#include <HemeBindingMover.hh>

Inheritance diagram for HemeBindingMover:

Public Member Functions
	HemeBindingMover ()

	HemeBindingMover (core::scoring::ScoreFunctionOP const &sfxn, protocols::backrub::BackrubMoverOP &brm, protocols::simple_moves::PackRotamersMoverOP &prm, core::Size n_it=1000, core::Real temperature=0.6)

	HemeBindingMover (core::scoring::ScoreFunctionOP const &sfxn, core::pack::task::TaskFactoryOP const &tf, core::Size n_it, core::Real temperature=0.6)

	HemeBindingMover (HemeBindingMover const &other)

virtual	~HemeBindingMover ()

void	score_function (core::scoring::ScoreFunctionOP other_score_function)

void	backrub_mover (protocols::backrub::BackrubMoverOP br_mover)

void	pack_rotamers_mover (protocols::simple_moves::PackRotamersMoverOP pr_mover)

void	num_iterations (core::Size n_it)

void	temperature (core::Real temp)

void	task_factory (core::pack::task::TaskFactoryOP tf)

core::scoring::ScoreFunctionCOP	score_function () const

protocols::backrub::BackrubMoverCOP	backrub_mover () const

protocols::simple_moves::PackRotamersMoverCOP	pack_rotamers_mover () const

core::Size	num_iterations () const

core::Real	temperature () const

core::pack::task::TaskFactoryCOP	task_factory () const

virtual protocols::moves::MoverOP	clone () const

virtual protocols::moves::MoverOP	fresh_instance () const

virtual void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const

void	add_initial_constraints (core::pose::Pose &pose, utility::vector1< core::Size > designable_residues, utility::vector1< core::Size > packable_residues)

void	initialize_from_options ()

	HemeBindingMover ()

	HemeBindingMover (core::scoring::ScoreFunctionOP const &sfxn, protocols::backrub::BackrubMoverOP &brm, protocols::simple_moves::MinPackMoverOP &mpm, core::Size n_it=1000, core::Real temperature=0.6)

	HemeBindingMover (core::scoring::ScoreFunctionOP const &sfxn, core::pack::task::TaskFactoryOP const &tf, core::Size n_it, core::Real temperature=0.6)

	HemeBindingMover (HemeBindingMover const &other)

virtual	~HemeBindingMover ()

void	score_function (core::scoring::ScoreFunctionOP other_score_function)

void	backrub_mover (protocols::backrub::BackrubMoverOP br_mover)

void	minpack_mover (protocols::simple_moves::MinPackMoverOP mp_mover)

void	num_iterations (core::Size n_it)

void	temperature (core::Real temp)

void	task_factory (core::pack::task::TaskFactoryOP tf)

core::scoring::ScoreFunctionCOP	score_function () const

protocols::backrub::BackrubMoverCOP	backrub_mover () const

protocols::simple_moves::MinPackMoverCOP	minpack_mover () const

core::Size	num_iterations () const

core::Real	temperature () const

core::pack::task::TaskFactoryCOP	task_factory () const

virtual protocols::moves::MoverOP	clone () const

virtual protocols::moves::MoverOP	fresh_instance () const

virtual void	apply (core::pose::Pose &pose)

virtual std::string	get_name () const

Private Attributes
core::scoring::ScoreFunctionOP	score_function_

core::scoring::ScoreFunctionOP	design_score_function_

core::scoring::ScoreFunctionOP	repack_score_function_

protocols::backrub::BackrubMoverOP	backrub_mover_

protocols::simple_moves::PackRotamersMoverOP	pack_rotamers_mover_

core::Size	num_iterations_

core::Real	temperature_

core::Real	prob_br_

core::pack::task::TaskFactoryOP	tf_

protocols::simple_moves::PackRotamersMoverOP	design_mover_

utility::vector1< std::string >	atoms_to_constrain_

core::scoring::constraints::BoundFuncOP	dist_func_

core::scoring::func::CircularHarmonicFuncOP	dihedral_func_

core::scoring::func::CircularHarmonicFuncOP	dihedral_func_2_

core::scoring::constraints::ConstraintCOPs	current_constraints_

protocols::simple_moves::MinPackMoverOP	minpack_mover_

Constructor & Destructor Documentation

◆ HemeBindingMover() [1/8]

HemeBindingMover::HemeBindingMover ( )

References design_score_function_, basic::database::full_name(), initialize_from_options(), repack_score_function_, score_function_, and TR.

Referenced by clone(), and fresh_instance().

◆ HemeBindingMover() [2/8]

HemeBindingMover::HemeBindingMover	(	core::scoring::ScoreFunctionOP const &	sfxn,
		protocols::backrub::BackrubMoverOP &	brm,
		protocols::simple_moves::PackRotamersMoverOP &	prm,
		core::Size	n_it = `1000`,
		core::Real	temperature = `0.6`
	)

References backrub_mover_, design_mover_, design_score_function_, basic::database::full_name(), initialize_from_options(), num_iterations_, pack_rotamers_mover_, repack_score_function_, score_function_, test.T120_core::sfxn, temperature(), temperature_, and tf_.

◆ HemeBindingMover() [3/8]

HemeBindingMover::HemeBindingMover	(	core::scoring::ScoreFunctionOP const &	sfxn,
		core::pack::task::TaskFactoryOP const &	tf,
		core::Size	n_it,
		core::Real	temperature = `0.6`
	)

References backrub_mover_, design_mover_, design_score_function_, basic::database::full_name(), initialize_from_options(), num_iterations_, pack_rotamers_mover_, repack_score_function_, score_function_, test.T120_core::sfxn, temperature(), temperature_, test.G200_Module_Region::tf, and tf_.

◆ HemeBindingMover() [4/8]

HemeBindingMover::HemeBindingMover ( HemeBindingMover const & other )

References backrub_mover(), backrub_mover_, design_mover_, design_score_function_, basic::database::full_name(), initialize_from_options(), num_iterations(), num_iterations_, pack_rotamers_mover(), pack_rotamers_mover_, repack_score_function_, score_function(), score_function_, task_factory(), temperature(), temperature_, and tf_.

◆ ~HemeBindingMover() [1/2]

HemeBindingMover::~HemeBindingMover ( )

virtual

◆ HemeBindingMover() [5/8]

HemeBindingMover::HemeBindingMover ( )

◆ HemeBindingMover() [6/8]

HemeBindingMover::HemeBindingMover	(	core::scoring::ScoreFunctionOP const &	sfxn,
		protocols::backrub::BackrubMoverOP &	brm,
		protocols::simple_moves::MinPackMoverOP &	mpm,
		core::Size	n_it = `1000`,
		core::Real	temperature = `0.6`
	)

◆ HemeBindingMover() [7/8]

HemeBindingMover::HemeBindingMover	(	core::scoring::ScoreFunctionOP const &	sfxn,
		core::pack::task::TaskFactoryOP const &	tf,
		core::Size	n_it,
		core::Real	temperature = `0.6`
	)

◆ HemeBindingMover() [8/8]

HemeBindingMover::HemeBindingMover ( HemeBindingMover const & other )

◆ ~HemeBindingMover() [2/2]

virtual HemeBindingMover::~HemeBindingMover ( )

virtual

Member Function Documentation

◆ add_initial_constraints()

void HemeBindingMover::add_initial_constraints	(	core::pose::Pose &	pose,
		utility::vector1< core::Size >	designable_residues,
		utility::vector1< core::Size >	packable_residues
	)

References atoms_to_constrain_, current_constraints_, cal_NBR_radius::current_res, dihedral_func_, dihedral_func_2_, dist_func_, create_a3b_hbs::i, create_a3b_hbs::j, beta_nonlocal::pose, predPRE::resnum, runtime_assert, and TR.

◆ apply() [1/2]

void HemeBindingMover::apply ( core::pose::Pose & pose )

virtual

◆ apply() [2/2]

virtual void HemeBindingMover::apply ( core::pose::Pose & pose )

virtual

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ backrub_mover() [1/4]

protocols::backrub::BackrubMoverCOP HemeBindingMover::backrub_mover ( ) const

References backrub_mover_.

◆ backrub_mover() [2/4]

protocols::backrub::BackrubMoverCOP HemeBindingMover::backrub_mover ( ) const

◆ backrub_mover() [3/4]

void HemeBindingMover::backrub_mover ( protocols::backrub::BackrubMoverOP br_mover )

References backrub_mover_.

Referenced by HemeBindingMover().

◆ backrub_mover() [4/4]

void HemeBindingMover::backrub_mover ( protocols::backrub::BackrubMoverOP br_mover )

◆ clone() [1/2]

protocols::moves::MoverOP HemeBindingMover::clone ( ) const

virtual

References HemeBindingMover().

◆ clone() [2/2]

virtual protocols::moves::MoverOP HemeBindingMover::clone ( ) const

virtual

◆ fresh_instance() [1/2]

protocols::moves::MoverOP HemeBindingMover::fresh_instance ( ) const

virtual

References HemeBindingMover().

◆ fresh_instance() [2/2]

virtual protocols::moves::MoverOP HemeBindingMover::fresh_instance ( ) const

virtual

◆ get_name() [1/2]

std::string HemeBindingMover::get_name ( ) const

virtual

◆ get_name() [2/2]

virtual std::string HemeBindingMover::get_name ( ) const

virtual

◆ initialize_from_options()

void HemeBindingMover::initialize_from_options ( )

References dihedral_func_, dihedral_func_2_, dist_func_, local::mc_temperature, local::num_iterations, num_iterations_, basic::options::option, prob_br_, local::prob_br_move, numeric::conversions::radians(), temperature_, TR, and value.

Referenced by HemeBindingMover().

◆ minpack_mover() [1/2]

protocols::simple_moves::MinPackMoverCOP HemeBindingMover::minpack_mover ( ) const

◆ minpack_mover() [2/2]

void HemeBindingMover::minpack_mover ( protocols::simple_moves::MinPackMoverOP mp_mover )

◆ num_iterations() [1/4]

core::Size HemeBindingMover::num_iterations ( ) const

References num_iterations_.

◆ num_iterations() [2/4]

core::Size HemeBindingMover::num_iterations ( ) const

◆ num_iterations() [3/4]

void HemeBindingMover::num_iterations ( core::Size n_it )

References num_iterations_.

Referenced by HemeBindingMover().

◆ num_iterations() [4/4]

void HemeBindingMover::num_iterations ( core::Size n_it )

◆ pack_rotamers_mover() [1/2]

protocols::simple_moves::PackRotamersMoverCOP HemeBindingMover::pack_rotamers_mover ( ) const

References pack_rotamers_mover_.

◆ pack_rotamers_mover() [2/2]

void HemeBindingMover::pack_rotamers_mover ( protocols::simple_moves::PackRotamersMoverOP pr_mover )

References pack_rotamers_mover_.

Referenced by HemeBindingMover().

◆ score_function() [1/4]

core::scoring::ScoreFunctionCOP HemeBindingMover::score_function ( ) const

References score_function_.

Referenced by pyrosetta.distributed.tasks.score.ScorePoseTask::execute().

◆ score_function() [2/4]

core::scoring::ScoreFunctionCOP HemeBindingMover::score_function ( ) const

Referenced by pyrosetta.distributed.tasks.score.ScorePoseTask::execute().

◆ score_function() [3/4]

void HemeBindingMover::score_function ( core::scoring::ScoreFunctionOP other_score_function )

References score_function_.

Referenced by pyrosetta.distributed.tasks.score.ScorePoseTask::execute(), and HemeBindingMover().

◆ score_function() [4/4]

void HemeBindingMover::score_function ( core::scoring::ScoreFunctionOP other_score_function )

Referenced by pyrosetta.distributed.tasks.score.ScorePoseTask::execute().

◆ task_factory() [1/4]

core::pack::task::TaskFactoryCOP HemeBindingMover::task_factory ( ) const

References tf_.

◆ task_factory() [2/4]

core::pack::task::TaskFactoryCOP HemeBindingMover::task_factory ( ) const

◆ task_factory() [3/4]

void HemeBindingMover::task_factory ( core::pack::task::TaskFactoryOP tf )

References test.G200_Module_Region::tf, and tf_.

Referenced by HemeBindingMover().

◆ task_factory() [4/4]

void HemeBindingMover::task_factory ( core::pack::task::TaskFactoryOP tf )

◆ temperature() [1/4]

core::Real HemeBindingMover::temperature ( ) const

References temperature_.

Referenced by schema.Temperature::__repr__(), schema.Temperature::formatted(), and HemeBindingMover().

◆ temperature() [2/4]

core::Real HemeBindingMover::temperature ( ) const

Referenced by schema.Temperature::__repr__(), and schema.Temperature::formatted().

◆ temperature() [3/4]

void HemeBindingMover::temperature ( core::Real temp )

References erraser_analysis::temp, and temperature_.

Referenced by schema.Temperature::__repr__(), schema.Temperature::formatted(), and HemeBindingMover().

◆ temperature() [4/4]

void HemeBindingMover::temperature ( core::Real temp )

Referenced by schema.Temperature::__repr__(), and schema.Temperature::formatted().

Member Data Documentation

◆ atoms_to_constrain_

utility::vector1< std::string > HemeBindingMover::atoms_to_constrain_

private

Referenced by add_initial_constraints().

◆ backrub_mover_

protocols::backrub::BackrubMoverOP HemeBindingMover::backrub_mover_

private

Referenced by apply(), backrub_mover(), and HemeBindingMover().

◆ current_constraints_

core::scoring::constraints::ConstraintCOPs HemeBindingMover::current_constraints_

private

Referenced by add_initial_constraints().

◆ design_mover_

protocols::simple_moves::PackRotamersMoverOP HemeBindingMover::design_mover_

private

Referenced by apply(), and HemeBindingMover().

◆ design_score_function_

core::scoring::ScoreFunctionOP HemeBindingMover::design_score_function_

private

Referenced by apply(), and HemeBindingMover().

◆ dihedral_func_

core::scoring::func::CircularHarmonicFuncOP HemeBindingMover::dihedral_func_

private

Referenced by add_initial_constraints(), and initialize_from_options().

◆ dihedral_func_2_

core::scoring::func::CircularHarmonicFuncOP HemeBindingMover::dihedral_func_2_

private

Referenced by add_initial_constraints(), and initialize_from_options().

◆ dist_func_

core::scoring::constraints::BoundFuncOP HemeBindingMover::dist_func_

private

Referenced by add_initial_constraints(), and initialize_from_options().

◆ minpack_mover_

protocols::simple_moves::MinPackMoverOP HemeBindingMover::minpack_mover_

private

◆ num_iterations_

core::Size HemeBindingMover::num_iterations_

private

Referenced by apply(), HemeBindingMover(), initialize_from_options(), and num_iterations().

◆ pack_rotamers_mover_

protocols::simple_moves::PackRotamersMoverOP HemeBindingMover::pack_rotamers_mover_

private

Referenced by apply(), HemeBindingMover(), and pack_rotamers_mover().

◆ prob_br_

core::Real HemeBindingMover::prob_br_

private

Referenced by apply(), and initialize_from_options().

◆ repack_score_function_

core::scoring::ScoreFunctionOP HemeBindingMover::repack_score_function_

private

Referenced by apply(), and HemeBindingMover().

◆ score_function_

core::scoring::ScoreFunctionOP HemeBindingMover::score_function_

private

Referenced by apply(), HemeBindingMover(), and score_function().

◆ temperature_

core::Real HemeBindingMover::temperature_

private

Referenced by apply(), HemeBindingMover(), initialize_from_options(), and temperature().

◆ tf_

core::pack::task::TaskFactoryOP HemeBindingMover::tf_

private

Referenced by apply(), HemeBindingMover(), and task_factory().

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

src/apps/pilot/guffysl/heme_binding.cc
src/apps/pilot/guffysl/HemeBindingMover.hh

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ HemeBindingMover() [1/8]

◆ HemeBindingMover() [2/8]

◆ HemeBindingMover() [3/8]

◆ HemeBindingMover() [4/8]

◆ ~HemeBindingMover() [1/2]

◆ HemeBindingMover() [5/8]

◆ HemeBindingMover() [6/8]

◆ HemeBindingMover() [7/8]

◆ HemeBindingMover() [8/8]

◆ ~HemeBindingMover() [2/2]

Member Function Documentation

◆ add_initial_constraints()

◆ apply() [1/2]

◆ apply() [2/2]

◆ backrub_mover() [1/4]

◆ backrub_mover() [2/4]

◆ backrub_mover() [3/4]

◆ backrub_mover() [4/4]

◆ clone() [1/2]

◆ clone() [2/2]

◆ fresh_instance() [1/2]

◆ fresh_instance() [2/2]

◆ get_name() [1/2]

◆ get_name() [2/2]

◆ initialize_from_options()

◆ minpack_mover() [1/2]

◆ minpack_mover() [2/2]

◆ num_iterations() [1/4]

◆ num_iterations() [2/4]

◆ num_iterations() [3/4]

◆ num_iterations() [4/4]

◆ pack_rotamers_mover() [1/2]

◆ pack_rotamers_mover() [2/2]

◆ score_function() [1/4]

◆ score_function() [2/4]

◆ score_function() [3/4]

◆ score_function() [4/4]

◆ task_factory() [1/4]

◆ task_factory() [2/4]

◆ task_factory() [3/4]

◆ task_factory() [4/4]

◆ temperature() [1/4]

◆ temperature() [2/4]

◆ temperature() [3/4]

◆ temperature() [4/4]

Member Data Documentation

◆ atoms_to_constrain_

◆ backrub_mover_

◆ current_constraints_

◆ design_mover_

◆ design_score_function_

◆ dihedral_func_

◆ dihedral_func_2_

◆ dist_func_

◆ minpack_mover_

◆ num_iterations_

◆ pack_rotamers_mover_

◆ prob_br_

◆ repack_score_function_

◆ score_function_

◆ temperature_

◆ tf_