util.hh File Reference

#include <protocols/magnesium/params.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/types.hh>
#include <numeric/UniformRotationSampler.fwd.hh>
#include <utility/vector1.fwd.hh>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::magnesium

Functions
void	protocols::magnesium::fixup_magnesiums (pose::Pose &pose)
core::scoring::ScoreFunctionOP	protocols::magnesium::get_mg_scorefxn ()
numeric::UniformRotationSamplerCOP	protocols::magnesium::get_water_uniform_rotation_sampler ()
numeric::UniformRotationSamplerCOP	protocols::magnesium::get_octahedral_uniform_rotation_sampler (core::Real const rotstep, bool const remove_redundant)
core::conformation::ResidueOP	protocols::magnesium::get_useful_HOH_coords (Vector &Oc, Vector &OH1c, Vector &OH2c, core::chemical::ResidueTypeSet const &residue_set)
void	protocols::magnesium::add_single_magnesium (pose::Pose &pose)
void	protocols::magnesium::strip_out_magnesiums (pose::Pose &pose)
utility::vector1< std::pair < Size, Size > >	protocols::magnesium::get_mg_water_pairs (pose::Pose const &pose)
utility::vector1< std::pair < Size, Size > >	protocols::magnesium::get_mg_water_pairs (pose::Pose const &pose, vector1< Size > const &mg_res)
utility::vector1 < core::id::AtomID >	protocols::magnesium::get_mg_ligands (pose::Pose const &pose, Size const i, bool const filter_for_acceptors)
utility::vector1 < core::id::AtomID >	protocols::magnesium::filter_acceptor_ligands (pose::Pose const &pose, utility::vector1< core::id::AtomID > const &ligands)
void	protocols::magnesium::instantiate_water_at_octahedral_vertex (pose::Pose &pose, Size const mg_res, Size const n, Distance const hoh_distance)
core::conformation::ResidueOP	protocols::magnesium::get_mg_rsd ()
utility::vector1< Size >	protocols::magnesium::get_mg_res (pose::Pose const &pose)
utility::vector1< Size >	protocols::magnesium::get_water_res (pose::Pose const &pose)
void	protocols::magnesium::remove_waters_except_mg_bound (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &mg_water_pairs)
void	protocols::magnesium::remove_mg_bound_waters (pose::Pose &pose, utility::vector1< Size > const &mg_res, bool const leave_other_waters)
void	protocols::magnesium::update_numbers_in_pdb_info (pose::Pose &pose, bool const reset_waters)
utility::vector1< core::Size >	protocols::magnesium::pdbslice (core::pose::Pose &pose, core::Size const center_res, core::Distance distance_cutoff)
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)

Detailed Description

Detailed:

Author

Rhiju Das, rhiju.nosp@m.@sta.nosp@m.nford.nosp@m..edu