generalized_kinematic_closure

• filter
• perturber
• selector

Bindings for protocols::generalized_kinematic_closure namespace

pyrosetta.rosetta.protocols.generalized_kinematic_closure.copy_loop_pose_to_original(original_pose: pyrosetta.rosetta.core.pose.Pose, loop_pose: pyrosetta.rosetta.core.pose.Pose, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, tail_residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

Copy the atom positions of the residues in the loop pose to the original pose.

C++: protocols::generalized_kinematic_closure::copy_loop_pose_to_original(class core::pose::Pose &, const 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> > > &, 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.generalized_kinematic_closure.correct_polymer_dependent_atoms_in_pose_segment(original_pose: pyrosetta.rosetta.core.pose.Pose, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → None

Update the polymer bond-dependent atom positions for every residue in the

residue map.

C++: protocols::generalized_kinematic_closure::correct_polymer_dependent_atoms_in_pose_segment(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.generalized_kinematic_closure.general_set_phi(pose: pyrosetta.rosetta.core.pose.Pose, residue_index: int, phi_value: float) → None

Sets phi for an L-alpha amino acid, even if the nitrogen has a nonstandard connection.

C++: protocols::generalized_kinematic_closure::general_set_phi(class core::pose::Pose &, const unsigned long, const double &) –> void

pyrosetta.rosetta.protocols.generalized_kinematic_closure.general_set_psi(pose: pyrosetta.rosetta.core.pose.Pose, residue_index: int, psi_value: float) → None

Sets psi for an L-alpha amino acid, even if the carbonyl carbon has a nonstandard connection.

C++: protocols::generalized_kinematic_closure::general_set_psi(class core::pose::Pose &, const unsigned long, const double &) –> void

pyrosetta.rosetta.protocols.generalized_kinematic_closure.get_original_pose_rsd(perturbedloop_rsd: int, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → int

Given a residue_map vector of pairs, where each pair is < residue_index_in_perturbedloop_pose, residue_index_in_original_pose >,

and a residue index in the perturbed loop, return the corresponding residue index in the original pose.

C++: protocols::generalized_kinematic_closure::get_original_pose_rsd(const unsigned long, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> unsigned long

pyrosetta.rosetta.protocols.generalized_kinematic_closure.is_in_list(val: int, list: pyrosetta.rosetta.utility.vector1_unsigned_long) → bool

Function to determine whether a value is in a list.

C++: protocols::generalized_kinematic_closure::is_in_list(const unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> bool

pyrosetta.rosetta.protocols.generalized_kinematic_closure.original_pose_residue_is_in_residue_map(residue_index: int, residue_map: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) → bool

function to determine whether a residue index from the original pose is in the residue_map list.

C++: protocols::generalized_kinematic_closure::original_pose_residue_is_in_residue_map(const unsigned long, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) –> bool

pyrosetta.rosetta.protocols.generalized_kinematic_closure.set_loop_pose(*args, **kwargs)

Overloaded function.

1. set_loop_pose(pose: pyrosetta.rosetta.core.pose.Pose, atomlist: pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t, t_ang: pyrosetta.rosetta.utility.vector1_double, b_ang: pyrosetta.rosetta.utility.vector1_double, b_len: pyrosetta.rosetta.utility.vector1_double) -> None

Set the loop pose conformation based on a set of results from kinematic closure.

– A pose consisting of the loop to be closed only.

—A list of AtomIDs and corresponding xyz coordinates (though we don’t use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.

– The torsion angles values to set.

—The bond angle values to set.

– The bond length values to set.

C++: protocols::generalized_kinematic_closure::set_loop_pose(class core::pose::Pose &, const class utility::vector1<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> > > > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) –> void

2. set_loop_pose(pose: pyrosetta.rosetta.core.pose.Pose, atomlist: pyrosetta.rosetta.utility.vector1_std_pair_core_id_AtomID_numeric_xyzVector_double_t, t_ang: pyrosetta.rosetta.utility.vector1_double) -> None

Set the loop pose conformation based on a set of results from kinematic closure.

This version ONLY sets mainchain torsions, and does no rebuilding of mainchain O or H atoms.

—A pose consisting of the loop to be closed only.

– A list of AtomIDs and corresponding xyz coordinates (though we don’t use the latter) of the chain of atoms closed by KIC. Note that the residue indices refer to the loop pose, not the original pose.

—The torsion angles values to set.

C++: protocols::generalized_kinematic_closure::set_loop_pose(class core::pose::Pose &, const class utility::vector1<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> >, class std::allocator<struct std::pair<class core::id::AtomID, class numeric::xyzVector<double> > > > &, const class utility::vector1<double, class std::allocator<double> > &) –> void