.

References DockingInitialPerturbation().

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

virtual

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

Implements protocols::moves::Mover.

void protocols::docking::DockingInitialPerturbation::init ( void )

Calls set_dault, register_from_options and init_from_options.

References init_from_options(), and set_default().

Referenced by DockingInitialPerturbation().

void protocols::docking::DockingInitialPerturbation::init_from_options ( )

Assigns user specified values to primitive members using command line options.

References option, set_center(), set_dock_pert(), set_randomize1(), set_randomize2(), set_spin(), set_uniform_trans(), set_use_ellipsoidal_randomization(), protocols::TR, and user.

Referenced by init().

void protocols::docking::DockingInitialPerturbation::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data_map,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)