Transform a pose into membrane coordinates based on the current embedding of the protein. More...

#include <TransformIntoMembraneMover.hh>

Inheritance diagram for protocols::membrane::TransformIntoMembraneMover:

[legend]

Public Member Functions
	TransformIntoMembraneMover ()
	Constructors ///. More...

	TransformIntoMembraneMover (core::Size jump)

	TransformIntoMembraneMover (protocols::membrane::geometry::EmbeddingDefOP current_embedding)
	Transform the protein with a user-specified protein embedding into a default membrane (defined by MEM) More...

	TransformIntoMembraneMover (core::Vector new_mem_cntr, core::Vector new_mem_norm)
	Transform the protein into user-specified membrane coordinates. More...

	TransformIntoMembraneMover (protocols::membrane::geometry::EmbeddingDefOP current_embedding, core::Vector new_mem_cntr, core::Vector new_mem_norm)
	Transform the protein into user-specified membrane coordinates. More...

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

	~TransformIntoMembraneMover () override
	Destructor. More...

protocols::moves::MoverOP	clone () const override
	Rosetta Scripts Methods ///. 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
	Pase Rosetta Scripts Options for this Mover. More...

void	use_default_membrane (bool truefalse)
	Mover Methods ///. More...

void	apply (core::pose::Pose &pose) override
	Get the name of this Mover (TransformIntoMembraneMover) 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	register_options ()
	Setup Methods ///. More...

void	init_from_cmd ()
	Initialize Mover options from the commandline. More...

Private Attributes
core::Size	jump_

core::Vector	new_mem_cntr_

core::Vector	new_mem_norm_

protocols::membrane::geometry::EmbeddingDefOP	current_embedding_

bool	use_default_membrane_

bool	user_defined_membrane_

bool	flip_if_needed_ = false

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

Transform a pose into membrane coordinates based on the current embedding of the protein.

Constructor & Destructor Documentation

◆ TransformIntoMembraneMover() [1/6]

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( )

Constructors ///.

Transform the protein into a membrane defined by MEM

Transform the protein into membrane defined by MEM, protein embedding computed from structure and spanfile

◆ TransformIntoMembraneMover() [2/6]

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( core::Size jump )

◆ TransformIntoMembraneMover() [3/6]

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( protocols::membrane::geometry::EmbeddingDefOP current_embedding )

Transform the protein with a user-specified protein embedding into a default membrane (defined by MEM)

Transform the protein with a user-defined embedding (might have been optimized before) into the default membrane

◆ TransformIntoMembraneMover() [4/6]

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover	(	core::Vector	new_mem_cntr,
		core::Vector	new_mem_norm
	)

Transform the protein into user-specified membrane coordinates.

Transform the protein into a user-defined membrane, protein embedding is computed from structure and spanfile

◆ TransformIntoMembraneMover() [5/6]

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover	(	protocols::membrane::geometry::EmbeddingDefOP	current_embedding,
		core::Vector	new_mem_cntr,
		core::Vector	new_mem_norm
	)

Transform the protein into user-specified membrane coordinates.

Transform the protein into a user-defined membrane, protein embedding is computed from structure and spanfile

◆ TransformIntoMembraneMover() [6/6]

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( TransformIntoMembraneMover const & src )

default

Copy Constructor.

Create a deep copy of this mover

◆ ~TransformIntoMembraneMover()

protocols::membrane::TransformIntoMembraneMover::~TransformIntoMembraneMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ apply()

void protocols::membrane::TransformIntoMembraneMover::apply ( core::pose::Pose & pose )

overridevirtual

Get the name of this Mover (TransformIntoMembraneMover)

Move the pose into membrane coordinate frame.

Move the pose into membrane coordinate frame

Implements protocols::moves::Mover.

References protocols::membrane::compute_structure_based_embedding(), core::pose::Pose::conformation(), current_embedding_, flip_if_needed_, core::pose::Pose::fold_tree(), init_from_cmd(), core::conformation::Conformation::is_membrane(), protocols::membrane::is_membrane_fixed(), protocols::membrane::is_membrane_moveable_by_itself(), jump_, core::conformation::Conformation::membrane_info(), core::pose::Pose::membrane_info(), new_mem_cntr_, new_mem_norm_, protocols::membrane::pose_tilt_angle_and_center_distance(), register_options(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::show(), protocols::loops::start, protocols::TR(), use_default_membrane_, and user_defined_membrane_.

◆ clone()

protocols::moves::MoverOP protocols::membrane::TransformIntoMembraneMover::clone ( ) const

overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

protocols::moves::MoverOP protocols::membrane::TransformIntoMembraneMover::fresh_instance ( ) const

overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::membrane::TransformIntoMembraneMover::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::membrane::TransformIntoMembraneMover::init_from_cmd ( )

private

Initialize Mover options from the commandline.

Initialize Mover options from the comandline.

Initialize mover settings from the commandline mainly in the mp, setup group: center, normal, spanfiles, jumpnum

Initialize mover settings from the commandline mainly in the mp, setup group: center, normal, spanfile

References new_mem_cntr_, new_mem_norm_, and protocols::membrane::read_center_normal_from_cmd().

Referenced by apply().

◆ mover_name()

std::string protocols::membrane::TransformIntoMembraneMover::mover_name ( )

static

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

◆ parse_my_tag()

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

overridevirtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References flip_if_needed_, jump_, new_mem_cntr_, new_mem_norm_, protocols::membrane::read_center_normal_from_tag(), use_default_membrane_, and user_defined_membrane_.

◆ provide_xml_schema()

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

static

References protocols::membrane::AddMembraneMover::attributes_for_parse_center_normal_from_tag(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::membrane::TransformIntoMembraneMoverCreator::provide_xml_schema().

◆ register_options()

void protocols::membrane::TransformIntoMembraneMover::register_options ( )

private

Setup Methods ///.

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp, setup options: center, normal, spanfiles, jumpnum

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp, seutp options: center, normal, spanfile and

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

Referenced by apply().

◆ use_default_membrane()

void protocols::membrane::TransformIntoMembraneMover::use_default_membrane ( bool truefalse )

Mover Methods ///.

Use the default membrane (cntr 0,0,0 and normal 0,0,1) instead of the membrane from the MEM coordinates stored in MembraneInfo

References use_default_membrane_.

Member Data Documentation

◆ current_embedding_

protocols::membrane::geometry::EmbeddingDefOP protocols::membrane::TransformIntoMembraneMover::current_embedding_

private

Referenced by apply().

◆ flip_if_needed_

bool protocols::membrane::TransformIntoMembraneMover::flip_if_needed_ = false

private

Referenced by apply(), and parse_my_tag().

◆ jump_

core::Size protocols::membrane::TransformIntoMembraneMover::jump_

private

Referenced by apply(), and parse_my_tag().

◆ new_mem_cntr_

core::Vector protocols::membrane::TransformIntoMembraneMover::new_mem_cntr_

private

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

◆ new_mem_norm_

core::Vector protocols::membrane::TransformIntoMembraneMover::new_mem_norm_

private

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

◆ use_default_membrane_

bool protocols::membrane::TransformIntoMembraneMover::use_default_membrane_

private

Referenced by apply(), parse_my_tag(), and use_default_membrane().

◆ user_defined_membrane_

bool protocols::membrane::TransformIntoMembraneMover::user_defined_membrane_

private

Referenced by apply(), and parse_my_tag().

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

src/protocols/membrane/TransformIntoMembraneMover.hh
src/protocols/membrane/TransformIntoMembraneMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ TransformIntoMembraneMover() [1/6]

◆ TransformIntoMembraneMover() [2/6]

◆ TransformIntoMembraneMover() [3/6]

◆ TransformIntoMembraneMover() [4/6]

◆ TransformIntoMembraneMover() [5/6]

◆ TransformIntoMembraneMover() [6/6]

◆ ~TransformIntoMembraneMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ init_from_cmd()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ register_options()

◆ use_default_membrane()

Member Data Documentation

◆ current_embedding_

◆ flip_if_needed_

◆ jump_

◆ new_mem_cntr_

◆ new_mem_norm_

◆ use_default_membrane_

◆ user_defined_membrane_