Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
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::Sizefind_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::Sizeget_res_with_name (pose::Pose const &pose, std::string const &name)
 
utility::vector1< core::Sizeget_mg_res (pose::Pose const &pose)
 
utility::vector1< core::Sizeget_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::Sizepdbslice (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)
 
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

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< 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)
core::Size protocols::magnesium::append_mg_bound_water ( core::pose::Pose pose,
core::conformation::Residue const &  rsd,
core::Size const  mg_res 
)
std::map< core::Size, utility::vector1< core::Size > > protocols::magnesium::define_mg_water_map ( pose::Pose const &  pose)
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 
)
utility::vector1< core::Size > protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree ( pose::Pose const &  pose,
core::Size const  mg_res 
)
void protocols::magnesium::fix_water_jump ( pose::Pose pose,
core::Size const &  parent_res,
core::Size const &  water_res 
)
void protocols::magnesium::fixup_magnesiums ( pose::Pose pose)
core::Size protocols::magnesium::get_bound_water_res ( pose::Pose const &  pose,
core::Size const  mg_res,
core::Size const  n 
)
core::id::AtomID protocols::magnesium::get_closest_non_hoh_contact ( pose::Pose const &  pose,
core::Size const  i,
std::string const &  exclude_rsd 
)
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 
)
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 
)

Referenced by get_hoh_xyz(), and get_mg_water_pairs().

utility::vector1< core::Size > protocols::magnesium::get_mg_res ( pose::Pose const &  pose)
core::conformation::ResidueOP protocols::magnesium::get_mg_rsd ( )
core::scoring::ScoreFunctionOP protocols::magnesium::get_mg_scorefxn ( )
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 
)
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 
)
numeric::UniformRotationSamplerCOP protocols::magnesium::get_octahedral_uniform_rotation_sampler ( core::Real const  rotstep,
bool const  remove_redundant 
)
utility::vector1< core::Size > protocols::magnesium::get_res_with_name ( pose::Pose const &  pose,
std::string const &  name 
)
core::conformation::ResidueOP protocols::magnesium::get_useful_HOH_coords ( Vector Oc,
Vector OH1c,
Vector OH2c,
core::chemical::ResidueTypeSet const &  residue_set 
)
utility::vector1< core::Size > protocols::magnesium::get_water_res ( pose::Pose const &  pose)
numeric::UniformRotationSamplerCOP protocols::magnesium::get_water_uniform_rotation_sampler ( )
void protocols::magnesium::hydrate_magnesiums ( pose::Pose pose,
bool  use_virtual_waters_as_placeholders,
bool  test_all_mg_hydration_frames 
)
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 
)
bool protocols::magnesium::is_ligand ( core::pose::Pose const &  pose,
core::id::AtomID const &  ligand 
)
core::Distance const protocols::magnesium::MG_HOH_DISTANCE ( 2.  1)
core::Distance const protocols::magnesium::MG_LIGAND_DISTANCE_CUTOFF ( 3.  2)
core::Distance const protocols::magnesium::MG_V_DISTANCE ( 1.  0)
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 
)
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 
)
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 
)
utility::vector1< core::Size > protocols::magnesium::pdbslice ( core::pose::Pose pose,
core::Size const  center_res,
core::Distance  distance_cutoff 
)
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::remove_waters_except_mg_bound ( pose::Pose pose,
utility::vector1< std::pair< core::Size, core::Size > > const &  mg_water_pairs 
)
void protocols::magnesium::set_water_numbers_to_zero ( pose::Pose pose)
void protocols::magnesium::strip_out_magnesiums ( pose::Pose pose)
void protocols::magnesium::update_jump_atoms_for_mg_bound_water ( core::pose::Pose pose,
core::Size const  n 
)
void protocols::magnesium::update_mg_hoh_fold_tree ( pose::Pose pose)
void protocols::magnesium::update_numbers_in_pdb_info ( pose::Pose pose,
bool const  reset_waters 
)