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

#include <VisualizeMembraneMover.hh>

Inheritance diagram for protocols::membrane::visualize::VisualizeMembraneMover:

[legend]

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

	VisualizeMembraneMover (core::Real spacing, core::Real width, core::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 () 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
	Parse Rosetta Scripts Options for this Mover. More...

void	apply (core::pose::Pose &pose) override
	Mover Methods ///. More...

std::string	get_name () const override
	Return the name of this mover. 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 ()
	Helper Methods ///. More...

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

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

Private Attributes
core::Real	spacing_

core::Real	width_

core::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 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

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

Constructor & Destructor Documentation

◆ VisualizeMembraneMover() [1/3]

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 operator=().

◆ VisualizeMembraneMover() [2/3]

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

Construct with User specified spacing & width.

Construct membranes with a given spacing and width in angstroms

◆ VisualizeMembraneMover() [3/3]

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

default

Copy Constructor.

Creates a deep copy of the visualize membrane mover class

◆ ~VisualizeMembraneMover()

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

overridedefault

Destructor.

Member Function Documentation

◆ apply()

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

overridevirtual

Mover Methods ///.

Create a new copy of this mover.

Apply Visualize Transform "Move"

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

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

Mover name for Rosetta Scripts Mover Methods ///

Implements protocols::moves::Mover.

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

◆ clone()

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

overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

◆ create_membrane_virtual()

core::conformation::ResidueOP protocols::membrane::visualize::VisualizeMembraneMover::create_membrane_virtual	(	core::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(), and core::chemical::FA_STANDARD.

Referenced by apply().

◆ fresh_instance()

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

overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overridevirtual

Return the name of this mover.

Implements protocols::moves::Mover.

References mover_name().

◆ init_from_cmd()

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

private

Initialize Options from the Command Line.

Options allowed are vrt spacing and plane width

References spacing_, core::conformation::membrane::thickness, thickness_, and width_.

Referenced by VisualizeMembraneMover().

◆ mover_name()

std::string protocols::membrane::visualize::VisualizeMembraneMover::mover_name ( )

static

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

◆ operator=()

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

Assignment Operator.

Overloads "=" assignemnt for deep copying

References VisualizeMembraneMover().

◆ parse_my_tag()

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

overridevirtual

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References spacing_, thickness_, and width_.

◆ provide_xml_schema()

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

static

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

Referenced by protocols::membrane::visualize::VisualizeMembraneMoverCreator::provide_xml_schema().

◆ register_options()

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

private

Helper Methods ///.

Register Options with JD2

Referenced by VisualizeMembraneMover().

Member Data Documentation

◆ spacing_

core::Real protocols::membrane::visualize::VisualizeMembraneMover::spacing_

private

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

◆ thickness_

core::Real protocols::membrane::visualize::VisualizeMembraneMover::thickness_

private

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

◆ width_

core::Real protocols::membrane::visualize::VisualizeMembraneMover::width_

private

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

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

src/protocols/membrane/visualize/VisualizeMembraneMover.hh
src/protocols/membrane/visualize/VisualizeMembraneMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ VisualizeMembraneMover() [1/3]

◆ VisualizeMembraneMover() [2/3]

◆ VisualizeMembraneMover() [3/3]

◆ ~VisualizeMembraneMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ create_membrane_virtual()

◆ fresh_instance()

◆ get_name()

◆ init_from_cmd()

◆ mover_name()

◆ operator=()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ register_options()

Member Data Documentation

◆ spacing_

◆ thickness_

◆ width_