Docks two proteins together in the membrane bilayer. More...

#include <MPDockingMover.hh>

Inheritance diagram for protocols::docking::membrane::MPDockingMover:

[legend]

Public Member Functions
	MPDockingMover (bool lowres=true, bool highres=true)
	Constructors ///. More...

	MPDockingMover (core::Size jump_num, bool lowres=true, bool highres=true)
	Constructor with jump number to dock over. More...

	MPDockingMover (MPDockingMover const &src)
	Copy Constructor. More...

	~MPDockingMover () override
	Destructor. More...

protocols::moves::MoverOP	clone () const override
	Create a Clone of this mover. More...

protocols::moves::MoverOP	fresh_instance () const override
	Create a Fresh Instance of this Mover. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
	Rosetta Scripts Methods ///. More...

void	set_cycles_inner (core::Size cycles_inner)
	Mover Methods ///. More...

void	set_cycles_outer (core::Size cycles_outer)
	Set outer cycles in DockingProtocol. More...

void	apply (Pose &pose) override
	Add membrane components to the pose, then dock proteins along the flexible jump. 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...

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 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 Member Functions
void	set_defaults (const Pose &pose)

void	set_docking_protocol ()

void	register_options ()

void	init_from_cmd ()

void	finalize_setup ()

Private Attributes
protocols::membrane::AddMembraneMoverOP	add_membrane_mover_

DockingProtocolOP	docking_protocol_

bool	lowres_

bool	highres_

core::scoring::ScoreFunctionOP	lowres_scorefxn_

core::scoring::ScoreFunctionOP	highres_scorefxn_

core::Vector	center_

core::Vector	normal_

core::Size	jump_num_

core::pose::PoseOP	native_

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

Docks two proteins together in the membrane bilayer.

Requires running mpdocking_setup first to create a single pose; Should also run docking_prepack before

Constructor & Destructor Documentation

◆ MPDockingMover() [1/3]

protocols::docking::membrane::MPDockingMover::MPDockingMover	(	bool	lowres = `true`,
		bool	highres = `true`
	)

Constructors ///.

Default Constructor

Docks two proteins with default normal=(0,0,1) and center=(0,0,0)

◆ MPDockingMover() [2/3]

protocols::docking::membrane::MPDockingMover::MPDockingMover	(	core::Size	jump_num,
		bool	lowres = `true`,
		bool	highres = `true`
	)

Constructor with jump number to dock over.

Default Constructor.

Docks two proteins with default normal=(0,0,1) and center=(0,0,0)

◆ MPDockingMover() [3/3]

protocols::docking::membrane::MPDockingMover::MPDockingMover ( MPDockingMover const & src )

Copy Constructor.

Create a deep copy of this mover

◆ ~MPDockingMover()

protocols::docking::membrane::MPDockingMover::~MPDockingMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::docking::membrane::MPDockingMover::apply ( Pose & pose )

overridevirtual

Add membrane components to the pose, then dock proteins along the flexible jump.

Implements protocols::moves::Mover.

References add_membrane_mover_, docking_protocol_, finalize_setup(), core::pose::Pose::fold_tree(), highres_scorefxn_, init_from_cmd(), protocols::membrane::is_membrane_fixed(), lowres_scorefxn_, core::pose::Pose::membrane_info(), register_options(), core::kinematics::FoldTree::reorder(), set_defaults(), set_docking_protocol(), core::kinematics::FoldTree::show(), core::pose::Pose::size(), and protocols::docking::TR().

◆ clone()

protocols::moves::MoverOP protocols::docking::membrane::MPDockingMover::clone ( ) const

overridevirtual

Create a Clone of this mover.

Reimplemented from protocols::moves::Mover.

◆ finalize_setup()

void protocols::docking::membrane::MPDockingMover::finalize_setup ( )

private

References add_membrane_mover_, docking_protocol_, native_, core::id::to_string(), and protocols::docking::TR().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::docking::membrane::MPDockingMover::fresh_instance ( ) const

overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::docking::membrane::MPDockingMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ init_from_cmd()

void protocols::docking::membrane::MPDockingMover::init_from_cmd ( )

private

References highres_scorefxn_, lowres_scorefxn_, native_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::docking::TR().

Referenced by apply().

◆ mover_name()

std::string protocols::docking::membrane::MPDockingMover::mover_name ( )

static

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

◆ parse_my_tag()

void protocols::docking::membrane::MPDockingMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &
	)

overridevirtual

Rosetta Scripts Methods ///.

Pase Rosetta Scripts Options for this Mover.

Pase Rosetta Scripts Options for this Mover

Reimplemented from protocols::moves::Mover.

References core::conformation::membrane::center, center_, core::scoring::ScoreFunctionFactory::create_score_function(), highres_scorefxn_, jump_num_, lowres_scorefxn_, core::conformation::membrane::normal, and normal_.

◆ provide_xml_schema()

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

static

References mover_name(), protocols::docking::membrane::real_regex_pattern(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::docking::membrane::MPDockingMoverCreator::provide_xml_schema().

◆ register_options()

void protocols::docking::membrane::MPDockingMover::register_options ( )

private

Referenced by apply().

◆ set_cycles_inner()

void protocols::docking::membrane::MPDockingMover::set_cycles_inner ( core::Size cycles_inner )

Mover Methods ///.

Create a new copy of this mover.

Get the name of this Mover (MPDockingMover)

Setters for the DockingProtocol

These are set here because the mover doesn't inherit from the DockingProtocol

Return the Name of this mover (as seen by Rscripts)

Mover name for Rosetta Scripts Mover Methods ///

Get the name of this Mover (MPDockingMover)

References docking_protocol_.

◆ set_cycles_outer()

void protocols::docking::membrane::MPDockingMover::set_cycles_outer ( core::Size cycles_outer )

Set outer cycles in DockingProtocol.

References docking_protocol_.

◆ set_defaults()

void protocols::docking::membrane::MPDockingMover::set_defaults ( const Pose & pose )

private

References core::scoring::ScoreFunctionFactory::create_score_function(), highres_scorefxn_, lowres_scorefxn_, and native_.

Referenced by apply().

◆ set_docking_protocol()

void protocols::docking::membrane::MPDockingMover::set_docking_protocol ( )

private

References docking_protocol_, highres_, highres_scorefxn_, jump_num_, lowres_, lowres_scorefxn_, and protocols::docking::TR().

Referenced by apply().

Member Data Documentation

◆ add_membrane_mover_

protocols::membrane::AddMembraneMoverOP protocols::docking::membrane::MPDockingMover::add_membrane_mover_

private

Referenced by apply(), and finalize_setup().

◆ center_

core::Vector protocols::docking::membrane::MPDockingMover::center_

private

Referenced by parse_my_tag().

◆ docking_protocol_

DockingProtocolOP protocols::docking::membrane::MPDockingMover::docking_protocol_

private

Referenced by apply(), finalize_setup(), set_cycles_inner(), set_cycles_outer(), and set_docking_protocol().

◆ highres_

bool protocols::docking::membrane::MPDockingMover::highres_

private

Referenced by set_docking_protocol().

◆ highres_scorefxn_

core::scoring::ScoreFunctionOP protocols::docking::membrane::MPDockingMover::highres_scorefxn_

private

Referenced by apply(), init_from_cmd(), parse_my_tag(), set_defaults(), and set_docking_protocol().

◆ jump_num_

core::Size protocols::docking::membrane::MPDockingMover::jump_num_

private

Referenced by parse_my_tag(), and set_docking_protocol().

◆ lowres_

bool protocols::docking::membrane::MPDockingMover::lowres_

private

Referenced by set_docking_protocol().

◆ lowres_scorefxn_

core::scoring::ScoreFunctionOP protocols::docking::membrane::MPDockingMover::lowres_scorefxn_

private

Referenced by apply(), init_from_cmd(), parse_my_tag(), set_defaults(), and set_docking_protocol().

◆ native_

core::pose::PoseOP protocols::docking::membrane::MPDockingMover::native_

private

Referenced by finalize_setup(), init_from_cmd(), and set_defaults().

◆ normal_

core::Vector protocols::docking::membrane::MPDockingMover::normal_

private

Referenced by parse_my_tag().

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

src/protocols/docking/membrane/MPDockingMover.hh
src/protocols/docking/membrane/MPDockingMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MPDockingMover() [1/3]

◆ MPDockingMover() [2/3]

◆ MPDockingMover() [3/3]

◆ ~MPDockingMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ finalize_setup()

◆ fresh_instance()

◆ get_name()

◆ init_from_cmd()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ register_options()

◆ set_cycles_inner()

◆ set_cycles_outer()

◆ set_defaults()

◆ set_docking_protocol()

Member Data Documentation

◆ add_membrane_mover_

◆ center_

◆ docking_protocol_

◆ highres_

◆ highres_scorefxn_

◆ jump_num_

◆ lowres_

◆ lowres_scorefxn_

◆ native_

◆ normal_