Inheritance diagram for TestQuickRelaxMover:

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

	TestQuickRelaxMover (Real angle_max, std::string nmoves)
	Custom Constructor. More...

	TestQuickRelaxMover (Real angle_max, std::string nmoves, MoveMapOP movemap)
	Custom Constructor. More...

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

TestQuickRelaxMover &	operator= (TestQuickRelaxMover const &src)
	Assignment Operator. More...

	~TestQuickRelaxMover () override
	Destructor. More...

std::string	get_name () const override
	Rosetta Scripts Methods ///. More...

void	apply (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...

Private Member Functions
void	register_options ()
	Setup Methods ///. More...

void	set_defaults ()
	Set default values. More...

void	init_from_cmd ()
	Initialize from commandline. More...

utility::vector1< bool >	get_repack_residues (Pose &pose, core::SSize center1, core::SSize center2, core::SSize halfrange)
	Initialize from commandline. More...

Private Attributes
PoseOP	native_
	Native. More...

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...

Size	nmoves_

MoveMapOP	movemap_
	Movemap for Small and ShearMover. More...

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...

bool	repack_again_
	Additional round of repack which packs all residues simultaneously. More...

Constructor & Destructor Documentation

◆ TestQuickRelaxMover() [1/4]

TestQuickRelaxMover::TestQuickRelaxMover ( )

Constructors ///.

Default Constructor.

Default Constructor

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

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

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

Referenced by operator=().

◆ TestQuickRelaxMover() [2/4]

TestQuickRelaxMover::TestQuickRelaxMover	(	Real	angle_max,
		std::string	nmoves
	)

Custom Constructor.

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

References basic::options::OptionKeys::mp::quickrelax::angle_max, angle_max_, init_from_cmd(), moves_, basic::options::OptionKeys::mp::quickrelax::nmoves, register_options(), and set_defaults().

◆ TestQuickRelaxMover() [3/4]

TestQuickRelaxMover::TestQuickRelaxMover	(	Real	angle_max,
		std::string	nmoves,
		MoveMapOP	movemap
	)

Custom Constructor.

Custom constructor.

References basic::options::OptionKeys::mp::quickrelax::angle_max, angle_max_, init_from_cmd(), basic::options::OptionKeys::in::file::movemap, movemap_, moves_, basic::options::OptionKeys::mp::quickrelax::nmoves, register_options(), and set_defaults().

◆ TestQuickRelaxMover() [4/4]

TestQuickRelaxMover::TestQuickRelaxMover ( TestQuickRelaxMover const & src )

Copy Constructor.

Create a deep copy of this mover

◆ ~TestQuickRelaxMover()

TestQuickRelaxMover::~TestQuickRelaxMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ add_membrane_again()

void TestQuickRelaxMover::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 TestQuickRelaxMover::apply ( Pose & pose )

override

Flip the downstream partner in the membrane.

Mover Methods ///.

Run a quick relax on a membrane protein

Requires AddMembraneMover to be run beforehand

Referenced by pyrosetta.bindings.scores.simple_metrics.SimpleMetricDataAccessorBase::__setitem__(), pyrosetta.bindings.scores.base.PoseCacheAccessorBase::_maybe_delete_keys_from_sm_data(), and pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ get_name()

std::string TestQuickRelaxMover::get_name ( ) const

override

Rosetta Scripts Methods ///.

Mover Methods ///

Get the name of this Mover (TestQuickRelaxMover)

Create a Clone of this mover

Get the name of this Mover (TestQuickRelaxMover)

◆ get_repack_residues()

utility::vector1< bool > TestQuickRelaxMover::get_repack_residues	(	Pose &	pose,
		core::SSize	center1,
		core::SSize	center2,
		core::SSize	halfrange
	)

private

Initialize from commandline.

References create_a3b_hbs::i, create_a3b_hbs::j, kmeans_adaptive_kernel_density_bb_dependent_rotlib::m, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, create_a3b_hbs::nres, beta_nonlocal::pose, and TR.

Referenced by apply().

◆ init_from_cmd()

void TestQuickRelaxMover::init_from_cmd ( )

private

Initialize from commandline.

References basic::options::OptionKeys::mp::quickrelax::angle_max, angle_max_, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, cst_file_, basic::options::OptionKeys::constraints::cst_weight, cst_weight_, moves_, surface_app::native, native_, basic::options::OptionKeys::mp::quickrelax::nmoves, option, pyrosetta.distributed.io::pose_from_file(), basic::options::OptionKeys::mp::quickrelax::repack_again, repack_again_, utility::to_string(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by TestQuickRelaxMover().

◆ membrane_from_topology()

void TestQuickRelaxMover::membrane_from_topology ( bool yesno )

Run MembranePositionFromTopology again?

Will change the starting membrane position

References mem_from_topo_.

◆ operator=()

TestQuickRelaxMover & TestQuickRelaxMover::operator= ( TestQuickRelaxMover const & src )

Assignment Operator.

References TestQuickRelaxMover().

◆ optimize_membrane()

void TestQuickRelaxMover::optimize_membrane ( bool yesno )

Optimize membrane position before relax?

References opt_mem_.

◆ register_options()

void TestQuickRelaxMover::register_options ( )

private

Setup Methods ///.

Register Options from Command Line

References basic::options::OptionKeys::mp::quickrelax::angle_max, basic::options::OptionKeys::cluster::energy_based_clustering::cst_file, basic::options::OptionKeys::constraints::cst_weight, surface_app::native, basic::options::OptionKeys::mp::quickrelax::nmoves, option, and basic::options::OptionKeys::mp::quickrelax::repack_again.

Referenced by TestQuickRelaxMover().

◆ set_defaults()

void TestQuickRelaxMover::set_defaults ( )

private

Set default values.

References addmem_, angle_max_, pyrosetta.io::create_score_function, cst_weight_, mem_from_topo_, movemap_, moves_, opt_mem_, repack_again_, and sfxn_.

Referenced by TestQuickRelaxMover().

Member Data Documentation

◆ addmem_

bool TestQuickRelaxMover::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_

Real TestQuickRelaxMover::angle_max_

private

Maximum allowed dihedral angle change for Small and ShearMover.

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

◆ cst_file_

std::string TestQuickRelaxMover::cst_file_

private

constraint filename

Referenced by apply(), and init_from_cmd().

◆ cst_weight_

core::Real TestQuickRelaxMover::cst_weight_

private

constraint weight

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

◆ mem_from_topo_

bool TestQuickRelaxMover::mem_from_topo_

private

Run MembranePositionFromTopology?

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

◆ movemap_

MoveMapOP TestQuickRelaxMover::movemap_

private

Movemap for Small and ShearMover.

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

◆ moves_

std::string TestQuickRelaxMover::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(), set_defaults(), and TestQuickRelaxMover().

◆ native_

PoseOP TestQuickRelaxMover::native_

private

Native.

Referenced by apply(), and init_from_cmd().

◆ nmoves_

Size TestQuickRelaxMover::nmoves_

private

Referenced by apply().

◆ opt_mem_

bool TestQuickRelaxMover::opt_mem_

private

Optimize membrane before?

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

◆ repack_again_

bool TestQuickRelaxMover::repack_again_

private

Additional round of repack which packs all residues simultaneously.

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

◆ sfxn_

ScoreFunctionOP TestQuickRelaxMover::sfxn_

private

Scorefxn.

Referenced by apply(), and set_defaults().

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

src/apps/pilot/jkleman/mp_qrtest.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ TestQuickRelaxMover() [1/4]

◆ TestQuickRelaxMover() [2/4]

◆ TestQuickRelaxMover() [3/4]

◆ TestQuickRelaxMover() [4/4]

◆ ~TestQuickRelaxMover()

Member Function Documentation

◆ add_membrane_again()

◆ apply()

◆ get_name()

◆ get_repack_residues()

◆ init_from_cmd()

◆ membrane_from_topology()

◆ operator=()

◆ optimize_membrane()

◆ register_options()

◆ set_defaults()

Member Data Documentation

◆ addmem_

◆ angle_max_

◆ cst_file_

◆ cst_weight_

◆ mem_from_topo_

◆ movemap_

◆ moves_

◆ native_

◆ nmoves_

◆ opt_mem_

◆ repack_again_

◆ sfxn_