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Classes | Typedefs | Functions
protocols::magnesium Namespace Reference

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 fix_water_jump (pose::Pose &pose, core::Size const &parent_res, core::Size const &water_res)
 
void minimize_magnesium_and_hydration_shell (pose::Pose &pose, utility::vector1< core::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< core::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, core::Size const i, std::string const &exclude_rsd)
 
void minimize_magnesium_and_hydration_shell (core::pose::Pose &pose, utility::vector1< core::pose::PoseOP > &pose_list, utility::vector1< core::Size > const &mg_res, core::scoring::ScoreFunctionCOP minimize_scorefxn=nullptr, core::Distance const mg_coord_cst_dist=0.2)
 
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)
 
void fixup_magnesiums (pose::Pose &pose)
 
void hydrate_magnesiums (pose::Pose &pose, bool use_virtual_waters_as_placeholders, bool test_all_mg_hydration_frames)
 
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)
 
bool is_ligand (core::pose::Pose const &pose, core::id::AtomID const &ligand)
 
utility::vector1< std::pair< core::Size, core::id::AtomID > > filter_acceptor_ligands (pose::Pose const &pose, utility::vector1< std::pair< core::Size, core::id::AtomID > > const &ligands)
 
utility::vector1< core::id::AtomID > filter_acceptor_ligands (core::pose::Pose const &pose, utility::vector1< core::id::AtomID > const &ligands)
 
utility::vector1< std::pair< core::Size, core::id::AtomID > > 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 > > define_mg_water_map (pose::Pose const &pose)
 
utility::vector1< std::pair< core::Size, core::id::AtomID > > 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 > 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 > > get_mg_water_pairs (pose::Pose const &pose, bool const exclude_virtual_waters)
 
utility::vector1< std::pair< core::Size, core::Size > > get_mg_water_pairs (pose::Pose const &pose, vector1< core::Size > const &mg_res, bool const exclude_virtual_waters)
 
utility::vector1< core::Size > find_bound_waters_that_are_daughters_in_fold_tree (pose::Pose const &pose, core::Size const mg_res)
 
core::Size get_bound_water_res (pose::Pose const &pose, core::Size const mg_res, core::Size const n)
 
core::Size 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 update_jump_atoms_for_mg_bound_water (core::pose::Pose &pose, core::Size const n)
 
Size append_mg_bound_water (core::pose::Pose &pose, core::conformation::Residue const &rsd, core::Size const mg_res)
 
core::conformation::ResidueOP get_mg_rsd ()
 
void add_single_magnesium (pose::Pose &pose)
 
void strip_out_magnesiums (pose::Pose &pose)
 
utility::vector1< core::Size > get_res_with_name (pose::Pose const &pose, std::string const &name)
 
utility::vector1< core::Size > get_mg_res (pose::Pose const &pose)
 
utility::vector1< core::Size > get_water_res (pose::Pose const &pose)
 
void remove_waters_except_mg_bound (pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const &mg_water_pairs)
 
void remove_mg_bound_waters (pose::Pose &pose, utility::vector1< core::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, core::Size const pdb_mg_res, core::Size &nlig)
 
void 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)
 
core::conformation::ResidueOP get_useful_HOH_coords (core::Vector &Oc, core::Vector &OH1c, core::Vector &OH2c, core::chemical::ResidueTypeSet const &residue_set)
 
utility::vector1< std::pair< core::Size, core::Size > > get_mg_water_pairs (core::pose::Pose const &pose, utility::vector1< core::Size > const &mg_res, bool const exclude_virtual_waters=true)
 

Typedef Documentation

◆ MgHydraterCOP

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

◆ MgHydraterOP

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

◆ MgMinimizerCOP

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

◆ MgMinimizerOP

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

◆ MgMonteCarloCOP

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

◆ MgMonteCarloOP

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

◆ MgOrbitalFrameFinderCOP

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

◆ MgOrbitalFrameFinderOP

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

◆ MgScannerCOP

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

◆ MgScannerOP

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

◆ MgWaterHydrogenPackerCOP

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

◆ MgWaterHydrogenPackerOP

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

◆ SampleGridCOP

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

◆ SampleGridOP

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

Function Documentation

◆ add_single_magnesium()

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

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

◆ append_mg_bound_water()

core::Size protocols::magnesium::append_mg_bound_water ( core::pose::Pose &  pose,
core::conformation::Residue const &  rsd,
core::Size const  mg_res 
)

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::size(), and update_jump_atoms_for_mg_bound_water().

Referenced by protocols::magnesium::MgHydrater::hydrate_magnesium(), and instantiate_water_at_octahedral_vertex().

◆ define_mg_water_map()

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

References get_mg_water_pairs(), core::chemical::element::I, and TR().

Referenced by protocols::magnesium::MgHydrater::setup_virtual_waters_around_magnesiums().

◆ filter_acceptor_ligands() [1/2]

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

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_acceptor(), protocols::sewing::data_storage::ligand, and core::pose::Pose::residue().

Referenced by get_mg_ligands().

◆ filter_acceptor_ligands() [2/2]

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 
)

References is_ligand(), and protocols::sewing::data_storage::ligand.

◆ filter_water_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 
)

References core::conformation::Residue::atom_name(), protocols::sewing::data_storage::ligand, core::conformation::Residue::name3(), and core::pose::Pose::residue().

Referenced by get_mg_ligands().

◆ find_bound_waters_that_are_daughters_in_fold_tree()

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

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_h2o, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_parent_residue(), MG_LIGAND_DISTANCE_CUTOFF(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by protocols::magnesium::MgHydrater::fix_fold_tree_in_excised_pose_for_mg_bound_waters(), get_bound_water_res(), and protocols::magnesium::MgHydrater::setup_virtual_waters_around_magnesiums().

◆ fix_water_jump()

void protocols::magnesium::fix_water_jump ( pose::Pose &  pose,
core::Size const &  parent_res,
core::Size const &  water_res 
)

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::slide_jump(), and update_jump_atoms_for_mg_bound_water().

Referenced by protocols::magnesium::MgHydrater::fix_fold_tree_in_excised_pose_for_mg_bound_waters(), and protocols::magnesium::MgHydrater::setup_virtual_waters_around_magnesiums().

◆ fixup_magnesiums()

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

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

◆ get_bound_water_res()

core::Size protocols::magnesium::get_bound_water_res ( pose::Pose const &  pose,
core::Size const  mg_res,
core::Size const  n 
)

References core::pose::Pose::annotated_sequence(), find_bound_waters_that_are_daughters_in_fold_tree(), core::pose::Pose::fold_tree(), and TR().

Referenced by instantiate_water_at_octahedral_vertex().

◆ get_closest_non_hoh_contact()

core::id::AtomID protocols::magnesium::get_closest_non_hoh_contact ( pose::Pose const &  pose,
core::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::size(), and core::conformation::Residue::xyz().

Referenced by update_mg_hoh_fold_tree().

◆ get_hoh_xyz()

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

References get_mg_ligands(), protocols::sewing::data_storage::ligand, core::conformation::Residue::name3(), core::pose::pdb_to_pose(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by get_hydration_stats().

◆ get_hydration_stats()

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 
)

References core::chemical::element::F, get_hoh_xyz(), get_mg_res(), core::chemical::element::I, core::conformation::membrane::out, core::pose::Pose::pdb_info(), core::pose::pdb_to_pose(), and core::pose::pose_to_pdb().

◆ get_mg_ligands() [1/2]

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 
)

Referenced by get_hoh_xyz(), and get_mg_water_pairs().

◆ get_mg_ligands() [2/2]

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 
)

References core::conformation::Residue::aa(), core::chemical::aa_h2o, protocols::mpi_refinement::distance(), filter_acceptor_ligands(), filter_water_ligands(), core::conformation::Residue::is_virtual(), MG_LIGAND_DISTANCE_CUTOFF(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::size(), core::pose::Pose::xyz(), and core::conformation::Residue::xyz().

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

◆ get_mg_res()

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::MgMonteCarlo::apply(), protocols::magnesium::MgOrbitalFrameFinder::apply(), protocols::magnesium::MgWaterHydrogenPacker::apply(), get_hydration_stats(), get_mg_water_pairs(), hydrate_magnesiums(), protocols::magnesium::MgMonteCarlo::setup_mg_water_fold_tree(), and protocols::magnesium::MgHydrater::setup_virtual_waters_around_magnesiums().

◆ get_mg_rsd()

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

References core::conformation::ResidueFactory::create_residue(), and core::chemical::FA_STANDARD.

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

◆ get_mg_scorefxn()

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

References core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::geom_sol_fast, core::scoring::methods::EnergyMethodOptions::hbond_options(), core::scoring::hbond_sc, core::scoring::hoh_ref, core::scoring::mg_lig, core::scoring::mg_ref, core::scoring::mg_sol, and core::scoring::hbonds::HBondOptions::use_hb_env_dep().

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

◆ get_mg_water_pairs() [1/3]

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

◆ get_mg_water_pairs() [2/3]

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

References get_mg_res(), and get_mg_water_pairs().

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

◆ get_mg_water_pairs() [3/3]

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 
)

References get_mg_ligands().

Referenced by define_mg_water_map(), get_mg_water_pairs(), and remove_mg_bound_waters().

◆ get_octahedral_uniform_rotation_sampler()

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

References core::init::init().

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

◆ get_res_with_name()

utility::vector1< core::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::size().

Referenced by get_mg_res(), and get_water_res().

◆ get_useful_HOH_coords() [1/2]

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

◆ get_useful_HOH_coords() [2/2]

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(), and core::chemical::ResidueTypeSet::name_map().

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

◆ get_water_res()

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

References get_res_with_name().

Referenced by protocols::magnesium::MgMonteCarlo::apply(), and protocols::stepwise::modeler::freeze_waters().

◆ get_water_uniform_rotation_sampler()

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

References core::init::init().

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

◆ hydrate_magnesiums()

void protocols::magnesium::hydrate_magnesiums ( pose::Pose &  pose,
bool  use_virtual_waters_as_placeholders,
bool  test_all_mg_hydration_frames 
)

References protocols::magnesium::MgHydrater::apply(), get_mg_res(), remove_mg_bound_waters(), protocols::magnesium::MgHydrater::set_excise_mini_pose(), protocols::magnesium::MgHydrater::set_use_fast_frame_heuristic(), and protocols::magnesium::MgHydrater::set_use_virtual_waters_as_placeholders().

Referenced by protocols::stepwise::modeler::StepWiseMinimizer::do_minimize().

◆ instantiate_water_at_octahedral_vertex()

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 
)

References core::pose::add_variant_type_to_pose_residue(), append_mg_bound_water(), get_bound_water_res(), get_useful_HOH_coords(), core::kinematics::Stub::local2global(), core::chemical::ResidueTypeBase::mode(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), update_numbers_in_pdb_info(), core::chemical::VIRTUAL_RESIDUE_VARIANT, and core::conformation::Residue::xyz().

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

◆ is_ligand()

bool protocols::magnesium::is_ligand ( core::pose::Pose const &  pose,
core::id::AtomID const &  ligand 
)

References core::conformation::Residue::atom_type(), core::chemical::AtomType::is_acceptor(), protocols::sewing::data_storage::ligand, and core::pose::Pose::residue().

Referenced by core::scoring::elec::FA_ElecEnergy::atomistic_pair_energy(), core::scoring::etable::BaseEtableEnergy< Derived >::determine_crossover_behavior(), core::scoring::elec::FA_ElecEnergy::eval_intrares_derivatives(), core::scoring::elec::FA_ElecEnergy::eval_intrares_energy(), filter_acceptor_ligands(), core::scoring::elec::FA_ElecEnergy::get_intrares_countpair(), core::pose::Pose::set_chi(), and protocols::hybridization::HybridizeProtocol::validate_template().

◆ MG_HOH_DISTANCE()

core::Distance const protocols::magnesium::MG_HOH_DISTANCE ( 2.  1)

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

◆ MG_LIGAND_DISTANCE_CUTOFF()

core::Distance const protocols::magnesium::MG_LIGAND_DISTANCE_CUTOFF ( 3.  2)

Referenced by find_bound_waters_that_are_daughters_in_fold_tree(), and get_mg_ligands().

◆ MG_V_DISTANCE()

core::Distance const protocols::magnesium::MG_V_DISTANCE ( 1.  0)

Referenced by protocols::magnesium::MgHydrater::hydrate_magnesium_with_orbital_frame().

◆ minimize_magnesium_and_hydration_shell() [1/3]

void protocols::magnesium::minimize_magnesium_and_hydration_shell ( core::pose::Pose &  pose,
utility::vector1< core::pose::PoseOP > &  pose_list,
utility::vector1< core::Size > const &  mg_res,
core::scoring::ScoreFunctionCOP  minimize_scorefxn = nullptr,
core::Distance const  mg_coord_cst_dist = 0.2 
)

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().

◆ minimize_magnesium_and_hydration_shell() [2/3]

void protocols::magnesium::minimize_magnesium_and_hydration_shell ( pose::Pose &  pose,
utility::vector1< core::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().

◆ minimize_magnesium_and_hydration_shell() [3/3]

void protocols::magnesium::minimize_magnesium_and_hydration_shell ( pose::Pose &  pose,
utility::vector1< pose::PoseOP > &  pose_list,
utility::vector1< core::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().

◆ pdbslice()

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

References core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by protocols::magnesium::MgMonteCarlo::apply(), protocols::magnesium::MgWaterHydrogenPacker::apply(), protocols::membrane::chain_tm_com(), core::pose::rna::extract_rna_chains(), protocols::magnesium::MgHydrater::hydrate_magnesium(), remove_mg_bound_waters(), and remove_waters_except_mg_bound().

◆ remove_mg_bound_waters()

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

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::full_model_info_defined(), get_mg_water_pairs(), core::conformation::Residue::name3(), pdbslice(), core::pose::full_model_info::FullModelInfo::res_list(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::stepwise::modeler::slice_out_pose().

Referenced by hydrate_magnesiums().

◆ remove_waters_except_mg_bound()

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

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

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

◆ set_water_numbers_to_zero()

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

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

Referenced by update_numbers_in_pdb_info().

◆ strip_out_magnesiums()

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

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

◆ update_jump_atoms_for_mg_bound_water()

void protocols::magnesium::update_jump_atoms_for_mg_bound_water ( core::pose::Pose &  pose,
core::Size const  n 
)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::get_jump_that_builds_residue(), core::chemical::ResidueTypeBase::name3(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by append_mg_bound_water(), and fix_water_jump().

◆ update_mg_hoh_fold_tree()

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

References core::chemical::ResidueType::atom_name(), core::id::AtomID::atomno(), core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), get_closest_non_hoh_contact(), get_mg_ligands(), core::import_pose::get_tree(), core::io::pose_from_sfr::is_connected(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueTypeBase::name3(), core::kinematics::FoldTree::num_jump(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), core::pose::Pose::size(), core::kinematics::FoldTree::upstream_atom(), and core::kinematics::FoldTree::upstream_jump_residue().

◆ update_numbers_in_pdb_info()

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

References core::pose::Pose::pdb_info(), set_water_numbers_to_zero(), and core::pose::Pose::size().

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

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