#include <SymmetricAddMembraneMover.hh>

Inheritance diagram for protocols::membrane::symmetry::SymmetricAddMembraneMover:

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

	SymmetricAddMembraneMover (std::string spanfile)
	Custom Constructor for SymmetricAddMembraneMover. More...

	SymmetricAddMembraneMover (core::conformation::membrane::SpanningTopologyOP topology)
	Custom Constructor for SymmetricAddMembraneMover. More...

	SymmetricAddMembraneMover (SymmetricAddMembraneMover const &src)
	Copy Constructor for SymmetricAddMembraneMover. More...

	~SymmetricAddMembraneMover () 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 &dm) override
	Pase Rosetta Scripts Options for this Mover. More...

core::Size	add_membrane_virtual (core::pose::Pose &pose) override
	Mover Methods ///. More...

std::string	get_name () const override
	Mover Methods ///. More...

utility::vector1< core::SSize >	check_pdb_for_mem (core::pose::Pose &pose) override
	Helper Method - Check for Membrane residue already in the PDB. More...

Public Member Functions inherited from protocols::membrane::AddMembraneMover
	AddMembraneMover ()
	Create a default RosettaMP membrane setup. More...

	AddMembraneMover (std::string spanfile, core::Size membrane_rsd=0, std::string lipid_composition="DLPC", core::Real temperature=37.0)
	Create a RosettaMP setup from a user specified spanfile. More...

	AddMembraneMover (core::Size membrane_rsd, std::string lipid_composition="DLPC", core::Real temperature=37.0)
	Create a RosettaMP setup from an existing membrane residue. More...

	AddMembraneMover (core::conformation::membrane::SpanningTopologyOP topology, core::Size anchor_rsd=1, core::Size membrane_rsd=0)
	Create a RosettaMP setup from a user specified SpanningTopology. More...

	AddMembraneMover (core::Size anchor_rsd, bool anchor_format, bool second_anchor_format, core::Size membrane_rsd=0)
	Create a RosettaMP setup by setting the root of the fold tree to anchor_rsd and designating MEM as membrane_rsd. The two booleans are dummy variables intended to differentiate. More...

	AddMembraneMover (AddMembraneMover const &src)
	Create a deep copy of the data in this mover. More...

	~AddMembraneMover () override
	Destructor. More...

void	apply (core::pose::Pose &pose) override
	Initialize the RosettaMP elements with this pose. More...

std::string	get_spanfile () const
	Path to file with transmembrane span data. More...

void	spanfile (std::string spanfile)
	Set path to spanfile. More...

void	restore_lazaridis_IMM1_behavior (bool restore)

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::membrane::AddMembraneMover
static std::string	mover_name ()

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

static void	attributes_for_parse_center_normal_from_tag (utility::tag::AttributeList &attributes)

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 comandline. More...

Private Attributes
utility::vector1 < core::conformation::membrane::SpanOP >	spans_from_xml_

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...

Constructor & Destructor Documentation

protocols::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( )

Constructors ///.

Default constructor of SymmetricAddMembraneMover

Create a membrane pose, setting the membrane center at center=(0, 0, 0), normal=(0, 0, 1) and loads in spans and lips from the command line interface. Calls the default constructor of AddMembraneMover

References init_from_cmd(), and register_options().

protocols::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( std::string spanfile )

Custom Constructor for SymmetricAddMembraneMover.

Creates a membrane pose, setting the membrane center at center=(0, 0, 0), normal=(0, 0, 1). Uses the user provided spanfile in this constructor to load the spanning topology. Calls the analagous parent constructor in AddMembraneMover

References init_from_cmd(), and register_options().

protocols::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( core::conformation::membrane::SpanningTopologyOP topology )

Custom Constructor for SymmetricAddMembraneMover.

Creates a membrane pose, setting the membrane center at center=(0, 0, 0), normal=(0, 0, 1). Uses the user provided SpanningTopology to be set in MembraneInfo. Calls the analagous parent constructor in AddMembraneMover

References init_from_cmd(), and register_options().

protocols::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( SymmetricAddMembraneMover const & src )

default

Copy Constructor for SymmetricAddMembraneMover.

Create a deep copy of SymmetricAddMembraneMover

protocols::membrane::symmetry::SymmetricAddMembraneMover::~SymmetricAddMembraneMover ( )

overridedefault

Destructor.

Member Function Documentation

core::Size protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual ( core::pose::Pose & pose )

overridevirtual

Mover Methods ///.

Add a membrane virtual residue to the pose by inserting by jump.

Get the name of this Mover (SymmetricAddMembraneMover) Add a membrane virtual residue to the pose by inserting by jump

Adds a virtual residue to the pose by selecting the VRT_0_Base as the anchoring residue and nres_complex+1 as tne new sequence position Not equivalent to an append_by_jump!

Reimplemented from protocols::membrane::AddMembraneMover.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::insert_residue_by_jump(), core::pose::symmetry::is_symmetric(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::size(), and protocols::TR().

utility::vector1< core::SSize > protocols::membrane::symmetry::SymmetricAddMembraneMover::check_pdb_for_mem ( core::pose::Pose & pose )

overridevirtual

Helper Method - Check for Membrane residue already in the PDB.

If there is an MEM residue in the PDB at the end of the pose with property MEMBRANE, return a vector of all of those residues.

Reimplemented from protocols::membrane::AddMembraneMover.

protocols::moves::MoverOP protocols::membrane::symmetry::SymmetricAddMembraneMover::clone ( ) const

overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::membrane::AddMembraneMover.

protocols::moves::MoverOP protocols::membrane::symmetry::SymmetricAddMembraneMover::fresh_instance ( ) const

overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::membrane::AddMembraneMover.

std::string protocols::membrane::symmetry::SymmetricAddMembraneMover::get_name ( ) const

overridevirtual

Mover Methods ///.

Reimplemented from protocols::membrane::AddMembraneMover.

References mover_name().

void protocols::membrane::symmetry::SymmetricAddMembraneMover::init_from_cmd ( )

private

Initialize Mover options from the comandline.

Initialize mover settings from the commandline mainly in the mp, setup group: spans_from_structure, spanfile and lipsfiles paths

References protocols::membrane::AddMembraneMover::get_spanfile(), protocols::membrane::AddMembraneMover::spanfile(), and protocols::TR().

Referenced by SymmetricAddMembraneMover().

std::string protocols::membrane::symmetry::SymmetricAddMembraneMover::mover_name ( )

static

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

void protocols::membrane::symmetry::SymmetricAddMembraneMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	dm
	)

overridevirtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::membrane::AddMembraneMover.

References protocols::membrane::AddMembraneMover::parse_my_tag().

void protocols::membrane::symmetry::SymmetricAddMembraneMover::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_and_repeatable_subelements().

Referenced by protocols::membrane::symmetry::SymmetricAddMembraneMoverCreator::provide_xml_schema().

void protocols::membrane::symmetry::SymmetricAddMembraneMover::register_options ( )

private

Setup Methods ///.

Create a new copy of this mover.

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp seutp options: spanfiles, lipsfile, and spans_from_structure.

Return the Name of this mover (as seen by Rscripts) Mover name for Rosetta Scripts Mover Methods /// Get the name of this Mover (SymmetricAddMembraneMover) Setup Methods /// Register Options from Command Line

Register mover-relevant options with JD2 - includes mp seutp options: spanfiles, lipsfile, and spans_from_structure.

Referenced by SymmetricAddMembraneMover().

Member Data Documentation

utility::vector1< core::conformation::membrane::SpanOP > protocols::membrane::symmetry::SymmetricAddMembraneMover::spans_from_xml_

private

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

src/protocols/membrane/symmetry/SymmetricAddMembraneMover.hh
src/protocols/membrane/symmetry/SymmetricAddMembraneMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation