inverse¶

Bindings for core::kinematics::inverse namespace

class pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtom¶

Bases: pybind11_object

this class has the duty of logging atoms and their desired positions

We are using struct instead of class because AlignmentAtom has no invariants

property destination_xyz¶

property id¶

set(*args, **kwargs)¶

Overloaded function.

set(self: pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtom, atomid: pyrosetta.rosetta.core.id.AtomID, dest_xyz: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

C++: core::kinematics::inverse::AlignmentAtom::set(class core::id::AtomID, const class numeric::xyzVector<double>) –> void

set(self: pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtom, atomid: pyrosetta.rosetta.core.id.AtomID, conf: pyrosetta.rosetta.core.conformation.Conformation) -> None

C++: core::kinematics::inverse::AlignmentAtom::set(class core::id::AtomID, const class core::conformation::Conformation &) –> void

class pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray¶

Bases: pybind11_object

This class contains the 3 AlignmentAtoms that we want to use to define the new jump value.

In theory, the order of the atoms does not matter. We are using struct instead of class because AlignmentAtomArray has no invariants. We are also defining functions in the header because the function body does a better job of explaining the purpose than my comments do.

property atoms¶

create_destination_stub(self: pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray) → pyrosetta.rosetta.core.kinematics.Stub¶

Define the intended stub that represents the future pose _after_ updating the jump

C++: core::kinematics::inverse::AlignmentAtomArray::create_destination_stub() const –> class core::kinematics::Stub

create_stub_from_atom_ids(self: pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray, conf: pyrosetta.rosetta.core.conformation.Conformation) → pyrosetta.rosetta.core.kinematics.Stub¶

This utility function uses the current XYZ coordinates for the AtomIDs in the pose.

C++: core::kinematics::inverse::AlignmentAtomArray::create_stub_from_atom_ids(const class core::conformation::Conformation &) const –> class core::kinematics::Stub

class pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms¶

Bases: pybind11_object

property child¶

property grandparent¶

property parent¶

class pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry¶

Bases: pybind11_object

property A_B_C_D_torsion_angle_rad¶

property B_C_D_E_torsion_angle_rad¶

property B_C_D_bond_angle_rad¶

property C_D_E_F_torsion_angle_rad¶

property C_D_E_bond_angle_rad¶

property C_D_dist_Ang¶

init_from_current(self: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry, conformation: pyrosetta.rosetta.core.conformation.Conformation, ABC: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms, DEF: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms) → None¶

set all six values using their current configuration in the conformation

C++: core::kinematics::inverse::InternalCoordGeometry::init_from_current(const class core::conformation::Conformation &, const struct core::kinematics::inverse::InternalCoordAtoms &, const struct core::kinematics::inverse::InternalCoordAtoms &) –> void

pyrosetta.rosetta.core.kinematics.inverse.assert_atoms_are_downstream_of_jump(conformation: pyrosetta.rosetta.core.conformation.Conformation, jump_id: int, atom_arr: pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray) → None¶: C++: core::kinematics::inverse::assert_atoms_are_downstream_of_jump(const class core::conformation::Conformation &, const unsigned long, const struct core::kinematics::inverse::AlignmentAtomArray &) –> void

pyrosetta.rosetta.core.kinematics.inverse.assert_atoms_are_upstream_of_jump(conformation: pyrosetta.rosetta.core.conformation.Conformation, jump_id: int, atom_arr: pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray) → None¶: C++: core::kinematics::inverse::assert_atoms_are_upstream_of_jump(const class core::conformation::Conformation &, const unsigned long, const struct core::kinematics::inverse::AlignmentAtomArray &) –> void

pyrosetta.rosetta.core.kinematics.inverse.calc_new_atom_location(greatgrandparent: pyrosetta.rosetta.numeric.xyzVector_double_t, grandparent: pyrosetta.rosetta.numeric.xyzVector_double_t, parent: pyrosetta.rosetta.numeric.xyzVector_double_t, dist: float, bond_angle: float, torsion_angle: float) → pyrosetta.rosetta.numeric.xyzVector_double_t¶

Given internal coordinates and XYZs of the parents, calculate XYZ of a child

C++: core::kinematics::inverse::calc_new_atom_location(const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, double, double, double) –> class numeric::xyzVector<double>

pyrosetta.rosetta.core.kinematics.inverse.calculate_new_jump(conformation: pyrosetta.rosetta.core.conformation.Conformation, jump_id: int, atoms: pyrosetta.rosetta.core.kinematics.inverse.AlignmentAtomArray) → pyrosetta.rosetta.core.kinematics.Jump¶

Update a desired jump in the conformation to place the atoms in the AlignmentAtomArray to the desired position

protocol is described as comments in the body of the code.

Jack Maguire

C++: core::kinematics::inverse::calculate_new_jump(const class core::conformation::Conformation &, const unsigned long, const struct core::kinematics::inverse::AlignmentAtomArray &) –> class core::kinematics::Jump

pyrosetta.rosetta.core.kinematics.inverse.dummy_AlignmentAtomArrayInternalType(val: pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t) → pyrosetta.rosetta.std.array_core_kinematics_inverse_AlignmentAtom_3_t¶: C++: core::kinematics::inverse::dummy_AlignmentAtomArrayInternalType(struct std::array<struct core::kinematics::inverse::AlignmentAtom, 3>) –> struct std::array<struct core::kinematics::inverse::AlignmentAtom, 3>

pyrosetta.rosetta.core.kinematics.inverse.dummy_InternalCoordAtoms(val: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms) → pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms¶: C++: core::kinematics::inverse::dummy_InternalCoordAtoms(struct core::kinematics::inverse::InternalCoordAtoms) –> struct core::kinematics::inverse::InternalCoordAtoms

pyrosetta.rosetta.core.kinematics.inverse.dummy_InternalCoordGeometry(val: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry) → pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry¶: C++: core::kinematics::inverse::dummy_InternalCoordGeometry(struct core::kinematics::inverse::InternalCoordGeometry) –> struct core::kinematics::inverse::InternalCoordGeometry

pyrosetta.rosetta.core.kinematics.inverse.jump_from_internal_coords(conformation: pyrosetta.rosetta.core.conformation.Conformation, fixed_atoms: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms, moving_atoms: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordAtoms, geometry: pyrosetta.rosetta.core.kinematics.inverse.InternalCoordGeometry, jump_id: int) → pyrosetta.rosetta.core.kinematics.Jump¶

Utility function for calculating jumps by knowing desired internal coordinates of arbitrary atoms

fixed_atoms (A/B/C) are upstream of the jump, moving_atoms (D/E/F) are downstream.

The user provides distances, angles, and dihedral angles for the relationship between the two sets and the number of the jump the user wants to change. Rosetta then calculates the new value of this jump.

C++: core::kinematics::inverse::jump_from_internal_coords(const class core::conformation::Conformation &, const struct core::kinematics::inverse::InternalCoordAtoms &, const struct core::kinematics::inverse::InternalCoordAtoms &, struct core::kinematics::inverse::InternalCoordGeometry, unsigned long) –> class core::kinematics::Jump