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protocols::membrane::visualize::VisualizeMembraneMover Class Reference

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:
Inheritance graph
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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...
 
VisualizeMembraneMoveroperator= (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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

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=().

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

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

Copy Constructor.

Creates a deep copy of the visualize membrane mover class

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

Destructor.

Member Function Documentation

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_.

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

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

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, and core::chemical::FA_STANDARD.

Referenced by apply().

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

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

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

Return the name of this mover.

Implements protocols::moves::Mover.

References mover_name().

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().

std::string protocols::membrane::visualize::VisualizeMembraneMover::mover_name ( )
static
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 &   
)
overridevirtual

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References spacing_, thickness_, and width_.

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

Helper Methods ///.

Register Options with JD2

Referenced by VisualizeMembraneMover().

Member Data Documentation

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

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

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

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

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: