Add membrane planes to the pose represented by 2 layers of MEM virtual residues. More...

#include <VisualizeMembraneMover.hh>

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

	VisualizeMembraneMover (Real spacing, Real width, Real thicnkess)
	Construct with User specified spacing & width. More...

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

VisualizeMembraneMover &	operator= (VisualizeMembraneMover const &src)
	Assignment Operator. More...

	~VisualizeMembraneMover ()
	Destructor. More...

virtual protocols::moves::MoverOP	clone () const
	Rosetta Scripts Methods ///. More...

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

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 &)
	Pase Rosetta Scripts Options for this Mover. More...

virtual void	apply (Pose &pose)
	Mover Methods ///. More...

virtual std::string	get_name () const
	Return the name of this mover. 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...

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...

Private Member Functions
void	register_options ()
	Helper Methods ///. More...

void	init_from_cmd ()
	Initialize Options from the Command Line. More...

ResidueOP	create_membrane_virtual (Vector pos, bool fullatom)
	Create a Membrane Residue. More...

Private Attributes
Real	spacing_

Real	width_

Real	thickness_

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

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...

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

Add membrane planes to the pose represented by 2 layers of MEM virtual residues.

Constructor & Destructor Documentation

protocols::membrane::visualize::VisualizeMembraneMover::VisualizeMembraneMover ( )

Constructors ///.

Defualt Constructor

Construct membrane residues with spacing = 5, width = 100, and the pose membrane and center

Defualt Constructor

Construct membrane residues with spacing = 5, width = 100

References init_from_cmd(), and register_options().

Referenced by clone(), fresh_instance(), and operator=().

protocols::membrane::visualize::VisualizeMembraneMover::VisualizeMembraneMover	(	Real	spacing,
		Real	width,
		Real	thickness
	)

Construct with User specified spacing & width.

Construct membranes with a given spacing and width in angstroms

protocols::membrane::visualize::VisualizeMembraneMover::VisualizeMembraneMover ( VisualizeMembraneMover const & src )

Copy Constructor.

Creates a deep copy of the visualize membrane mover class

protocols::membrane::visualize::VisualizeMembraneMover::~VisualizeMembraneMover ( )

Destructor.

Member Function Documentation

void protocols::membrane::visualize::VisualizeMembraneMover::apply ( Pose & pose )

virtual

Mover Methods ///.

Apply Visualize Transform "Move"

Adds a series of virtiaul residues to the pose given a spacing and width specified at construction time

Implements protocols::moves::Mover.

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::conformation(), create_membrane_virtual(), fullatom, core::pose::Pose::is_fullatom(), core::conformation::Conformation::is_membrane(), spacing_, thickness_, core::pose::Pose::total_residue(), protocols::TR, utility_exit_with_message, and width_.

protocols::moves::MoverOP protocols::membrane::visualize::VisualizeMembraneMover::clone ( ) const

virtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

References VisualizeMembraneMover().

ResidueOP protocols::membrane::visualize::VisualizeMembraneMover::create_membrane_virtual	(	Vector	pos,
		bool	fullatom
	)

private

Create a Membrane Residue.

Given a centered position and residue typeset, return a ResidueOP with the xyz coordinate pos, type MEM, from typeset given

References core::chemical::CENTROID, core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::chemical::ChemicalManager::get_instance(), membrane, residue_type_set, and core::conformation::Residue::set_xyz().

Referenced by apply().

protocols::moves::MoverOP protocols::membrane::visualize::VisualizeMembraneMover::fresh_instance ( ) const

virtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

References VisualizeMembraneMover().

std::string protocols::membrane::visualize::VisualizeMembraneMover::get_name ( ) const

virtual

Return the name of this mover.

Implements protocols::moves::Mover.

void protocols::membrane::visualize::VisualizeMembraneMover::init_from_cmd ( )

private

Initialize Options from the Command Line.

Options allowed are vrt spacing and plane width

References option, spacing_, thickness_, user, and width_.

Referenced by VisualizeMembraneMover().

VisualizeMembraneMover & protocols::membrane::visualize::VisualizeMembraneMover::operator= ( VisualizeMembraneMover const & src )

Assignment Operator.

Overloads "=" assignemnt for deep copying

References VisualizeMembraneMover().

void protocols::membrane::visualize::VisualizeMembraneMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	,
		protocols::filters::Filters_map const &	,
		protocols::moves::Movers_map const &	,
		core::pose::Pose const &
	)