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| static basic::Tracer | TR ("protocols.magnesium.util") |
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| void | protocols::magnesium::fixup_magnesiums (pose::Pose &pose) |
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| void | protocols::magnesium::hydrate_magnesiums (pose::Pose &pose, bool use_virtual_waters_as_placeholders, bool test_all_mg_hydration_frames) |
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| core::scoring::ScoreFunctionOP | protocols::magnesium::get_mg_scorefxn () |
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| numeric::UniformRotationSamplerCOP | protocols::magnesium::get_water_uniform_rotation_sampler () |
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| numeric::UniformRotationSamplerCOP | protocols::magnesium::get_octahedral_uniform_rotation_sampler (core::Real const rotstep, bool const remove_redundant) |
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| core::conformation::ResidueOP | protocols::magnesium::get_useful_HOH_coords (Vector &Oc, Vector &OH1c, Vector &OH2c, core::chemical::ResidueTypeSet const &residue_set) |
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| bool | protocols::magnesium::is_ligand (core::pose::Pose const &pose, core::id::AtomID const &ligand) |
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| utility::vector1< std::pair< core::Size, core::id::AtomID > > | protocols::magnesium::filter_acceptor_ligands (pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::id::AtomID > > const &ligands) |
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| utility::vector1< core::id::AtomID > | protocols::magnesium::filter_acceptor_ligands (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const &ligands) |
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| utility::vector1< std::pair< core::Size, core::id::AtomID > > | protocols::magnesium::filter_water_ligands (pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::id::AtomID > > const &ligands) |
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| std::map< core::Size, vector1< core::Size > > | protocols::magnesium::define_mg_water_map (pose::Pose const &pose) |
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| utility::vector1< std::pair< core::Size, core::id::AtomID > > | protocols::magnesium::get_mg_ligands (pose::Pose const &pose, utility::vector1< core::Size > const mg_res, bool const filter_for_acceptors, bool const exclude_virtual_waters, bool const just_waters=false) |
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| utility::vector1< core::id::AtomID > | protocols::magnesium::get_mg_ligands (pose::Pose const &pose, core::Size const i, bool const filter_for_acceptors, bool const exclude_virtual_waters) |
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| utility::vector1< std::pair< core::Size, core::Size > > | protocols::magnesium::get_mg_water_pairs (pose::Pose const &pose, bool const exclude_virtual_waters) |
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| utility::vector1< std::pair< core::Size, core::Size > > | protocols::magnesium::get_mg_water_pairs (pose::Pose const &pose, vector1< core::Size > const &mg_res, bool const exclude_virtual_waters) |
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| utility::vector1< core::Size > | protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree (pose::Pose const &pose, core::Size const mg_res) |
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| core::Size | protocols::magnesium::get_bound_water_res (pose::Pose const &pose, core::Size const mg_res, core::Size const n) |
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| core::Size | protocols::magnesium::instantiate_water_at_octahedral_vertex (pose::Pose &pose, core::Size const mg_res, core::Size const n, Distance const hoh_distance, bool const replace_residue, bool const virtual_water) |
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| void | protocols::magnesium::update_jump_atoms_for_mg_bound_water (core::pose::Pose &pose, core::Size const n) |
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| Size | protocols::magnesium::append_mg_bound_water (core::pose::Pose &pose, core::conformation::Residue const &rsd, core::Size const mg_res) |
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| core::conformation::ResidueOP | protocols::magnesium::get_mg_rsd () |
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| void | protocols::magnesium::add_single_magnesium (pose::Pose &pose) |
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| void | protocols::magnesium::strip_out_magnesiums (pose::Pose &pose) |
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| utility::vector1< core::Size > | protocols::magnesium::get_res_with_name (pose::Pose const &pose, std::string const &name) |
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| utility::vector1< core::Size > | protocols::magnesium::get_mg_res (pose::Pose const &pose) |
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| utility::vector1< core::Size > | protocols::magnesium::get_water_res (pose::Pose const &pose) |
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| void | protocols::magnesium::remove_waters_except_mg_bound (pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &mg_water_pairs) |
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| void | protocols::magnesium::remove_mg_bound_waters (pose::Pose &pose, utility::vector1< core::Size > const &mg_res, bool const leave_other_waters) |
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| void | protocols::magnesium::set_water_numbers_to_zero (pose::Pose &pose) |
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| void | protocols::magnesium::update_numbers_in_pdb_info (pose::Pose &pose, bool const reset_waters) |
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| utility::vector1< core::Size > | protocols::magnesium::pdbslice (core::pose::Pose &pose, core::Size const center_res, core::Distance distance_cutoff) |
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| utility::vector1< numeric::xyzVector< core::Real > > | protocols::magnesium::get_hoh_xyz (pose::Pose const &pose, core::Size const pdb_mg_res, core::Size &nlig) |
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| void | protocols::magnesium::get_hydration_stats (pose::Pose const &pose, pose::Pose const &reference_pose, utility::vector1< core::Size > const &pdb_mg_res_list_in, std::string const &outfile) |
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