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protocols::membrane::FlipMover Class Reference

Takes a pose and flips the downstream partner around the axis between the COMs of the partners, projected into the membrane plane. CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!! More...

#include <FlipMover.hh>

Inheritance diagram for protocols::membrane::FlipMover:
Inheritance graph
[legend]

Public Member Functions

 FlipMover ()
 Constructors ///. More...
 
 FlipMover (core::Size jump_num)
 Custom Constructor. More...
 
 FlipMover (core::Size jump_num, core::Vector axis)
 Custom constructor. More...
 
 FlipMover (core::Size jump_num, core::Real angle)
 Custom constructor. More...
 
 FlipMover (core::Size jump_num, core::Vector axis, core::Real angle)
 Custom constructor. More...
 
 FlipMover (FlipMover const &src)
 Copy Constructor. More...
 
FlipMoveroperator= (FlipMover const &src)
 Assignment Operator. More...
 
 ~FlipMover () 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...
 
void set_random_membrane_flip_angle ()
 Set Random flip angle between 135 and 225 degrees to keep protein oriented in the membrane correctly. More...
 
void set_range (core::Real max_angle_dev)
 Set angle range. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
core::Size get_jump_num () const
 Get Methods ///. More...
 
core::Vector get_axis () const
 get rotation axis More...
 
core::Real get_angle () const
 get rotation angle More...
 
bool get_random_angle () const
 get random angle status More...
 
core::Real get_max_angle_dev () const
 get maximum angle deviation from 180 degrees 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 void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 Provide xml schema for RosettaScripts compatibility. More...
 
static std::string mover_name ()
 
- 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 set_defaults ()
 Set default values. More...
 

Private Attributes

core::Size jump_num_
 Jump number. More...
 
core::Vector axis_
 Rotation axis. More...
 
core::Real angle_
 Rotation angle in degrees. More...
 
bool random_angle_
 Random flip angle between 135 and 225 degrees in the membrane. More...
 
core::Real max_angle_dev_
 Maximum angle deviation from 180 degrees. More...
 

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

Takes a pose and flips the downstream partner around the axis between the COMs of the partners, projected into the membrane plane. CAUTION: THIS MOVER ONLY WORKS FOR A FIXED MEMBRANE WHERE THE MEMBRANE VIRTUAL RESIDUE IS AT THE ROOT OF THE FOLDTREE!!!

Constructor & Destructor Documentation

protocols::membrane::FlipMover::FlipMover ( )

Constructors ///.

Default Constructor

Defaults: jump = membrane jump, angle = 180 deg, axis = x-axis

References register_options(), and set_defaults().

Referenced by operator=().

protocols::membrane::FlipMover::FlipMover ( core::Size  jump_num)

Custom Constructor.

User can specify jump number

References jump_num_, register_options(), and set_defaults().

protocols::membrane::FlipMover::FlipMover ( core::Size  jump_num,
core::Vector  axis 
)

Custom constructor.

User can specify jump number and rotation axis

References axis_, jump_num_, register_options(), and set_defaults().

protocols::membrane::FlipMover::FlipMover ( core::Size  jump_num,
core::Real  angle 
)

Custom constructor.

User can specify jump number and angle

References angle_, jump_num_, register_options(), and set_defaults().

protocols::membrane::FlipMover::FlipMover ( core::Size  jump_num,
core::Vector  axis,
core::Real  angle 
)

Custom constructor.

User can specify jump number and rotation axis

References angle_, axis_, jump_num_, register_options(), and set_defaults().

protocols::membrane::FlipMover::FlipMover ( FlipMover const &  src)
default

Copy Constructor.

Create a deep copy of this mover

protocols::membrane::FlipMover::~FlipMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::membrane::FlipMover::apply ( core::pose::Pose pose)
overridevirtual

Mover Methods ///.

Create a new copy of this mover.

Get the name of this Mover (FlipMover) Flip the downstream partner in the membrane

Return the Name of this mover (as seen by Rscripts) Mover name for Rosetta Scripts Mover Methods /// Get the name of this Mover (FlipMover) Flip the downstream partner in the membrane

Implements protocols::moves::Mover.

References angle_, axis_, protocols::membrane::compute_structure_based_embedding(), core::pose::Pose::fold_tree(), protocols::membrane::is_membrane_fixed(), jump_num_, max_angle_dev_, core::pose::Pose::membrane_info(), random_angle_, core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::show(), protocols::membrane::split_topology_by_jump(), and protocols::TR().

protocols::moves::MoverOP protocols::membrane::FlipMover::clone ( ) const
overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::membrane::FlipMover::fresh_instance ( ) const
overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

core::Real protocols::membrane::FlipMover::get_angle ( ) const

get rotation angle

References angle_.

core::Vector protocols::membrane::FlipMover::get_axis ( ) const

get rotation axis

References axis_.

core::Size protocols::membrane::FlipMover::get_jump_num ( ) const

Get Methods ///.

get jump num

References jump_num_.

core::Real protocols::membrane::FlipMover::get_max_angle_dev ( ) const

get maximum angle deviation from 180 degrees

References max_angle_dev_.

std::string protocols::membrane::FlipMover::get_name ( ) const
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

References mover_name().

bool protocols::membrane::FlipMover::get_random_angle ( ) const

get random angle status

References random_angle_.

std::string protocols::membrane::FlipMover::mover_name ( )
static
FlipMover & protocols::membrane::FlipMover::operator= ( FlipMover const &  src)

Assignment Operator.

References FlipMover().

void protocols::membrane::FlipMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References angle_, axis_, jump_num_, max_angle_dev_, and random_angle_.

void protocols::membrane::FlipMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Provide xml schema for RosettaScripts compatibility.

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

Referenced by protocols::membrane::FlipMoverCreator::provide_xml_schema().

void protocols::membrane::FlipMover::register_options ( )
private

Setup Methods ///.

Register Options from Command Line

Referenced by FlipMover().

void protocols::membrane::FlipMover::set_defaults ( )
private

Set default values.

References angle_, axis_, jump_num_, max_angle_dev_, and random_angle_.

Referenced by FlipMover().

void protocols::membrane::FlipMover::set_random_membrane_flip_angle ( )

Set Random flip angle between 135 and 225 degrees to keep protein oriented in the membrane correctly.

Set Random flip angle between 160 and 200 degrees to keep protein oriented in the membrane correctly.

References random_angle_.

void protocols::membrane::FlipMover::set_range ( core::Real  max_angle_dev)

Set angle range.

Maximum angle deviation from 180 degrees

References max_angle_dev_.

Member Data Documentation

core::Real protocols::membrane::FlipMover::angle_
private

Rotation angle in degrees.

Referenced by apply(), FlipMover(), get_angle(), parse_my_tag(), and set_defaults().

core::Vector protocols::membrane::FlipMover::axis_
private

Rotation axis.

Referenced by apply(), FlipMover(), get_axis(), parse_my_tag(), and set_defaults().

core::Size protocols::membrane::FlipMover::jump_num_
private

Jump number.

Referenced by apply(), FlipMover(), get_jump_num(), parse_my_tag(), and set_defaults().

core::Real protocols::membrane::FlipMover::max_angle_dev_
private

Maximum angle deviation from 180 degrees.

Referenced by apply(), get_max_angle_dev(), parse_my_tag(), set_defaults(), and set_range().

bool protocols::membrane::FlipMover::random_angle_
private

Random flip angle between 135 and 225 degrees in the membrane.

Referenced by apply(), get_random_angle(), parse_my_tag(), set_defaults(), and set_random_membrane_flip_angle().


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