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protocols::docking::membrane::MPDockingMover Class Reference

Docks two proteins together in the membrane bilayer. More...

#include <MPDockingMover.hh>

Inheritance diagram for protocols::docking::membrane::MPDockingMover:
Inheritance graph
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Public Member Functions

 MPDockingMover (bool lowres=true, bool highres=true)
 Constructors ///. More...
 
 MPDockingMover (core::Size jump_num, bool lowres=true, bool highres=true)
 Constructor with jump number to dock over. More...
 
 MPDockingMover (MPDockingMover const &src)
 Copy Constructor. More...
 
 ~MPDockingMover () override
 Destructor. More...
 
protocols::moves::MoverOP clone () const override
 Create a Clone of this mover. 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
 Rosetta Scripts Methods ///. More...
 
void set_cycles_inner (core::Size cycles_inner)
 Mover Methods ///. More...
 
void set_cycles_outer (core::Size cycles_outer)
 Set outer cycles in DockingProtocol. More...
 
void apply (Pose &pose) override
 Add membrane components to the pose, then dock proteins along the flexible jump. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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 set_defaults (const Pose &pose)
 
void register_options ()
 
void init_from_cmd ()
 
void finalize_setup ()
 

Private Attributes

protocols::membrane::AddMembraneMoverOP add_membrane_mover_
 
DockingProtocolOP docking_protocol_
 
bool lowres_
 
bool highres_
 
core::scoring::ScoreFunctionOP lowres_scorefxn_
 
core::scoring::ScoreFunctionOP highres_scorefxn_
 
core::Vector center_
 
core::Vector normal_
 
core::Size jump_num_
 
core::pose::PoseOP native_
 

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

Docks two proteins together in the membrane bilayer.

Requires running mpdocking_setup first to create a single pose; Should also run docking_prepack before

Constructor & Destructor Documentation

protocols::docking::membrane::MPDockingMover::MPDockingMover ( bool  lowres = true,
bool  highres = true 
)

Constructors ///.

Default Constructor

Docks two proteins with default normal=(0,0,1) and center=(0,0,0)

protocols::docking::membrane::MPDockingMover::MPDockingMover ( core::Size  jump_num,
bool  lowres = true,
bool  highres = true 
)

Constructor with jump number to dock over.

Default Constructor.

Docks two proteins with default normal=(0,0,1) and center=(0,0,0)

protocols::docking::membrane::MPDockingMover::MPDockingMover ( MPDockingMover const &  src)

Copy Constructor.

Create a deep copy of this mover

protocols::docking::membrane::MPDockingMover::~MPDockingMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::docking::membrane::MPDockingMover::apply ( Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::docking::membrane::MPDockingMover::clone ( ) const
overridevirtual

Create a Clone of this mover.

Reimplemented from protocols::moves::Mover.

void protocols::docking::membrane::MPDockingMover::finalize_setup ( )
private
protocols::moves::MoverOP protocols::docking::membrane::MPDockingMover::fresh_instance ( ) const
overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

std::string protocols::docking::membrane::MPDockingMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::docking::membrane::MPDockingMover::init_from_cmd ( )
private
std::string protocols::docking::membrane::MPDockingMover::mover_name ( )
static
void protocols::docking::membrane::MPDockingMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual

Rosetta Scripts Methods ///.

Pase Rosetta Scripts Options for this Mover.

Pase Rosetta Scripts Options for this Mover

Reimplemented from protocols::moves::Mover.

References core::conformation::membrane::center, center_, core::scoring::ScoreFunctionFactory::create_score_function(), highres_scorefxn_, jump_num_, lowres_scorefxn_, core::conformation::membrane::normal, and normal_.

void protocols::docking::membrane::MPDockingMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::membrane::MPDockingMover::register_options ( )
private

Referenced by apply().

void protocols::docking::membrane::MPDockingMover::set_cycles_inner ( core::Size  cycles_inner)

Mover Methods ///.

Create a new copy of this mover.

Get the name of this Mover (MPDockingMover) Setters for the DockingProtocol

These are set here because the mover doesn't inherit from the DockingProtocol

Return the Name of this mover (as seen by Rscripts) Mover name for Rosetta Scripts Mover Methods /// Get the name of this Mover (MPDockingMover)

References docking_protocol_.

void protocols::docking::membrane::MPDockingMover::set_cycles_outer ( core::Size  cycles_outer)

Set outer cycles in DockingProtocol.

References docking_protocol_.

void protocols::docking::membrane::MPDockingMover::set_defaults ( const Pose pose)
private

Member Data Documentation

protocols::membrane::AddMembraneMoverOP protocols::docking::membrane::MPDockingMover::add_membrane_mover_
private

Referenced by apply(), and finalize_setup().

core::Vector protocols::docking::membrane::MPDockingMover::center_
private

Referenced by parse_my_tag().

DockingProtocolOP protocols::docking::membrane::MPDockingMover::docking_protocol_
private
bool protocols::docking::membrane::MPDockingMover::highres_
private

Referenced by set_defaults().

core::scoring::ScoreFunctionOP protocols::docking::membrane::MPDockingMover::highres_scorefxn_
private
core::Size protocols::docking::membrane::MPDockingMover::jump_num_
private
bool protocols::docking::membrane::MPDockingMover::lowres_
private

Referenced by set_defaults().

core::scoring::ScoreFunctionOP protocols::docking::membrane::MPDockingMover::lowres_scorefxn_
private
core::pose::PoseOP protocols::docking::membrane::MPDockingMover::native_
private
core::Vector protocols::docking::membrane::MPDockingMover::normal_
private

Referenced by parse_my_tag().


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