#include <RangeRelaxMover.hh>

Inheritance diagram for protocols::relax::RangeRelaxMover:

[legend]

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

	RangeRelaxMover (core::Size center_resnumber)
	Custom Constructor. More...

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

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

	~RangeRelaxMover () override
	Destructor. More...

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

void	apply (Pose &pose) override
	Run RangeRelax. More...

void	add_membrane_again (bool yesno)
	Run AddMembraneMover before? More...

void	optimize_membrane (bool yesno)
	Optimize membrane. More...

void	idealize (bool yesno)
	Idealize pose after run? More...

void	set_angle_max (core::Real angle_max)
	Set maximum dihedral angle perturbation. More...

void	set_nmoves (std::string nmoves)
	Set number of moves, can be "nres" or a number. More...

void	set_scorefunction (core::scoring::ScoreFunctionOP sfxn)
	Use scorefunction. More...

void	set_native (core::pose::PoseOP pose)
	Set native. 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 MoverOP	clone () const
	Return a clone of the Mover object. 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...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. 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

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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...

core::kinematics::FoldTree	finalize_setup (Pose &pose)
	Finalize setup. More...

void	constrain_to_reference (Pose &pose, Pose &ref_pose)
	Create constraints to reference pose. More...

void	repack_sequence_window (Pose &pose, protocols::moves::MonteCarloOP mc)
	Repack in a sequence window. More...

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

void	repack_spherical_range (Pose &pose, protocols::moves::MonteCarloOP mc)
	Repack in spherical range. More...

utility::vector1< bool >	get_spherical_repack_residues (Pose &pose, core::Real inner_radius, core::Real outer_radius)
	Initialize from commandline. More...

void	repack_all (Pose &pose, protocols::moves::MonteCarloOP mc)
	Repack all residues again. More...

void	idealize_pose (Pose &pose, core::optimization::MinimizerOptions minopts, core::optimization::AtomTreeMinimizer atm)
	Idealize pose. More...

void	print_score (Pose &pose)
	Print score to cout. More...

Private Attributes
core::pose::PoseOP	native_
	Native. More...

core::Size	center_resnumber_
	Center residue number. 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 for scoring. More...

core::scoring::ScoreFunctionOP	sfxn_nocst_
	Scorefunction without constraints. More...

std::string	cst_file_
	constraint filename More...

core::Real	cst_weight_
	constraint weight More...

bool	cst_to_start_
	constrain to starting coordinates More...

bool	cst_to_native_
	constrain to native More...

bool	addmem_
	Add Membrane to native? More...

bool	optmem_
	Optimize membrane for protein? More...

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

core::Size	cycles_
	Cycles for repacking and minimization. More...

core::Size	min_cycles_
	Cycles within the Minimizer. More...

bool	spherical_wave_
	Relax in centric wave pattern. More...

bool	idealize_
	Idealize decoy after run? 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

◆ RangeRelaxMover() [1/3]

protocols::relax::RangeRelaxMover::RangeRelaxMover ( )

Constructors ///.

Default Constructor

Defaults: dih angle_max = 0.1, 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=().

◆ RangeRelaxMover() [2/3]

protocols::relax::RangeRelaxMover::RangeRelaxMover ( core::Size center_resnumber )

Custom Constructor.

Takes the center residue to start relaxing from

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

◆ RangeRelaxMover() [3/3]

protocols::relax::RangeRelaxMover::RangeRelaxMover ( RangeRelaxMover const & src )

default

Copy Constructor.

Create a deep copy of this mover

◆ ~RangeRelaxMover()

protocols::relax::RangeRelaxMover::~RangeRelaxMover ( )

overridedefault

Destructor.

Member Function Documentation

◆ add_membrane_again()

void protocols::relax::RangeRelaxMover::add_membrane_again ( bool yesno )

Run AddMembraneMover before?

Run AddMembraneMover again?

If you want to keep your anchor point for MEM, then pick no This is only needed for the native, not the pose itself

If you want to keep your anchor point for MEM, then pick no

References addmem_.

◆ apply()

void protocols::relax::RangeRelaxMover::apply ( Pose & pose )

overridevirtual

Run RangeRelax.

Mover Methods ///.

Run RangeRelax

Implements protocols::moves::Mover.

References protocols::jd2::add_string_real_pair_to_current_job(), angle_max_, core::scoring::bb_rmsd(), core::pose::Pose::conformation(), cst_to_start_, cycles_, core::pose::Pose::energies(), core::scoring::fa_rep, finalize_setup(), core::pose::Pose::fold_tree(), idealize_, idealize_pose(), core::pose::Pose::is_centroid(), core::conformation::Conformation::is_membrane(), core::optimization::MinimizerOptions::max_iter(), min_cycles_, movemap_, native_, nmoves_, core::pose::nres_protein(), optmem_, print_score(), protocols::rigid::random, repack_again_, repack_all(), repack_sequence_window(), repack_spherical_range(), core::optimization::AtomTreeMinimizer::run(), sfxn_, core::kinematics::FoldTree::show(), spherical_wave_, core::scoring::Energies::total_energies(), core::scoring::Energies::total_energy(), and protocols::relax::TR().

◆ constrain_to_reference()

void protocols::relax::RangeRelaxMover::constrain_to_reference	(	Pose &	pose,
		Pose &	ref_pose
	)

private

Create constraints to reference pose.

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom(), core::scoring::coordinate_constraint, core::pose::nres_protein(), core::pose::Pose::residue(), sfxn_, sfxn_nocst_, and core::conformation::Atom::xyz().

Referenced by finalize_setup().

◆ finalize_setup()

core::kinematics::FoldTree protocols::relax::RangeRelaxMover::finalize_setup ( Pose & pose )

private

Finalize setup.

References addmem_, core::scoring::angle_constraint, core::scoring::atom_pair_constraint, center_resnumber_, core::pose::Pose::clone(), core::pose::Pose::conformation(), constrain_to_reference(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, cst_file_, cst_to_native_, cst_to_start_, cst_weight_, core::scoring::dihedral_constraint, core::pose::Pose::fold_tree(), core::conformation::Conformation::is_membrane(), protocols::membrane::is_membrane_fixed(), moves_, native_, nmoves_, core::pose::nres_protein(), core::kinematics::FoldTree::reorder(), core::conformation::symmetry::residue_center_of_mass(), protocols::membrane::rsd_closest_to_pose_tm_com(), protocols::membrane::setup_foldtree_pose_com(), sfxn_, sfxn_nocst_, core::kinematics::FoldTree::show(), and protocols::relax::TR().

Referenced by apply().

◆ get_name()

std::string protocols::relax::RangeRelaxMover::get_name ( ) const

overridevirtual

Rosetta Scripts Methods ///.

Mover Methods ///

Get the name of this Mover (RangeRelaxMover)

Create a Clone of this mover

Get the name of this Mover (RangeRelaxMover)

Implements protocols::moves::Mover.

◆ get_spherical_repack_residues()

utility::vector1< bool > protocols::relax::RangeRelaxMover::get_spherical_repack_residues	(	Pose &	pose,
		core::Real	inner_radius,
		core::Real	outer_radius
	)

private

Initialize from commandline.

References center_resnumber_, protocols::simple_filters::coords(), core::kinematics::distance(), core::pose::nres_protein(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::relax::TR(), and core::conformation::Residue::xyz().

Referenced by repack_spherical_range().

◆ get_window_repack_residues()

utility::vector1< bool > protocols::relax::RangeRelaxMover::get_window_repack_residues	(	Pose &	pose,
		core::SSize	center1,
		core::SSize	center2,
		core::SSize	halfrange
	)

private

Initialize from commandline.

References core::pose::Pose::size(), and protocols::relax::TR().

Referenced by repack_sequence_window().

◆ idealize()

void protocols::relax::RangeRelaxMover::idealize ( bool yesno )

Idealize pose after run?

Might lead to better decoy but takes longer

References idealize_.

◆ idealize_pose()

void protocols::relax::RangeRelaxMover::idealize_pose	(	Pose &	pose,
		core::optimization::MinimizerOptions	minopts,
		core::optimization::AtomTreeMinimizer	atm
	)

private

◆ init_from_cmd()

void protocols::relax::RangeRelaxMover::init_from_cmd ( )

private

Initialize from commandline.

References addmem_, angle_max_, cst_file_, cst_to_native_, cst_to_start_, cst_weight_, cycles_, idealize_, min_cycles_, moves_, native_, optmem_, core::import_pose::PDB_file, core::import_pose::pose_from_file(), repack_again_, spherical_wave_, and protocols::relax::TR().

Referenced by RangeRelaxMover().

◆ operator=()

RangeRelaxMover & protocols::relax::RangeRelaxMover::operator= ( RangeRelaxMover const & src )

Assignment Operator.

References RangeRelaxMover().

◆ optimize_membrane()

void protocols::relax::RangeRelaxMover::optimize_membrane ( bool yesno )

Optimize membrane.

References optmem_.

◆ print_score()

void protocols::relax::RangeRelaxMover::print_score ( Pose & pose )

private

Print score to cout.

References core::pose::Pose::energies(), core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::Energies::show_total_headers(), core::scoring::Energies::show_totals(), core::scoring::Energies::total_energies(), and protocols::relax::TR().

Referenced by apply(), repack_all(), repack_sequence_window(), and repack_spherical_range().

◆ register_options()

void protocols::relax::RangeRelaxMover::register_options ( )

private

Setup Methods ///.

Register Options from Command Line

Referenced by RangeRelaxMover().

◆ repack_all()

void protocols::relax::RangeRelaxMover::repack_all	(	Pose &	pose,
		protocols::moves::MonteCarloOP	mc
	)

private

Repack all residues again.

References core::pack::task::TaskFactory::create_packer_task(), core::pack::pack_rotamers(), print_score(), sfxn_, and protocols::relax::TR().

Referenced by apply().

◆ repack_sequence_window()

void protocols::relax::RangeRelaxMover::repack_sequence_window	(	Pose &	pose,
		protocols::moves::MonteCarloOP	mc
	)

private

Repack in a sequence window.

References center_resnumber_, core::pack::task::TaskFactory::create_packer_task(), get_window_repack_residues(), core::pack::pack_rotamers(), print_score(), protocols::sic_dock::range(), protocols::antibody::design::repack, sfxn_, core::pose::Pose::size(), and protocols::relax::TR().

Referenced by apply().

◆ repack_spherical_range()

void protocols::relax::RangeRelaxMover::repack_spherical_range	(	Pose &	pose,
		protocols::moves::MonteCarloOP	mc
	)

private

Repack in spherical range.

References center_resnumber_, protocols::simple_filters::coords(), core::pack::task::TaskFactory::create_packer_task(), get_spherical_repack_residues(), core::pack::pack_rotamers(), print_score(), protocols::antibody::design::repack, core::pose::Pose::residue(), sfxn_, core::pose::Pose::size(), protocols::relax::TR(), and core::conformation::Residue::xyz().

Referenced by apply().

◆ set_angle_max()

void protocols::relax::RangeRelaxMover::set_angle_max ( core::Real angle_max )

Set maximum dihedral angle perturbation.

References angle_max_.

◆ set_defaults()

void protocols::relax::RangeRelaxMover::set_defaults ( )

private

Set default values.

References addmem_, angle_max_, center_resnumber_, cst_file_, cst_to_native_, cst_to_start_, cst_weight_, cycles_, core::scoring::get_score_function(), idealize_, min_cycles_, movemap_, moves_, native_, optmem_, repack_again_, sfxn_, sfxn_nocst_, and spherical_wave_.

Referenced by RangeRelaxMover().

◆ set_native()

void protocols::relax::RangeRelaxMover::set_native ( core::pose::PoseOP pose )

Set native.

References native_.

◆ set_nmoves()

void protocols::relax::RangeRelaxMover::set_nmoves ( std::string nmoves )

Set number of moves, can be "nres" or a number.

References moves_.

◆ set_scorefunction()

void protocols::relax::RangeRelaxMover::set_scorefunction ( core::scoring::ScoreFunctionOP sfxn )

Use scorefunction.

Use membrane scorefunction.

References sfxn_, and sfxn_nocst_.

Member Data Documentation

◆ addmem_

bool protocols::relax::RangeRelaxMover::addmem_

private

Add Membrane to native?

Referenced by add_membrane_again(), finalize_setup(), init_from_cmd(), and set_defaults().

◆ angle_max_

core::Real protocols::relax::RangeRelaxMover::angle_max_

private

Maximum allowed dihedral angle change for Small and ShearMover.

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

◆ center_resnumber_

core::Size protocols::relax::RangeRelaxMover::center_resnumber_

private

Center residue number.

Referenced by finalize_setup(), get_spherical_repack_residues(), RangeRelaxMover(), repack_sequence_window(), repack_spherical_range(), and set_defaults().

◆ cst_file_

std::string protocols::relax::RangeRelaxMover::cst_file_

private

constraint filename

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

◆ cst_to_native_

bool protocols::relax::RangeRelaxMover::cst_to_native_

private

constrain to native

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

◆ cst_to_start_

bool protocols::relax::RangeRelaxMover::cst_to_start_

private

constrain to starting coordinates

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

◆ cst_weight_

core::Real protocols::relax::RangeRelaxMover::cst_weight_

private

constraint weight

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

◆ cycles_

core::Size protocols::relax::RangeRelaxMover::cycles_

private

Cycles for repacking and minimization.

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

◆ idealize_

bool protocols::relax::RangeRelaxMover::idealize_

private

Idealize decoy after run?

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

◆ min_cycles_

core::Size protocols::relax::RangeRelaxMover::min_cycles_

private

Cycles within the Minimizer.

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

◆ movemap_

core::kinematics::MoveMapOP protocols::relax::RangeRelaxMover::movemap_

private

Movemap for Small and ShearMover.

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

◆ moves_

std::string protocols::relax::RangeRelaxMover::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 finalize_setup(), init_from_cmd(), set_defaults(), and set_nmoves().

◆ native_

core::pose::PoseOP protocols::relax::RangeRelaxMover::native_

private

Native.

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

◆ nmoves_

core::Size protocols::relax::RangeRelaxMover::nmoves_

private

Referenced by apply(), and finalize_setup().

◆ optmem_

bool protocols::relax::RangeRelaxMover::optmem_

private

Optimize membrane for protein?

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

◆ repack_again_

bool protocols::relax::RangeRelaxMover::repack_again_

private

Additional round of repack which packs all residues simultaneously.

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

◆ sfxn_

core::scoring::ScoreFunctionOP protocols::relax::RangeRelaxMover::sfxn_

private

Scorefxn for scoring.

Referenced by apply(), constrain_to_reference(), finalize_setup(), idealize_pose(), repack_all(), repack_sequence_window(), repack_spherical_range(), set_defaults(), and set_scorefunction().

◆ sfxn_nocst_

core::scoring::ScoreFunctionOP protocols::relax::RangeRelaxMover::sfxn_nocst_

private

Scorefunction without constraints.

Referenced by constrain_to_reference(), finalize_setup(), set_defaults(), and set_scorefunction().

◆ spherical_wave_

bool protocols::relax::RangeRelaxMover::spherical_wave_

private

Relax in centric wave pattern.

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

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

src/protocols/relax/RangeRelaxMover.hh
src/protocols/relax/RangeRelaxMover.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ RangeRelaxMover() [1/3]

◆ RangeRelaxMover() [2/3]

◆ RangeRelaxMover() [3/3]

◆ ~RangeRelaxMover()

Member Function Documentation

◆ add_membrane_again()

◆ apply()

◆ constrain_to_reference()

◆ finalize_setup()

◆ get_name()

◆ get_spherical_repack_residues()

◆ get_window_repack_residues()

◆ idealize()

◆ idealize_pose()

◆ init_from_cmd()

◆ operator=()

◆ optimize_membrane()

◆ print_score()

◆ register_options()

◆ repack_all()

◆ repack_sequence_window()

◆ repack_spherical_range()

◆ set_angle_max()

◆ set_defaults()

◆ set_native()

◆ set_nmoves()

◆ set_scorefunction()

Member Data Documentation

◆ addmem_

◆ angle_max_

◆ center_resnumber_

◆ cst_file_

◆ cst_to_native_

◆ cst_to_start_

◆ cst_weight_

◆ cycles_

◆ idealize_

◆ min_cycles_

◆ movemap_

◆ moves_

◆ native_

◆ nmoves_

◆ optmem_

◆ repack_again_

◆ sfxn_

◆ sfxn_nocst_

◆ spherical_wave_