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

#include <OptimizeMembranePositionMover.hh>

Inheritance diagram for protocols::membrane::OptimizeMembranePositionMover:
Inheritance graph

Public Member Functions

 OptimizeMembranePositionMover ()
 Constructors ///. More...
 OptimizeMembranePositionMover (OptimizeMembranePositionMover const &src)
 Copy Constructor. More...
OptimizeMembranePositionMoveroperator= (OptimizeMembranePositionMover const &src)
 Assignment Operator. More...
 ~OptimizeMembranePositionMover () 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 (core::pose::Pose &pose) override
 Flip the downstream partner in the membrane. More...
core::scoring::ScoreFunctionOP get_sfxn () const
 Get Methods ///. More...
core::Real get_score_best () const
 Get score_best for this Mover. More...
core::Real get_starting_z () const
 Get starting_z for this Mover. More...
core::Real get_best_z () const
 Get best_z for this Mover. More...
core::Real get_stepsize_z () const
 Get stepsize_z for this Mover. More...
core::Real get_stepsize_angle () const
 Get stepsize_angle for this Mover. 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...

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 optimize_membrane_center (core::pose::Pose &pose)
 optimize membrane center More...
void optimize_membrane_normal (core::pose::Pose &pose)
 Optimize membrane normal. More...

Private Attributes

core::kinematics::FoldTree ft_
 Original foldtree before optimization. More...
core::scoring::ScoreFunctionOP sfxn_
 Scorefunction. More...
core::Real score_best_
core::Real starting_z_
 center search More...
core::Real best_z_
core::Real stepsize_z_
core::Vector best_center_
core::Real stepsize_angle_
 Normal search. More...
core::Vector best_normal_

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

◆ OptimizeMembranePositionMover() [1/2]

protocols::membrane::OptimizeMembranePositionMover::OptimizeMembranePositionMover ( )

Constructors ///.

Default Constructor

Defaults: scorefxn = smooth2012

References register_options(), and set_defaults().

Referenced by operator=().

◆ OptimizeMembranePositionMover() [2/2]

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

Copy Constructor.

Create a deep copy of this mover

◆ ~OptimizeMembranePositionMover()

protocols::membrane::OptimizeMembranePositionMover::~OptimizeMembranePositionMover ( )


Member Function Documentation

◆ apply()

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

◆ clone()

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

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

◆ fresh_instance()

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

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_best_z()

core::Real protocols::membrane::OptimizeMembranePositionMover::get_best_z ( ) const

Get best_z for this Mover.

References best_z_.

◆ get_name()

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

Mover Methods ///.

Get the name of this Mover (OptimizeMembranePositionMover)

Implements protocols::moves::Mover.

◆ get_score_best()

core::Real protocols::membrane::OptimizeMembranePositionMover::get_score_best ( ) const

Get score_best for this Mover.

References score_best_.

◆ get_sfxn()

core::scoring::ScoreFunctionOP protocols::membrane::OptimizeMembranePositionMover::get_sfxn ( ) const

Get Methods ///.

Get Scorefunction for this Mover

References sfxn_.

◆ get_starting_z()

core::Real protocols::membrane::OptimizeMembranePositionMover::get_starting_z ( ) const

Get starting_z for this Mover.

References starting_z_.

◆ get_stepsize_angle()

core::Real protocols::membrane::OptimizeMembranePositionMover::get_stepsize_angle ( ) const

Get stepsize_angle for this Mover.

References stepsize_angle_.

◆ get_stepsize_z()

core::Real protocols::membrane::OptimizeMembranePositionMover::get_stepsize_z ( ) const

Get stepsize_z for this Mover.

References stepsize_z_.

◆ operator=()

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

Assignment Operator.

References OptimizeMembranePositionMover().

◆ optimize_membrane_center()

void protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_center ( core::pose::Pose pose)

optimize membrane center

Optimize membrane center.

References best_center_, best_z_, core::pose::Pose::conformation(), core::pose::Pose::membrane_info(), score_best_, sfxn_, starting_z_, stepsize_z_, and protocols::TR().

Referenced by apply().

◆ optimize_membrane_normal()

void protocols::membrane::OptimizeMembranePositionMover::optimize_membrane_normal ( core::pose::Pose pose)

◆ parse_my_tag()

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

Parse Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

References best_z_, core::scoring::ScoreFunctionFactory::create_score_function(), score_best_, sfxn_, starting_z_, stepsize_angle_, and stepsize_z_.

◆ provide_xml_schema()

void protocols::membrane::OptimizeMembranePositionMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ register_options()

void protocols::membrane::OptimizeMembranePositionMover::register_options ( )

Setup Methods ///.

Register Options from Command Line

Referenced by OptimizeMembranePositionMover().

◆ set_defaults()

void protocols::membrane::OptimizeMembranePositionMover::set_defaults ( )

Member Data Documentation

◆ best_center_

core::Vector protocols::membrane::OptimizeMembranePositionMover::best_center_

◆ best_normal_

core::Vector protocols::membrane::OptimizeMembranePositionMover::best_normal_

◆ best_z_

core::Real protocols::membrane::OptimizeMembranePositionMover::best_z_

◆ ft_

core::kinematics::FoldTree protocols::membrane::OptimizeMembranePositionMover::ft_

Original foldtree before optimization.

Will be reset to original after the optimization

◆ score_best_

core::Real protocols::membrane::OptimizeMembranePositionMover::score_best_

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::membrane::OptimizeMembranePositionMover::sfxn_

◆ starting_z_

core::Real protocols::membrane::OptimizeMembranePositionMover::starting_z_

◆ stepsize_angle_

core::Real protocols::membrane::OptimizeMembranePositionMover::stepsize_angle_

◆ stepsize_z_

core::Real protocols::membrane::OptimizeMembranePositionMover::stepsize_z_

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