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

#include <DockingInitialPerturbation.hh>

Inheritance diagram for protocols::docking::DockingInitialPerturbation:

[legend]

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, bool const autofoldtree=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 () override

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

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

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	or_randomize2 (bool randomize2)

void	set_use_ellipsoidal_randomization (bool use_ellipsoidal_randomization)

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

void	set_tilt (utility::vector1< core::Real > const &tilt)

void	set_tilt1_center (std::string const &tilt_center)

void	set_tilt2_center (std::string const &tilt_center)

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 &) override
	zhe for rosetta_scripts More...

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

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...

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

static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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...

bool	autofoldtree_
	adjust foldtree in Ellipsoidal docking? 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_

utility::vector1< core::Real >	tilt_

std::string	tilt1_center_

std::string	tilt2_center_

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 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

◆ DockingInitialPerturbation() [1/3]

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

Default constructor.

References init(), movable_jumps_, and multiple_jumps_.

◆ DockingInitialPerturbation() [2/3]

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_, and multiple_jumps_.

◆ DockingInitialPerturbation() [3/3]

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation	(	DockJumps const	movable_jumps,
		bool const	slide = `true`,
		bool const	autofoldtree = `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_, and multiple_jumps_.

◆ ~DockingInitialPerturbation()

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

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Make starting perturbations for rigid body moves.

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++

Author: Monica Berrondo June 14 2007

Implements protocols::moves::Mover.

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

Referenced by protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs().

◆ apply_body()

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::RigidBodyTiltMover::apply(), protocols::rigid::UniformSphereTransMover::apply(), autofoldtree_, 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(), core::pose::parse_resnum(), protocols::rigid::partner_downstream, protocols::rigid::partner_upstream, randomize1_, randomize2_, rot(), protocols::rigid::RigidBodySpinMover::rot_center(), slide_, slide_axis_, spin_, protocols::rigid::RigidBodyTiltMover::spin_axis(), protocols::rigid::RigidBodySpinMover::spin_axis(), spin_center_, tilt1_center_, tilt2_center_, tilt_, protocols::docking::TR(), trans(), uniform_trans_, and use_ellipsoidal_randomization_.

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::docking::DockingInitialPerturbation::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.

◆ get_name()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ init()

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().

◆ init_from_options()

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

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

References or_randomize2(), set_center(), set_dock_pert(), set_randomize1(), set_spin(), set_tilt(), set_tilt1_center(), set_tilt2_center(), set_uniform_trans(), set_use_ellipsoidal_randomization(), and protocols::docking::TR().

Referenced by init().

◆ mover_name()

std::string protocols::docking::DockingInitialPerturbation::mover_name ( )

static

Referenced by get_name(), protocols::docking::DockingInitialPerturbationCreator::keyname(), and provide_xml_schema().

◆ or_randomize2()

void protocols::docking::DockingInitialPerturbation::or_randomize2 ( bool randomize2 )

inline

References randomize2_.

Referenced by init_from_options().

◆ parse_my_tag()

void protocols::docking::DockingInitialPerturbation::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data_map
	)

overridevirtual

zhe for rosetta_scripts

Reimplemented from protocols::moves::Mover.

References dock_pert_, rigid_body_info_, set_center(), set_dock_pert(), set_randomize1(), set_randomize2(), set_spin(), set_uniform_trans(), set_use_ellipsoidal_randomization(), slide_, and protocols::docking::TR().

◆ provide_xml_schema()

void protocols::docking::DockingInitialPerturbation::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::docking::DockingInitialPerturbationCreator::provide_xml_schema().

◆ register_options()

void protocols::docking::DockingInitialPerturbation::register_options ( )

static

Associates relevant options with the DockingInitialPerturbation class.

◆ set_center()

void protocols::docking::DockingInitialPerturbation::set_center ( bool center )

inline

References core::conformation::membrane::center, and center_at_interface_.

Referenced by init_from_options(), and parse_my_tag().

◆ set_default()

void protocols::docking::DockingInitialPerturbation::set_default ( )

Sets members to default values.

References center_at_interface_, if_dock_pert_, if_uniform_trans_, randomize1_, randomize2_, slide_axis_, spin_, spin_center_, and use_ellipsoidal_randomization_.

Referenced by init().

◆ set_dock_pert()

void protocols::docking::DockingInitialPerturbation::set_dock_pert ( utility::vector1< core::Real > const & dock_pert )

inline

References dock_pert_, and if_dock_pert_.

Referenced by init_from_options(), and parse_my_tag().

◆ set_randomize1()

void protocols::docking::DockingInitialPerturbation::set_randomize1 ( bool randomize1 )

inline

set functions

References randomize1_.

Referenced by init_from_options(), and parse_my_tag().

◆ set_randomize2()

void protocols::docking::DockingInitialPerturbation::set_randomize2 ( bool randomize2 )

inline

References randomize2_.

Referenced by parse_my_tag().

◆ set_spin()

void protocols::docking::DockingInitialPerturbation::set_spin ( bool spin )

inline

References spin_.

Referenced by init_from_options(), and parse_my_tag().

◆ set_tilt()

void protocols::docking::DockingInitialPerturbation::set_tilt ( utility::vector1< core::Real > const & tilt )

inline

References tilt_.

Referenced by init_from_options().

◆ set_tilt1_center()

void protocols::docking::DockingInitialPerturbation::set_tilt1_center ( std::string const & tilt_center )

inline

References tilt1_center_.

Referenced by init_from_options().

◆ set_tilt2_center()

void protocols::docking::DockingInitialPerturbation::set_tilt2_center ( std::string const & tilt_center )

inline

References tilt2_center_.

Referenced by init_from_options().

◆ set_uniform_trans()

void protocols::docking::DockingInitialPerturbation::set_uniform_trans ( core::Real uniform_trans )

inline

References if_uniform_trans_, and uniform_trans_.

Referenced by init_from_options(), and parse_my_tag().

◆ set_use_ellipsoidal_randomization()

void protocols::docking::DockingInitialPerturbation::set_use_ellipsoidal_randomization ( bool use_ellipsoidal_randomization )

inline

References use_ellipsoidal_randomization_.

Referenced by init_from_options(), and parse_my_tag().

Member Data Documentation

◆ autofoldtree_

bool protocols::docking::DockingInitialPerturbation::autofoldtree_

private

adjust foldtree in Ellipsoidal docking?

Referenced by apply_body().

◆ center_at_interface_

bool protocols::docking::DockingInitialPerturbation::center_at_interface_

private

Referenced by apply_body(), set_center(), and set_default().

◆ dock_pert_

utility::vector1< core::Real > protocols::docking::DockingInitialPerturbation::dock_pert_

private

Referenced by apply_body(), parse_my_tag(), and set_dock_pert().

◆ if_dock_pert_

bool protocols::docking::DockingInitialPerturbation::if_dock_pert_

private

Referenced by apply_body(), set_default(), and set_dock_pert().

◆ if_uniform_trans_

bool protocols::docking::DockingInitialPerturbation::if_uniform_trans_

private

Referenced by apply_body(), set_default(), and set_uniform_trans().

◆ movable_jumps_

DockJumps protocols::docking::DockingInitialPerturbation::movable_jumps_

private

Referenced by apply(), and DockingInitialPerturbation().

◆ multiple_jumps_

bool protocols::docking::DockingInitialPerturbation::multiple_jumps_

private

Referenced by DockingInitialPerturbation().

◆ randomize1_

bool protocols::docking::DockingInitialPerturbation::randomize1_

private

Referenced by apply_body(), set_default(), and set_randomize1().

◆ randomize2_

bool protocols::docking::DockingInitialPerturbation::randomize2_

private

Referenced by apply_body(), or_randomize2(), set_default(), and set_randomize2().

◆ rigid_body_info_

protocols::docking::RigidBodyInfoOP protocols::docking::DockingInitialPerturbation::rigid_body_info_

private

Referenced by apply(), and parse_my_tag().

◆ slide_

bool protocols::docking::DockingInitialPerturbation::slide_

private

do slide into context?

Referenced by apply_body(), and parse_my_tag().

◆ slide_axis_

core::Vector protocols::docking::DockingInitialPerturbation::slide_axis_

private

Referenced by apply_body(), and set_default().

◆ spin_

bool protocols::docking::DockingInitialPerturbation::spin_

private

Referenced by apply_body(), set_default(), and set_spin().

◆ spin_center_

core::Vector protocols::docking::DockingInitialPerturbation::spin_center_

private

Referenced by apply_body(), and set_default().

◆ tilt1_center_

std::string protocols::docking::DockingInitialPerturbation::tilt1_center_

private

Referenced by apply_body(), and set_tilt1_center().

◆ tilt2_center_

std::string protocols::docking::DockingInitialPerturbation::tilt2_center_

private

Referenced by apply_body(), and set_tilt2_center().

◆ tilt_

utility::vector1< core::Real > protocols::docking::DockingInitialPerturbation::tilt_

private

Referenced by apply_body(), and set_tilt().

◆ uniform_trans_

core::Real protocols::docking::DockingInitialPerturbation::uniform_trans_

private

Referenced by apply_body(), and set_uniform_trans().

◆ use_ellipsoidal_randomization_

bool protocols::docking::DockingInitialPerturbation::use_ellipsoidal_randomization_

private

Referenced by apply_body(), set_default(), and set_use_ellipsoidal_randomization().

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

src/protocols/docking/DockingInitialPerturbation.hh
src/protocols/docking/DockingInitialPerturbation.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DockingInitialPerturbation() [1/3]

◆ DockingInitialPerturbation() [2/3]

◆ DockingInitialPerturbation() [3/3]

◆ ~DockingInitialPerturbation()

Member Function Documentation

◆ apply()

◆ apply_body()

◆ clone()

◆ get_name()

◆ init()

◆ init_from_options()

◆ mover_name()

◆ or_randomize2()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ register_options()

◆ set_center()

◆ set_default()

◆ set_dock_pert()

◆ set_randomize1()

◆ set_randomize2()

◆ set_spin()

◆ set_tilt()

◆ set_tilt1_center()

◆ set_tilt2_center()

◆ set_uniform_trans()

◆ set_use_ellipsoidal_randomization()

Member Data Documentation

◆ autofoldtree_

◆ center_at_interface_

◆ dock_pert_

◆ if_dock_pert_

◆ if_uniform_trans_

◆ movable_jumps_

◆ multiple_jumps_

◆ randomize1_

◆ randomize2_

◆ rigid_body_info_

◆ slide_

◆ slide_axis_

◆ spin_

◆ spin_center_

◆ tilt1_center_

◆ tilt2_center_

◆ tilt_

◆ uniform_trans_

◆ use_ellipsoidal_randomization_