Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::membrane::visualize::VisualizeMembraneMover Class Reference

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...
 
VisualizeMembraneMoveroperator= (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)
 
Moveroperator= (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 Stringsinfo ()
 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::stringStrings
 
- 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 &   
)
virtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References spacing_, thickness_, and width_.

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

Helper Methods ///.

Register Options with JD2

References utility::options::OptionCollection::add_relevant(), and option.

Referenced by VisualizeMembraneMover().

Member Data Documentation

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

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

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

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

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: