#include <OptimizeMembranePositionMover.hh>

Inheritance diagram for protocols::membrane::OptimizeMembranePositionMover:

[legend]

Public Member Functions
	OptimizeMembranePositionMover ()
	Constructors ///. More...

	OptimizeMembranePositionMover (OptimizeMembranePositionMover const &src)
	Copy Constructor. More...

OptimizeMembranePositionMover &	operator= (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 Strings &	info ()
	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 )

default

Copy Constructor.

Create a deep copy of this mover

◆ ~OptimizeMembranePositionMover()

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

overridedefault

Destructor.

Member Function Documentation

◆ apply()

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

overridevirtual

Flip the downstream partner in the membrane.

Implements protocols::moves::Mover.

References core::conformation::membrane::center, protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom(), core::pose::Pose::fold_tree(), protocols::membrane::is_membrane_fixed(), core::conformation::membrane::normal, optimize_membrane_center(), optimize_membrane_normal(), core::kinematics::FoldTree::reorder(), sfxn_, core::kinematics::FoldTree::show(), and protocols::TR().

◆ clone()

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

overridevirtual

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

overridevirtual

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

overridevirtual

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 )

private

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 )

private

Optimize membrane normal.

References best_center_, best_normal_, core::pose::Pose::conformation(), core::pose::Pose::membrane_info(), score_best_, sfxn_, stepsize_angle_, and protocols::TR().

Referenced by apply().

◆ parse_my_tag()

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

overridevirtual

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 )

static

Provide xml schema for RosettaScripts compatibility.

References protocols::membrane::OptimizeMembranePositionMoverCreator::mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

◆ register_options()

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

private

Setup Methods ///.

Register Options from Command Line

Referenced by OptimizeMembranePositionMover().

◆ set_defaults()

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

private

Set default values.

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

Referenced by OptimizeMembranePositionMover().

Member Data Documentation

◆ best_center_

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

private

Referenced by optimize_membrane_center(), and optimize_membrane_normal().

◆ best_normal_

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

private

Referenced by optimize_membrane_normal().

◆ best_z_

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

private

Referenced by get_best_z(), optimize_membrane_center(), parse_my_tag(), and set_defaults().

◆ ft_

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

private

Original foldtree before optimization.

Will be reset to original after the optimization

◆ score_best_

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

private

Referenced by get_score_best(), optimize_membrane_center(), optimize_membrane_normal(), parse_my_tag(), and set_defaults().

◆ sfxn_

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

private

Scorefunction.

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

◆ starting_z_

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

private

center search

Referenced by get_starting_z(), optimize_membrane_center(), parse_my_tag(), and set_defaults().

◆ stepsize_angle_

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

private

Normal search.

Referenced by get_stepsize_angle(), optimize_membrane_normal(), parse_my_tag(), and set_defaults().

◆ stepsize_z_

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

private

Referenced by get_stepsize_z(), optimize_membrane_center(), parse_my_tag(), and set_defaults().

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

src/protocols/membrane/OptimizeMembranePositionMover.hh
src/protocols/membrane/OptimizeMembranePositionMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ OptimizeMembranePositionMover() [1/2]

◆ OptimizeMembranePositionMover() [2/2]

◆ ~OptimizeMembranePositionMover()

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_best_z()

◆ get_name()

◆ get_score_best()

◆ get_sfxn()

◆ get_starting_z()

◆ get_stepsize_angle()

◆ get_stepsize_z()

◆ operator=()

◆ optimize_membrane_center()

◆ optimize_membrane_normal()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ register_options()

◆ set_defaults()

Member Data Documentation

◆ best_center_

◆ best_normal_

◆ best_z_

◆ ft_

◆ score_best_

◆ sfxn_

◆ starting_z_

◆ stepsize_angle_

◆ stepsize_z_