Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::membrane::MPQuickRelaxMover Class Reference

#include <MPQuickRelaxMover.hh>

Inheritance diagram for protocols::membrane::MPQuickRelaxMover:
Inheritance graph

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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

◆ MPQuickRelaxMover() [1/4]

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=().

◆ MPQuickRelaxMover() [2/4]

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().

◆ MPQuickRelaxMover() [3/4]

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().

◆ MPQuickRelaxMover() [4/4]

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

Copy Constructor.

Create a deep copy of this mover

◆ ~MPQuickRelaxMover()

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


Member Function Documentation

◆ add_membrane_again()

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_.

◆ apply()

void protocols::membrane::MPQuickRelaxMover::apply ( core::pose::Pose pose)

◆ clone()

protocols::moves::MoverOP protocols::membrane::MPQuickRelaxMover::clone ( ) const

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

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

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

Mover Methods ///.

Get the name of this Mover (MPQuickRelaxMover)

Implements protocols::moves::Mover.

◆ init_from_cmd()

void protocols::membrane::MPQuickRelaxMover::init_from_cmd ( )

◆ membrane_from_topology()

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

Run MembranePositionFromTopology again?

Will change the starting membrane position

References mem_from_topo_.

◆ operator=()

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

Assignment Operator.

References MPQuickRelaxMover().

◆ optimize_membrane()

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

Optimize membrane position before relax?

References opt_mem_.

◆ parse_my_tag()

void protocols::membrane::MPQuickRelaxMover::parse_my_tag ( utility::tag::TagCOP  tag,

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

◆ register_options()

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

Setup Methods ///.

Register Options from Command Line

Referenced by MPQuickRelaxMover().

◆ set_defaults()

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

Member Data Documentation

◆ addmem_

bool protocols::membrane::MPQuickRelaxMover::addmem_

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().

◆ angle_max_

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

Maximum allowed dihedral angle change for Small and ShearMover.

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

◆ cst_file_

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

constraint filename

Referenced by apply(), and init_from_cmd().

◆ cst_weight_

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

constraint weight

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

◆ mem_from_topo_

bool protocols::membrane::MPQuickRelaxMover::mem_from_topo_

Run MembranePositionFromTopology?

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

◆ movemap_

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

Movemap for Small and ShearMover.

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

◆ moves_

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

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().

◆ native_

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


Referenced by apply(), and init_from_cmd().

◆ nmoves_

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

Referenced by apply().

◆ opt_mem_

bool protocols::membrane::MPQuickRelaxMover::opt_mem_

Optimize membrane before?

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

◆ sfxn_

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


Referenced by apply(), and set_defaults().

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