magnesium

Bindings for protocols::magnesium namespace

pyrosetta.rosetta.protocols.magnesium.add_single_magnesium(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::add_single_magnesium(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.append_mg_bound_water(pose: pyrosetta.rosetta.core.pose.Pose, rsd: pyrosetta.rosetta.core.conformation.Residue, mg_res: int) → int

C++: protocols::magnesium::append_mg_bound_water(class core::pose::Pose &, const class core::conformation::Residue &, const unsigned long) –> unsigned long

pyrosetta.rosetta.protocols.magnesium.define_mg_water_map(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_unsigned_long_utility_vector1_unsigned_long_std_allocator_unsigned_long_t

C++: protocols::magnesium::define_mg_water_map(const class core::pose::Pose &) –> class std::map<unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> > > > >

pyrosetta.rosetta.protocols.magnesium.filter_acceptor_ligands(pose: pyrosetta.rosetta.core.pose.Pose, ligands: pyrosetta.rosetta.utility.vector1_core_id_AtomID) → pyrosetta.rosetta.utility.vector1_core_id_AtomID

C++: protocols::magnesium::filter_acceptor_ligands(const class core::pose::Pose &, const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.protocols.magnesium.find_bound_waters_that_are_daughters_in_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::find_bound_waters_that_are_daughters_in_fold_tree(const class core::pose::Pose &, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.fixup_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::fixup_magnesiums(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.get_closest_non_hoh_contact(*args, **kwargs)

Overloaded function.

  1. get_closest_non_hoh_contact(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> pyrosetta.rosetta.core.id.AtomID
  2. get_closest_non_hoh_contact(pose: pyrosetta.rosetta.core.pose.Pose, i: int, exclude_rsd: str) -> pyrosetta.rosetta.core.id.AtomID

C++: protocols::magnesium::get_closest_non_hoh_contact(const class core::pose::Pose &, const unsigned long, const class std::basic_string<char> &) –> class core::id::AtomID

pyrosetta.rosetta.protocols.magnesium.get_hydration_stats(pose: pyrosetta.rosetta.core.pose.Pose, reference_pose: pyrosetta.rosetta.core.pose.Pose, pdb_mg_res_list_in: pyrosetta.rosetta.utility.vector1_unsigned_long, outfile: str) → None

C++: protocols::magnesium::get_hydration_stats(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.magnesium.get_mg_ligands(*args, **kwargs)

Overloaded function.

  1. get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID
  2. get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int, filter_for_acceptors: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID
  3. get_mg_ligands(pose: pyrosetta.rosetta.core.pose.Pose, i: int, filter_for_acceptors: bool, exclude_virtual_waters: bool) -> pyrosetta.rosetta.utility.vector1_core_id_AtomID

C++: protocols::magnesium::get_mg_ligands(const class core::pose::Pose &, const unsigned long, const bool, const bool) –> class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> >

pyrosetta.rosetta.protocols.magnesium.get_mg_res(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::get_mg_res(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.get_mg_rsd() → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::magnesium::get_mg_rsd() –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.protocols.magnesium.get_mg_scorefxn() → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::magnesium::get_mg_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

pyrosetta.rosetta.protocols.magnesium.get_mg_water_pairs(*args, **kwargs)

Overloaded function.

  1. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
  2. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose, exclude_virtual_waters: bool) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::magnesium::get_mg_water_pairs(const class core::pose::Pose &, const bool) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

  1. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
  2. get_mg_water_pairs(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, exclude_virtual_waters: bool) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t

C++: protocols::magnesium::get_mg_water_pairs(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >

pyrosetta.rosetta.protocols.magnesium.get_octahedral_uniform_rotation_sampler(*args, **kwargs)

Overloaded function.

  1. get_octahedral_uniform_rotation_sampler() -> pyrosetta.rosetta.numeric.UniformRotationSampler
  2. get_octahedral_uniform_rotation_sampler(rotstep: float) -> pyrosetta.rosetta.numeric.UniformRotationSampler
  3. get_octahedral_uniform_rotation_sampler(rotstep: float, remove_redundant: bool) -> pyrosetta.rosetta.numeric.UniformRotationSampler

C++: protocols::magnesium::get_octahedral_uniform_rotation_sampler(const double, const bool) –> class std::shared_ptr<const class numeric::UniformRotationSampler>

pyrosetta.rosetta.protocols.magnesium.get_useful_HOH_coords(Oc: pyrosetta.rosetta.numeric.xyzVector_double_t, OH1c: pyrosetta.rosetta.numeric.xyzVector_double_t, OH2c: pyrosetta.rosetta.numeric.xyzVector_double_t, residue_set: pyrosetta.rosetta.core.chemical.ResidueTypeSet) → pyrosetta.rosetta.core.conformation.Residue

C++: protocols::magnesium::get_useful_HOH_coords(class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &, const class core::chemical::ResidueTypeSet &) –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.protocols.magnesium.get_water_res(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::get_water_res(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.get_water_uniform_rotation_sampler() → pyrosetta.rosetta.numeric.UniformRotationSampler

C++: protocols::magnesium::get_water_uniform_rotation_sampler() –> class std::shared_ptr<const class numeric::UniformRotationSampler>

pyrosetta.rosetta.protocols.magnesium.hydrate_magnesiums(*args, **kwargs)

Overloaded function.

  1. hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose) -> None
  2. hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose, use_virtual_waters_as_placeholders: bool) -> None
  3. hydrate_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose, use_virtual_waters_as_placeholders: bool, test_all_mg_hydration_frames: bool) -> None

C++: protocols::magnesium::hydrate_magnesiums(class core::pose::Pose &, bool, bool) –> void

pyrosetta.rosetta.protocols.magnesium.instantiate_water_at_octahedral_vertex(*args, **kwargs)

Overloaded function.

  1. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int) -> int
  2. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float) -> int
  3. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float, replace_residue: bool) -> int
  4. instantiate_water_at_octahedral_vertex(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: int, n: int, hoh_distance: float, replace_residue: bool, virtual_water: bool) -> int

C++: protocols::magnesium::instantiate_water_at_octahedral_vertex(class core::pose::Pose &, const unsigned long, const unsigned long, const double, const bool, const bool) –> unsigned long

pyrosetta.rosetta.protocols.magnesium.minimize_magnesium_and_hydration_shell(*args, **kwargs)

Overloaded function.

  1. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
  2. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  3. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mg_coord_cst_dist: float) -> None

C++: protocols::magnesium::minimize_magnesium_and_hydration_shell(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const double) –> void

  1. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
  2. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None
  3. minimize_magnesium_and_hydration_shell(pose: pyrosetta.rosetta.core.pose.Pose, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, minimize_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mg_coord_cst_dist: float) -> None

C++: protocols::magnesium::minimize_magnesium_and_hydration_shell(class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const double) –> void

pyrosetta.rosetta.protocols.magnesium.pdbslice(*args, **kwargs)

Overloaded function.

  1. pdbslice(pose: pyrosetta.rosetta.core.pose.Pose, center_res: int) -> pyrosetta.rosetta.utility.vector1_unsigned_long
  2. pdbslice(pose: pyrosetta.rosetta.core.pose.Pose, center_res: int, distance_cutoff: float) -> pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::magnesium::pdbslice(class core::pose::Pose &, const unsigned long, double) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.magnesium.remove_mg_bound_waters(*args, **kwargs)

Overloaded function.

  1. remove_mg_bound_waters(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
  2. remove_mg_bound_waters(pose: pyrosetta.rosetta.core.pose.Pose, mg_res: pyrosetta.rosetta.utility.vector1_unsigned_long, leave_other_waters: bool) -> None

C++: protocols::magnesium::remove_mg_bound_waters(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool) –> void

pyrosetta.rosetta.protocols.magnesium.remove_waters_except_mg_bound(pose: pyrosetta.rosetta.core.pose.Pose, mg_water_pairs: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

C++: protocols::magnesium::remove_waters_except_mg_bound(class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> void

pyrosetta.rosetta.protocols.magnesium.strip_out_magnesiums(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::strip_out_magnesiums(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.update_jump_atoms_for_mg_bound_water(pose: pyrosetta.rosetta.core.pose.Pose, n: int) → None

C++: protocols::magnesium::update_jump_atoms_for_mg_bound_water(class core::pose::Pose &, const unsigned long) –> void

pyrosetta.rosetta.protocols.magnesium.update_mg_hoh_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::magnesium::update_mg_hoh_fold_tree(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.magnesium.update_numbers_in_pdb_info(*args, **kwargs)

Overloaded function.

  1. update_numbers_in_pdb_info(pose: pyrosetta.rosetta.core.pose.Pose) -> None
  2. update_numbers_in_pdb_info(pose: pyrosetta.rosetta.core.pose.Pose, reset_waters: bool) -> None

C++: protocols::magnesium::update_numbers_in_pdb_info(class core::pose::Pose &, const bool) –> void