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protocols::relax::membrane::MPRangeRelaxMover Class Reference

#include <MPRangeRelaxMover.hh>

Inheritance diagram for protocols::relax::membrane::MPRangeRelaxMover:
Inheritance graph
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Public Member Functions

 MPRangeRelaxMover ()
 Constructors ///. More...
 
 MPRangeRelaxMover (MPRangeRelaxMover const &src)
 Copy Constructor. More...
 
MPRangeRelaxMoveroperator= (MPRangeRelaxMover const &src)
 Assignment Operator. More...
 
 ~MPRangeRelaxMover () 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...
 
std::string get_name () const override
 Mover Methods ///. More...
 
void apply (Pose &pose) override
 Do a RangeRelax of a membrane protein. More...
 
void optimize_membrane (bool yesno)
 Optimize membrane. More...
 
core::pose::PoseOP get_native () const
 Get Methods ///. More...
 
core::scoring::ScoreFunctionOP get_sfxn () const
 Get scorefxn. More...
 
core::Size get_center_resnumber () const
 Get center residue number. More...
 
bool get_set_tm_helical () const
 Get yes/no for set helical secondary structure in TM region. More...
 
bool get_optmem () const
 Get yes/no for optimize membrane option. 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 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...
 
void init_from_cmd ()
 Init from commandline. More...
 

Private Attributes

core::pose::PoseOP native_
 Native. More...
 
core::scoring::ScoreFunctionOP sfxn_
 Scorefxn. More...
 
core::Size center_resnumber_
 Center residue number. More...
 
bool set_tm_helical_
 Set helical secondary structure in TM region. More...
 
bool optmem_
 optimize membrane? 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...
 

Constructor & Destructor Documentation

protocols::relax::membrane::MPRangeRelaxMover::MPRangeRelaxMover ( )

Constructors ///.

Default Constructor

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

Referenced by operator=().

protocols::relax::membrane::MPRangeRelaxMover::MPRangeRelaxMover ( MPRangeRelaxMover const &  src)
default

Copy Constructor.

Create a deep copy of this mover

protocols::relax::membrane::MPRangeRelaxMover::~MPRangeRelaxMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::relax::membrane::MPRangeRelaxMover::apply ( Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::relax::membrane::MPRangeRelaxMover::clone ( ) const
overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::relax::membrane::MPRangeRelaxMover::fresh_instance ( ) const
overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

core::Size protocols::relax::membrane::MPRangeRelaxMover::get_center_resnumber ( ) const

Get center residue number.

References center_resnumber_.

std::string protocols::relax::membrane::MPRangeRelaxMover::get_name ( ) const
overridevirtual

Mover Methods ///.

Create a new copy of this mover.

Get the name of this Mover (MPRangeRelaxMover)

Mover Methods /// Get the name of this Mover (MPRangeRelaxMover)

Implements protocols::moves::Mover.

core::pose::PoseOP protocols::relax::membrane::MPRangeRelaxMover::get_native ( ) const

Get Methods ///.

Get native

References native_.

bool protocols::relax::membrane::MPRangeRelaxMover::get_optmem ( ) const

Get yes/no for optimize membrane option.

References optmem_.

bool protocols::relax::membrane::MPRangeRelaxMover::get_set_tm_helical ( ) const

Get yes/no for set helical secondary structure in TM region.

References set_tm_helical_.

core::scoring::ScoreFunctionOP protocols::relax::membrane::MPRangeRelaxMover::get_sfxn ( ) const

Get scorefxn.

References sfxn_.

void protocols::relax::membrane::MPRangeRelaxMover::init_from_cmd ( )
private

Init from commandline.

Set default values.

References native_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), and set_tm_helical_.

Referenced by MPRangeRelaxMover().

MPRangeRelaxMover & protocols::relax::membrane::MPRangeRelaxMover::operator= ( MPRangeRelaxMover const &  src)

Assignment Operator.

References MPRangeRelaxMover().

void protocols::relax::membrane::MPRangeRelaxMover::optimize_membrane ( bool  yesno)

Optimize membrane.

References optmem_.

void protocols::relax::membrane::MPRangeRelaxMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::relax::membrane::MPRangeRelaxMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static

Provide xml schema for RosettaScripts compatibility.

References protocols::moves::xsd_type_definition_w_attributes().

void protocols::relax::membrane::MPRangeRelaxMover::register_options ( )
private

Setup Methods ///.

Register Options from Command Line.

Register Options from Command Line

Referenced by MPRangeRelaxMover().

void protocols::relax::membrane::MPRangeRelaxMover::set_defaults ( )
private

Set default values.

Setup Methods ///.

Set default values

References center_resnumber_, core::scoring::ScoreFunctionFactory::create_score_function(), native_, optmem_, set_tm_helical_, and sfxn_.

Referenced by MPRangeRelaxMover().

Member Data Documentation

core::Size protocols::relax::membrane::MPRangeRelaxMover::center_resnumber_
private

Center residue number.

Referenced by get_center_resnumber(), parse_my_tag(), and set_defaults().

core::pose::PoseOP protocols::relax::membrane::MPRangeRelaxMover::native_
private
bool protocols::relax::membrane::MPRangeRelaxMover::optmem_
private

optimize membrane?

Referenced by get_optmem(), optimize_membrane(), parse_my_tag(), and set_defaults().

bool protocols::relax::membrane::MPRangeRelaxMover::set_tm_helical_
private

Set helical secondary structure in TM region.

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

core::scoring::ScoreFunctionOP protocols::relax::membrane::MPRangeRelaxMover::sfxn_
private

Scorefxn.

Referenced by apply(), get_sfxn(), parse_my_tag(), and set_defaults().


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