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protocols::membrane::MPQuickRelaxMover Class Reference

#include <MPQuickRelaxMover.hh>

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

Public Member Functions

 MPQuickRelaxMover ()
 Constructors ///. More...
 
 MPQuickRelaxMover (core::Real angle_max, std::string nmoves)
 Custom Constructor. More...
 
 MPQuickRelaxMover (core::Real angle_max, std::string nmoves, core::kinematics::MoveMapOP movemap)
 Custom Constructor. More...
 
 MPQuickRelaxMover (MPQuickRelaxMover const &src)
 Copy Constructor. More...
 
MPQuickRelaxMoveroperator= (MPQuickRelaxMover const &src)
 Assignment Operator. More...
 
 ~MPQuickRelaxMover () 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...
 
std::string get_name () const override
 Mover Methods ///. More...
 
void apply (core::pose::Pose &pose) override
 Flip the downstream partner in the membrane. More...
 
void add_membrane_again (bool yesno)
 Run AddMembraneMover before? More...
 
void membrane_from_topology (bool yesno)
 Run MembranePositionFromTopology again? More...
 
void optimize_membrane (bool yesno)
 Optimize membrane position before relax? 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...
 

Private Member Functions

void register_options ()
 Setup Methods ///. More...
 
void set_defaults ()
 Set default values. More...
 
void init_from_cmd ()
 Initialize from commandline. More...
 

Private Attributes

core::pose::PoseOP native_
 Native. More...
 
core::Real angle_max_
 Maximum allowed dihedral angle change for Small and ShearMover. More...
 
std::string moves_
 Number of moves Small and ShearMover can make. More...
 
core::Size nmoves_
 
core::kinematics::MoveMapOP movemap_
 Movemap for Small and ShearMover. More...
 
core::scoring::ScoreFunctionOP sfxn_
 Scorefxn. More...
 
std::string cst_file_
 constraint filename More...
 
core::Real cst_weight_
 constraint weight More...
 
bool addmem_
 Run AddMembraneMover again? More...
 
bool mem_from_topo_
 Run MembranePositionFromTopology? More...
 
bool opt_mem_
 Optimize membrane before? 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
 
- 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...
 
- 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::membrane::MPQuickRelaxMover::MPQuickRelaxMover ( )

Constructors ///.

Default Constructor

Defaults: dih angle_max = 1, nmoves = "nres", movemap = bb and all chi

Default Constructor

Defaults: dih angle_max = 1, nmoves = nres, movemap = bb and all chi

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

Referenced by operator=().

protocols::membrane::MPQuickRelaxMover::MPQuickRelaxMover ( core::Real  angle_max,
std::string  nmoves 
)

Custom Constructor.

nmoves is a string because it can either be "nres" or an integer

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

protocols::membrane::MPQuickRelaxMover::MPQuickRelaxMover ( core::Real  angle_max,
std::string  nmoves,
core::kinematics::MoveMapOP  movemap 
)

Custom Constructor.

Custom constructor.

References angle_max_, init_from_cmd(), movemap_, moves_, register_options(), and set_defaults().

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

Copy Constructor.

Create a deep copy of this mover

protocols::membrane::MPQuickRelaxMover::~MPQuickRelaxMover ( )
overridedefault

Destructor.

Member Function Documentation

void protocols::membrane::MPQuickRelaxMover::add_membrane_again ( bool  yesno)

Run AddMembraneMover before?

Run AddMembraneMover again?

If you want to keep your anchor point for MEM, then pick no

References addmem_.

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

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

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

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

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

Mover Methods ///.

Get the name of this Mover (MPQuickRelaxMover)

Implements protocols::moves::Mover.

void protocols::membrane::MPQuickRelaxMover::init_from_cmd ( )
private
void protocols::membrane::MPQuickRelaxMover::membrane_from_topology ( bool  yesno)

Run MembranePositionFromTopology again?

Will change the starting membrane position

References mem_from_topo_.

MPQuickRelaxMover & protocols::membrane::MPQuickRelaxMover::operator= ( MPQuickRelaxMover const &  src)

Assignment Operator.

References MPQuickRelaxMover().

void protocols::membrane::MPQuickRelaxMover::optimize_membrane ( bool  yesno)

Optimize membrane position before relax?

References opt_mem_.

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

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

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

Setup Methods ///.

Register Options from Command Line

Referenced by MPQuickRelaxMover().

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

Member Data Documentation

bool protocols::membrane::MPQuickRelaxMover::addmem_
private

Run AddMembraneMover again?

This is stupid: we need this as a workaround for attaching the MEM at the correct anchor point, neither sliding the jump nor removing the MEM and re-attaching it works. :(

Referenced by add_membrane_again(), apply(), and set_defaults().

core::Real protocols::membrane::MPQuickRelaxMover::angle_max_
private

Maximum allowed dihedral angle change for Small and ShearMover.

Referenced by apply(), init_from_cmd(), MPQuickRelaxMover(), and set_defaults().

std::string protocols::membrane::MPQuickRelaxMover::cst_file_
private

constraint filename

Referenced by apply(), and init_from_cmd().

core::Real protocols::membrane::MPQuickRelaxMover::cst_weight_
private

constraint weight

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

bool protocols::membrane::MPQuickRelaxMover::mem_from_topo_
private

Run MembranePositionFromTopology?

Referenced by apply(), membrane_from_topology(), and set_defaults().

core::kinematics::MoveMapOP protocols::membrane::MPQuickRelaxMover::movemap_
private

Movemap for Small and ShearMover.

Referenced by apply(), MPQuickRelaxMover(), and set_defaults().

std::string protocols::membrane::MPQuickRelaxMover::moves_
private

Number of moves Small and ShearMover can make.

moves_ is a string and can take 'nres' as well as a number nmoves_ is the actual number that is taken after conversion

Referenced by apply(), init_from_cmd(), MPQuickRelaxMover(), and set_defaults().

core::pose::PoseOP protocols::membrane::MPQuickRelaxMover::native_
private

Native.

Referenced by apply(), and init_from_cmd().

core::Size protocols::membrane::MPQuickRelaxMover::nmoves_
private

Referenced by apply().

bool protocols::membrane::MPQuickRelaxMover::opt_mem_
private

Optimize membrane before?

Referenced by apply(), optimize_membrane(), and set_defaults().

core::scoring::ScoreFunctionOP protocols::membrane::MPQuickRelaxMover::sfxn_
private

Scorefxn.

Referenced by apply(), and set_defaults().


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