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util.cc File Reference
#include <protocols/magnesium/util.hh>
#include <protocols/magnesium/MgWaterHydrogenPacker.hh>
#include <protocols/magnesium/MgOrbitalFrameFinder.hh>
#include <protocols/magnesium/MgHydrater.hh>
#include <protocols/stepwise/modeler/util.hh>
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/ChemicalManager.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/id/AtomID.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/methods/EnergyMethodOptions.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/variant_util.hh>
#include <core/id/NamedAtomID.hh>
#include <core/pose/subpose_manipulation_util.hh>
#include <core/pose/full_model_info/FullModelInfo.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/tools/make_vector1.hh>
#include <basic/Tracer.hh>
#include <numeric/UniformRotationSampler.hh>
#include <numeric/xyzMatrix.io.hh>
#include <ObjexxFCL/format.hh>

Namespaces

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

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 

Functions

static basic::Tracer TR ("protocols.magnesium.util")
 
void protocols::magnesium::fixup_magnesiums (pose::Pose &pose)
 
void protocols::magnesium::hydrate_magnesiums (pose::Pose &pose, bool use_virtual_waters_as_placeholders, bool test_all_mg_hydration_frames)
 
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)
 
bool protocols::magnesium::is_ligand (core::pose::Pose const &pose, core::id::AtomID const &ligand)
 
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)
 
utility::vector1
< core::id::AtomID
protocols::magnesium::filter_acceptor_ligands (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const &ligands)
 
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)
 
std::map< core::Size, vector1
< core::Size > > 
protocols::magnesium::define_mg_water_map (pose::Pose const &pose)
 
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)
 
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)
 
utility::vector1< std::pair
< core::Size, core::Size > > 
protocols::magnesium::get_mg_water_pairs (pose::Pose const &pose, bool const exclude_virtual_waters)
 
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)
 
utility::vector1< core::Sizeprotocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree (pose::Pose const &pose, core::Size const mg_res)
 
core::Size protocols::magnesium::get_bound_water_res (pose::Pose const &pose, core::Size const mg_res, core::Size const n)
 
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)
 
void protocols::magnesium::update_jump_atoms_for_mg_bound_water (core::pose::Pose &pose, core::Size const n)
 
Size protocols::magnesium::append_mg_bound_water (core::pose::Pose &pose, core::conformation::Residue const &rsd, core::Size const mg_res)
 
core::conformation::ResidueOP protocols::magnesium::get_mg_rsd ()
 
void protocols::magnesium::add_single_magnesium (pose::Pose &pose)
 
void protocols::magnesium::strip_out_magnesiums (pose::Pose &pose)
 
utility::vector1< core::Sizeprotocols::magnesium::get_res_with_name (pose::Pose const &pose, std::string const &name)
 
utility::vector1< core::Sizeprotocols::magnesium::get_mg_res (pose::Pose const &pose)
 
utility::vector1< core::Sizeprotocols::magnesium::get_water_res (pose::Pose const &pose)
 
void protocols::magnesium::remove_waters_except_mg_bound (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< core::Size > const &mg_res, bool const leave_other_waters)
 
void protocols::magnesium::set_water_numbers_to_zero (pose::Pose &pose)
 
void protocols::magnesium::update_numbers_in_pdb_info (pose::Pose &pose, bool const reset_waters)
 
utility::vector1< core::Sizeprotocols::magnesium::pdbslice (core::pose::Pose &pose, core::Size const center_res, core::Distance distance_cutoff)
 
utility::vector1
< numeric::xyzVector
< core::Real > > 
protocols::magnesium::get_hoh_xyz (pose::Pose const &pose, core::Size const pdb_mg_res, core::Size &nlig)
 
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)
 

Detailed Description

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

Typedef Documentation

using Matrix = numeric::xyzMatrix<Real>

Function Documentation

static basic::Tracer TR ( "protocols.magnesium.util"  )
static