Classes
class	MgHydrater

class	MgMinimizer

class	MgMonteCarlo

class	MgOrbitalFrameFinder

class	MgScanner

class	MgWaterHydrogenPacker

class	SampleGrid

Typedefs
typedef utility::pointer::shared_ptr < MgHydrater >	MgHydraterOP

typedef utility::pointer::shared_ptr < MgHydrater const >	MgHydraterCOP

typedef utility::pointer::shared_ptr < MgMinimizer >	MgMinimizerOP

typedef utility::pointer::shared_ptr < MgMinimizer const >	MgMinimizerCOP

typedef utility::pointer::shared_ptr < MgMonteCarlo >	MgMonteCarloOP

typedef utility::pointer::shared_ptr < MgMonteCarlo const >	MgMonteCarloCOP

typedef utility::pointer::shared_ptr < MgOrbitalFrameFinder >	MgOrbitalFrameFinderOP

typedef utility::pointer::shared_ptr < MgOrbitalFrameFinder const >	MgOrbitalFrameFinderCOP

typedef utility::pointer::shared_ptr < MgScanner >	MgScannerOP

typedef utility::pointer::shared_ptr < MgScanner const >	MgScannerCOP

typedef utility::pointer::shared_ptr < MgWaterHydrogenPacker >	MgWaterHydrogenPackerOP

typedef utility::pointer::shared_ptr < MgWaterHydrogenPacker const >	MgWaterHydrogenPackerCOP

typedef utility::pointer::shared_ptr < SampleGrid >	SampleGridOP

typedef utility::pointer::shared_ptr < SampleGrid const >	SampleGridCOP

Functions
void	minimize_magnesium_and_hydration_shell (pose::Pose &pose, utility::vector1< Size > const mg_res, core::scoring::ScoreFunctionCOP minimize_scorefxn, core::Distance const mg_coord_cst_dist)

void	minimize_magnesium_and_hydration_shell (pose::Pose &pose, utility::vector1< pose::PoseOP > &pose_list, utility::vector1< Size > const mg_res, core::scoring::ScoreFunctionCOP minimize_scorefxn, core::Distance const mg_coord_cst_dist)

void	update_mg_hoh_fold_tree (pose::Pose &pose)

core::id::AtomID	get_closest_non_hoh_contact (pose::Pose const &pose, Size const i, std::string const exclude_rsd)

void	fixup_magnesiums (pose::Pose &pose)

core::scoring::ScoreFunctionOP	get_mg_scorefxn ()

numeric::UniformRotationSamplerCOP	get_water_uniform_rotation_sampler ()

numeric::UniformRotationSamplerCOP	get_octahedral_uniform_rotation_sampler (core::Real const rotstep, bool const remove_redundant)

core::conformation::ResidueOP	get_useful_HOH_coords (Vector &Oc, Vector &OH1c, Vector &OH2c, core::chemical::ResidueTypeSet const &residue_set)

utility::vector1< std::pair < Size, Size > >	get_mg_water_pairs (pose::Pose const &pose)

utility::vector1< std::pair < Size, Size > >	get_mg_water_pairs (pose::Pose const &pose, vector1< Size > const &mg_res)

utility::vector1 < core::id::AtomID >	filter_acceptor_ligands (pose::Pose const &pose, utility::vector1< core::id::AtomID > const &ligands)

utility::vector1 < core::id::AtomID >	get_mg_ligands (pose::Pose const &pose, Size const i, bool const filter_for_acceptors)

void	instantiate_water_at_octahedral_vertex (pose::Pose &pose, Size const mg_res, Size const n, Distance const hoh_distance)

core::conformation::ResidueOP	get_mg_rsd ()

void	add_single_magnesium (pose::Pose &pose)

void	strip_out_magnesiums (pose::Pose &pose)

utility::vector1< Size >	get_res_with_name (pose::Pose const &pose, std::string const &name)

utility::vector1< Size >	get_mg_res (pose::Pose const &pose)

utility::vector1< Size >	get_water_res (pose::Pose const &pose)

void	remove_waters_except_mg_bound (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > const &mg_water_pairs)

void	remove_mg_bound_waters (pose::Pose &pose, utility::vector1< Size > const &mg_res, bool const leave_other_waters)

void	set_water_numbers_to_zero (pose::Pose &pose)

void	update_numbers_in_pdb_info (pose::Pose &pose, bool const reset_waters)

utility::vector1< core::Size >	pdbslice (core::pose::Pose &pose, core::Size const center_res, core::Distance distance_cutoff)

utility::vector1 < numeric::xyzVector < core::Real > >	get_hoh_xyz (pose::Pose const &pose, Size const pdb_mg_res, Size &nlig)

void	get_hydration_stats (pose::Pose const &pose, pose::Pose const &reference_pose, utility::vector1< Size > const &pdb_mg_res_list_in, std::string const outfile)

void	remove_waters_except_mg_bound (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &mg_water_pairs)

Variables
core::Distance const	MG_HOH_DISTANCE (2.1)

core::Distance const	MG_LIGAND_DISTANCE_CUTOFF (3.2)

core::Distance const	MG_V_DISTANCE (1.0)

Typedef Documentation

typedef utility::pointer::shared_ptr< MgHydrater const > protocols::magnesium::MgHydraterCOP

typedef utility::pointer::shared_ptr< MgHydrater > protocols::magnesium::MgHydraterOP

typedef utility::pointer::shared_ptr< MgMinimizer const > protocols::magnesium::MgMinimizerCOP

typedef utility::pointer::shared_ptr< MgMinimizer > protocols::magnesium::MgMinimizerOP

typedef utility::pointer::shared_ptr< MgMonteCarlo const > protocols::magnesium::MgMonteCarloCOP

typedef utility::pointer::shared_ptr< MgMonteCarlo > protocols::magnesium::MgMonteCarloOP

typedef utility::pointer::shared_ptr< MgOrbitalFrameFinder const > protocols::magnesium::MgOrbitalFrameFinderCOP

typedef utility::pointer::shared_ptr< MgOrbitalFrameFinder > protocols::magnesium::MgOrbitalFrameFinderOP

typedef utility::pointer::shared_ptr< MgScanner const > protocols::magnesium::MgScannerCOP

typedef utility::pointer::shared_ptr< MgScanner > protocols::magnesium::MgScannerOP

typedef utility::pointer::shared_ptr< MgWaterHydrogenPacker const > protocols::magnesium::MgWaterHydrogenPackerCOP

typedef utility::pointer::shared_ptr< MgWaterHydrogenPacker > protocols::magnesium::MgWaterHydrogenPackerOP

typedef utility::pointer::shared_ptr< SampleGrid const > protocols::magnesium::SampleGridCOP

typedef utility::pointer::shared_ptr< SampleGrid > protocols::magnesium::SampleGridOP

Function Documentation

void protocols::magnesium::add_single_magnesium ( pose::Pose & pose )

References core::pose::Pose::append_residue_by_jump(), get_mg_rsd(), and core::pose::Pose::total_residue().

utility::vector1< core::id::AtomID > protocols::magnesium::filter_acceptor_ligands	(	pose::Pose const &	pose,
		utility::vector1< core::id::AtomID > const &	ligands
	)

References core::id::AtomID::atomno(), core::pose::Pose::residue(), and core::id::AtomID::rsd().

Referenced by get_mg_ligands().

void protocols::magnesium::fixup_magnesiums ( pose::Pose & pose )

References protocols::magnesium::MgOrbitalFrameFinder::apply(), and protocols::magnesium::MgWaterHydrogenPacker::apply().

core::id::AtomID protocols::magnesium::get_closest_non_hoh_contact	(	pose::Pose const &	pose,
		Size const	i,
		std::string const	exclude_rsd
	)

References core::conformation::Residue::heavyatom_has_polar_hydrogens(), core::conformation::Residue::heavyatom_is_an_acceptor(), core::conformation::Residue::name3(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by update_mg_hoh_fold_tree().

utility::vector1< numeric::xyzVector< core::Real > > protocols::magnesium::get_hoh_xyz	(	pose::Pose const &	pose,
		Size const	pdb_mg_res,
		Size &	nlig
	)

References core::id::AtomID::atomno(), get_mg_ligands(), core::conformation::Residue::name3(), pdb_to_pose(), core::pose::Pose::residue(), core::id::AtomID::rsd(), and core::conformation::Residue::xyz().

Referenced by get_hydration_stats().

void protocols::magnesium::get_hydration_stats	(	pose::Pose const &	pose,
		pose::Pose const &	reference_pose,
		utility::vector1< Size > const &	pdb_mg_res_list_in,
		std::string const	outfile
	)

References utility::io::ozstream::close(), F, get_hoh_xyz(), get_mg_res(), I, core::pose::Pose::pdb_info(), pdb_to_pose(), and pose_to_pdb().

utility::vector1< core::id::AtomID > protocols::magnesium::get_mg_ligands	(	pose::Pose const &	pose,
		Size const	i,
		bool const	filter_for_acceptors
	)

References distance(), filter_acceptor_ligands(), core::conformation::Residue::is_virtual(), MG_LIGAND_DISTANCE_CUTOFF, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::magnesium::MgMonteCarlo::apply(), protocols::magnesium::MgOrbitalFrameFinder::determine_mg_orbital_frame(), get_hoh_xyz(), get_mg_water_pairs(), and update_mg_hoh_fold_tree().

utility::vector1< core::Size > protocols::magnesium::get_mg_res ( pose::Pose const & pose )

References get_res_with_name().

Referenced by protocols::magnesium::MgMinimizer::apply(), protocols::magnesium::MgOrbitalFrameFinder::apply(), protocols::magnesium::MgWaterHydrogenPacker::apply(), protocols::magnesium::MgMonteCarlo::apply(), get_hydration_stats(), get_mg_water_pairs(), and protocols::magnesium::MgMonteCarlo::setup_mg_water_fold_tree().

core::conformation::ResidueOP protocols::magnesium::get_mg_rsd ( )

References core::conformation::ResidueFactory::create_residue(), and FA_RNA.

Referenced by add_single_magnesium(), protocols::magnesium::MgScanner::get_single_mg_pose(), and protocols::magnesium::MgScanner::output_mg_into_one_PDB().

core::scoring::ScoreFunctionOP protocols::magnesium::get_mg_scorefxn ( )

References fa_atr, fa_rep, geom_sol_fast, hbond_sc, hoh_ref, mg_lig, mg_ref, mg_sol, and options.

Referenced by protocols::magnesium::MgMonteCarlo::apply(), protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), and protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose().

utility::vector1< std::pair< core::Size, core::Size > > protocols::magnesium::get_mg_water_pairs ( pose::Pose const & pose )

References get_mg_res(), and get_mg_water_pairs().

Referenced by protocols::magnesium::MgWaterHydrogenPacker::apply(), and protocols::magnesium::MgWaterHydrogenPacker::remove_waters_except_mg_bound().

utility::vector1< std::pair< core::Size, core::Size > > protocols::magnesium::get_mg_water_pairs	(	pose::Pose const &	pose,
		vector1< Size > const &	mg_res
	)

References core::id::AtomID::atomno(), get_mg_ligands(), core::pose::Pose::residue(), core::id::AtomID::rsd(), and core::conformation::Residue::xyz().

Referenced by get_mg_water_pairs(), and remove_mg_bound_waters().

numeric::UniformRotationSamplerCOP protocols::magnesium::get_octahedral_uniform_rotation_sampler	(	core::Real const	rotstep,
		bool const	remove_redundant
	)

References protocols::init::init(), radians(), and rotation_matrix().

Referenced by protocols::magnesium::MgHydrater::hydrate_magnesium_in_pose(), and protocols::magnesium::MgOrbitalFrameFinder::sample_orbital_frame().

utility::vector1< Size > protocols::magnesium::get_res_with_name	(	pose::Pose const &	pose,
		std::string const &	name
	)

References core::conformation::Residue::name3(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by get_mg_res(), and get_water_res().

core::conformation::ResidueOP protocols::magnesium::get_useful_HOH_coords	(	Vector &	Oc,
		Vector &	OH1c,
		Vector &	OH2c,
		core::chemical::ResidueTypeSet const &	residue_set
	)

References core::conformation::ResidueFactory::create_residue(), numeric::xyzVector< class >::dot(), numeric::xyzVector< class >::length(), core::chemical::ResidueTypeSet::name_map(), numeric::xyzMatrix< class >::rows(), and runtime_assert.

Referenced by instantiate_water_at_octahedral_vertex(), and protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose().

utility::vector1< core::Size > protocols::magnesium::get_water_res ( pose::Pose const & pose )

References get_res_with_name().

Referenced by protocols::magnesium::MgMonteCarlo::apply().

numeric::UniformRotationSamplerCOP protocols::magnesium::get_water_uniform_rotation_sampler ( )

References protocols::init::init(), and numeric::xyzMatrix< class >::rows().

Referenced by protocols::magnesium::MgWaterHydrogenPacker::pack_mg_water_hydrogens_in_pose().

void protocols::magnesium::instantiate_water_at_octahedral_vertex	(	pose::Pose &	pose,
		Size const	mg_res,
		Size const	n,
		Distance const	hoh_distance
	)

References core::pose::Pose::append_residue_by_jump(), numeric::xyzMatrix< Real >::cols(), cross(), get_useful_HOH_coords(), core::kinematics::Stub::local2global(), core::pose::Pose::residue(), core::conformation::Residue::residue_type_set(), runtime_assert, update_numbers_in_pdb_info(), x(), core::conformation::Residue::xyz(), y(), and z().

Referenced by protocols::magnesium::MgMonteCarlo::apply(), and protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame().

void protocols::magnesium::minimize_magnesium_and_hydration_shell	(	pose::Pose &	pose,
		utility::vector1< Size > const	mg_res,
		core::scoring::ScoreFunctionCOP	minimize_scorefxn,
		core::Distance const	mg_coord_cst_dist
	)

References protocols::magnesium::MgMinimizer::apply(), protocols::magnesium::MgMinimizer::set_mg_coord_cst_dist(), protocols::magnesium::MgMinimizer::set_mg_res(), and protocols::magnesium::MgMinimizer::set_minimize_scorefxn().

Referenced by protocols::magnesium::MgScanner::apply(), and protocols::magnesium::MgScanner::get_score().

void protocols::magnesium::minimize_magnesium_and_hydration_shell	(	pose::Pose &	pose,
		utility::vector1< pose::PoseOP > &	pose_list,
		utility::vector1< Size > const	mg_res,
		core::scoring::ScoreFunctionCOP	minimize_scorefxn,
		core::Distance const	mg_coord_cst_dist
	)

References protocols::magnesium::MgMinimizer::apply(), protocols::magnesium::MgMinimizer::set_mg_coord_cst_dist(), protocols::magnesium::MgMinimizer::set_mg_res(), and protocols::magnesium::MgMinimizer::set_minimize_scorefxn().

utility::vector1< core::Size > protocols::magnesium::pdbslice	(	core::pose::Pose &	pose,
		core::Size const	center_res,
		core::Distance	distance_cutoff
	)

References utility::vector1< T, class >::has_value(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by protocols::magnesium::MgMonteCarlo::apply(), protocols::stepwise::modeler::align::StepWiseLegacyClusterer::do_some_clustering(), protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::do_some_clustering(), protocols::magnesium::MgHydrater::hydrate_magnesium(), protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose(), remove_mg_bound_waters(), and remove_waters_except_mg_bound().

void protocols::magnesium::remove_mg_bound_waters	(	pose::Pose &	pose,
		utility::vector1< Size > const &	mg_res,
		bool const	leave_other_waters
	)

References get_mg_water_pairs(), utility::vector1< T, class >::has_value(), core::conformation::Residue::name3(), pdbslice(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void protocols::magnesium::remove_waters_except_mg_bound	(	core::pose::Pose &	pose,
		utility::vector1< std::pair< core::Size, core::Size > > const &	mg_water_pairs
	)