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protocols::docking::membrane::MPDockingSetupMover Class Reference

Setup for MPDocking. More...

#include <MPDockingSetupMover.hh>

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

 MPDockingSetupMover ()
 Constructors ///. More...
 
 MPDockingSetupMover (MPDockingSetupMover const &src)
 Copy Constructor. More...
 
 ~MPDockingSetupMover () 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
 Parse Rosetta Scripts Options for this Mover. More...
 
bool get_optimize1 () const
 Get Methods ///. More...
 
bool get_optimize2 () const
 get optimize1 More...
 
utility::vector1
< core::pose::PoseOP
get_poses () const
 get pose vector More...
 
utility::vector1< std::string > get_spanfiles () const
 get spanfile vector More...
 
void apply (Pose &pose) override
 Mover Methods ///. 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 read_poses ()
 
void read_spanfiles ()
 
void init_from_cmd ()
 
void transform_pose_into_membrane (core::pose::Pose &pose, core::Vector center, core::Vector normal, std::string spanfile, core::Size partner)
 

Private Attributes

utility::vector1
< core::pose::PoseOP
poses_
 
utility::vector1< std::string > spanfiles_
 
bool optimize1_
 
bool optimize2_
 

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

Setup for MPDocking.

Reads in 2 poses and 2 spanfiles, concatenates the poses and spanfiles and prints them out CURRENTLY ONLY WORKS FOR 2 POSES!!!

Constructor & Destructor Documentation

protocols::docking::membrane::MPDockingSetupMover::MPDockingSetupMover ( )

Constructors ///.

Default Constructor

protocols::docking::membrane::MPDockingSetupMover::MPDockingSetupMover ( MPDockingSetupMover const &  src)
default

Copy Constructor.

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

Destructor.

Member Function Documentation

void protocols::docking::membrane::MPDockingSetupMover::apply ( Pose pose)
overridevirtual

Mover Methods ///.

Create a new copy of this mover.

Get the name of this Mover (MPDockingSetupMover) Reads in 2 poses and 2 spanfiles, concatenates the poses and spanfiles and prints them out

Return the Name of this mover (as seen by Rscripts) Mover name for Rosetta Scripts Mover Methods /// Get the name of this Mover (MPDockingSetupMover) Add membrane components to the pose, then dock proteins along the flexible jump

Implements protocols::moves::Mover.

References core::pose::append_pose_to_pose(), protocols::toolbox::CA_superimpose(), core::conformation::membrane::center, core::pose::Pose::fold_tree(), init_from_cmd(), protocols::membrane::is_membrane_fixed(), core::conformation::membrane::normal, poses_, read_poses(), read_spanfiles(), core::pose::renumber_pdbinfo_based_on_conf_chains(), protocols::membrane::reorder_membrane_foldtree(), core::kinematics::FoldTree::show(), spanfiles_, protocols::docking::TR(), and transform_pose_into_membrane().

protocols::moves::MoverOP protocols::docking::membrane::MPDockingSetupMover::clone ( ) const
overridevirtual

Create a Clone of this mover.

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::docking::membrane::MPDockingSetupMover::fresh_instance ( ) const
overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

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

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::docking::membrane::MPDockingSetupMover::get_optimize1 ( ) const

Get Methods ///.

get optimize1

References optimize1_.

bool protocols::docking::membrane::MPDockingSetupMover::get_optimize2 ( ) const

get optimize1

References optimize2_.

utility::vector1< core::pose::PoseOP > protocols::docking::membrane::MPDockingSetupMover::get_poses ( ) const

get pose vector

References poses_.

utility::vector1< std::string > protocols::docking::membrane::MPDockingSetupMover::get_spanfiles ( ) const

get spanfile vector

References spanfiles_.

void protocols::docking::membrane::MPDockingSetupMover::init_from_cmd ( )
private

References optimize1_, and optimize2_.

Referenced by apply().

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

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References optimize1_, optimize2_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), poses_, and spanfiles_.

void protocols::docking::membrane::MPDockingSetupMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::membrane::MPDockingSetupMover::read_poses ( )
private
void protocols::docking::membrane::MPDockingSetupMover::read_spanfiles ( )
private
void protocols::docking::membrane::MPDockingSetupMover::transform_pose_into_membrane ( core::pose::Pose pose,
core::Vector  center,
core::Vector  normal,
std::string  spanfile,
core::Size  partner 
)
private

Member Data Documentation

bool protocols::docking::membrane::MPDockingSetupMover::optimize1_
private
bool protocols::docking::membrane::MPDockingSetupMover::optimize2_
private
utility::vector1< core::pose::PoseOP > protocols::docking::membrane::MPDockingSetupMover::poses_
private
utility::vector1< std::string > protocols::docking::membrane::MPDockingSetupMover::spanfiles_
private

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