#include <MPQuickRelaxMover.hh>

Inheritance diagram for protocols::membrane::MPQuickRelaxMover:

[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...

MPQuickRelaxMover &	operator= (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 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...

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 )

default

Copy Constructor.

Create a deep copy of this mover

◆ ~MPQuickRelaxMover()

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

overridedefault

Destructor.

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 )

overridevirtual

Flip the downstream partner in the membrane.

Mover Methods ///.

Run a quick relax on a membrane protein

Requires AddMembraneMover to be run beforehand

Implements protocols::moves::Mover.

References protocols::jd2::add_string_real_pair_to_current_job(), addmem_, core::scoring::angle_constraint, angle_max_, core::scoring::atom_pair_constraint, core::scoring::bb_rmsd(), core::pose::Pose::constraint_set(), cst_file_, cst_weight_, core::scoring::dihedral_constraint, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, protocols::moves::FAIL_DO_NOT_RETRY, core::pose::Pose::fold_tree(), protocols::membrane::is_membrane_fixed(), mem_from_topo_, movemap_, moves_, native_, nmoves_, core::pose::nres_protein(), opt_mem_, core::pack::pack_rotamers(), protocols::antibody::design::repack, core::optimization::AtomTreeMinimizer::run(), protocols::moves::Mover::set_last_move_status(), sfxn_, core::kinematics::FoldTree::show(), core::scoring::Energies::show_total_headers(), core::scoring::Energies::show_totals(), core::id::to_string(), core::scoring::Energies::total_energies(), core::scoring::Energies::total_energy(), and protocols::TR().

◆ clone()

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

overridevirtual

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

overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

◆ get_name()

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

overridevirtual

Mover Methods ///.

Get the name of this Mover (MPQuickRelaxMover)

Implements protocols::moves::Mover.

◆ init_from_cmd()

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

private

Initialize from commandline.

References angle_max_, cst_file_, cst_weight_, moves_, native_, core::pose::nres_protein(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and core::id::to_string().

Referenced by MPQuickRelaxMover().

◆ 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,
		basic::datacache::DataMap &
	)

overridevirtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

◆ register_options()

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

private

Setup Methods ///.

Register Options from Command Line

Referenced by MPQuickRelaxMover().

◆ set_defaults()

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

private

Set default values.

References addmem_, angle_max_, core::scoring::ScoreFunctionFactory::create_score_function(), cst_weight_, mem_from_topo_, movemap_, moves_, opt_mem_, and sfxn_.

Referenced by MPQuickRelaxMover().

Member Data Documentation

◆ addmem_

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().

◆ angle_max_

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().

◆ cst_file_

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

private

constraint filename

Referenced by apply(), and init_from_cmd().

◆ cst_weight_

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

private

constraint weight

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

◆ mem_from_topo_

bool protocols::membrane::MPQuickRelaxMover::mem_from_topo_

private

Run MembranePositionFromTopology?

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

◆ movemap_

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

private

Movemap for Small and ShearMover.

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

◆ moves_

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().

◆ native_

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

private

Native.

Referenced by apply(), and init_from_cmd().

◆ nmoves_

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

private

Referenced by apply().

◆ opt_mem_

bool protocols::membrane::MPQuickRelaxMover::opt_mem_

private

Optimize membrane before?

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

◆ sfxn_

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:

src/protocols/membrane/MPQuickRelaxMover.hh
src/protocols/membrane/MPQuickRelaxMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ MPQuickRelaxMover() [1/4]

◆ MPQuickRelaxMover() [2/4]

◆ MPQuickRelaxMover() [3/4]

◆ MPQuickRelaxMover() [4/4]

◆ ~MPQuickRelaxMover()

Member Function Documentation

◆ add_membrane_again()

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ init_from_cmd()

◆ membrane_from_topology()

◆ operator=()

◆ optimize_membrane()

◆ parse_my_tag()

◆ register_options()

◆ set_defaults()

Member Data Documentation

◆ addmem_

◆ angle_max_

◆ cst_file_

◆ cst_weight_

◆ mem_from_topo_

◆ movemap_

◆ moves_

◆ native_

◆ nmoves_

◆ opt_mem_

◆ sfxn_