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protocols::membrane::TransformIntoMembraneMover Class Reference

Transform a pose into membrane coordinates based on the current embedding of the protein. More...

#include <TransformIntoMembraneMover.hh>

Inheritance diagram for protocols::membrane::TransformIntoMembraneMover:
Inheritance graph
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Public Member Functions

 TransformIntoMembraneMover ()
 Constructors ///. More...
 
 TransformIntoMembraneMover (core::Size jump)
 
 TransformIntoMembraneMover (protocols::membrane::geometry::EmbeddingDefOP current_embedding)
 Transform the protein with a user-specified protein embedding into a default membrane (defined by MEM) More...
 
 TransformIntoMembraneMover (core::Vector new_mem_cntr, core::Vector new_mem_norm)
 Transform the protein into user-specified membrane coordinates. More...
 
 TransformIntoMembraneMover (protocols::membrane::geometry::EmbeddingDefOP current_embedding, core::Vector new_mem_cntr, core::Vector new_mem_norm)
 Transform the protein into user-specified membrane coordinates. More...
 
 TransformIntoMembraneMover (TransformIntoMembraneMover const &src)
 Copy Constructor. More...
 
 ~TransformIntoMembraneMover () 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
 Pase Rosetta Scripts Options for this Mover. More...
 
void use_default_membrane (bool truefalse)
 Mover Methods ///. More...
 
void apply (core::pose::Pose &pose) override
 Get the name of this Mover (TransformIntoMembraneMover) 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 register_options ()
 Setup Methods ///. More...
 
void init_from_cmd ()
 Initialize Mover options from the commandline. More...
 

Private Attributes

core::Size jump_
 
core::Vector new_mem_cntr_
 
core::Vector new_mem_norm_
 
protocols::membrane::geometry::EmbeddingDefOP current_embedding_
 
bool use_default_membrane_
 
bool user_defined_membrane_
 
bool flip_if_needed_ = false
 

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

Transform a pose into membrane coordinates based on the current embedding of the protein.

Constructor & Destructor Documentation

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( )

Constructors ///.

Transform the protein into a membrane defined by MEM

Transform the protein into membrane defined by MEM, protein embedding computed from structure and spanfile

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( core::Size  jump)
protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( protocols::membrane::geometry::EmbeddingDefOP  current_embedding)

Transform the protein with a user-specified protein embedding into a default membrane (defined by MEM)

Transform the protein with a user-defined embedding (might have been optimized before) into the default membrane

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( core::Vector  new_mem_cntr,
core::Vector  new_mem_norm 
)

Transform the protein into user-specified membrane coordinates.

Transform the protein into a user-defined membrane, protein embedding is computed from structure and spanfile

protocols::membrane::TransformIntoMembraneMover::TransformIntoMembraneMover ( protocols::membrane::geometry::EmbeddingDefOP  current_embedding,
core::Vector  new_mem_cntr,
core::Vector  new_mem_norm 
)

Transform the protein into user-specified membrane coordinates.

Transform the protein into a user-defined membrane, protein embedding is computed from structure and spanfile

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

Copy Constructor.

Create a deep copy of this mover

protocols::membrane::TransformIntoMembraneMover::~TransformIntoMembraneMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::membrane::TransformIntoMembraneMover::apply ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::membrane::TransformIntoMembraneMover::clone ( ) const
overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

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

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

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

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::membrane::TransformIntoMembraneMover::init_from_cmd ( )
private

Initialize Mover options from the commandline.

Initialize Mover options from the comandline.

Initialize mover settings from the commandline mainly in the mp, setup group: center, normal, spanfiles, jumpnum

Initialize mover settings from the commandline mainly in the mp, setup group: center, normal, spanfile

References new_mem_cntr_, new_mem_norm_, and protocols::membrane::read_center_normal_from_cmd().

Referenced by apply().

std::string protocols::membrane::TransformIntoMembraneMover::mover_name ( )
static
void protocols::membrane::TransformIntoMembraneMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::membrane::TransformIntoMembraneMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::membrane::TransformIntoMembraneMover::register_options ( )
private

Setup Methods ///.

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp, setup options: center, normal, spanfiles, jumpnum

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp, seutp options: center, normal, spanfile and

References core::conformation::membrane::center, and core::conformation::membrane::normal.

Referenced by apply().

void protocols::membrane::TransformIntoMembraneMover::use_default_membrane ( bool  truefalse)

Mover Methods ///.

Use the default membrane (cntr 0,0,0 and normal 0,0,1) instead of the membrane from the MEM coordinates stored in MembraneInfo

References use_default_membrane_.

Member Data Documentation

protocols::membrane::geometry::EmbeddingDefOP protocols::membrane::TransformIntoMembraneMover::current_embedding_
private

Referenced by apply().

bool protocols::membrane::TransformIntoMembraneMover::flip_if_needed_ = false
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::membrane::TransformIntoMembraneMover::jump_
private

Referenced by apply(), and parse_my_tag().

core::Vector protocols::membrane::TransformIntoMembraneMover::new_mem_cntr_
private

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

core::Vector protocols::membrane::TransformIntoMembraneMover::new_mem_norm_
private

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

bool protocols::membrane::TransformIntoMembraneMover::use_default_membrane_
private
bool protocols::membrane::TransformIntoMembraneMover::user_defined_membrane_
private

Referenced by apply(), and parse_my_tag().


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