numpy_utils

pyrosetta.toolbox.numpy_utils.calc_dihedral(c)

Compute a dihedral angle from four points in space.

Args:

c (np.mat): Coordinates of four points in space (atoms)

Returns:

The dihedral angle as a float

pyrosetta.toolbox.numpy_utils.get_coordinates_from_pose(p, resNo=1)

Pack atomic coordinates in a single residue into a numpy matrix.

Args:

p (Pose): Pose from coordinates will be extracted resNo (int): the pose-numbered residue of interest

Returns:

Set of coordinates (np.mat) for the atoms in the Pose

pyrosetta.toolbox.numpy_utils.numpy_to_rosetta(np_arr)

Pack values in a numpy data structure into the analogous Rosetta data structure.

Args:

np_arry (np.mat or np.array): One- (1 x 3) or two-dimensional (3 x 3)

numpy matrix

Returns:

The values in the appropriate Rosetta container

(numeric.xyzVector_double_t or numeric.xyzMatrix_double_t)

pyrosetta.toolbox.numpy_utils.rigid_transform_3D(A, B)

Compute the translation and rotation to optimally superpose two sets of points using singular value decomposition.

Args:

A (np.mat): A set of points B (np.mat): A set of points (must have a one-to-one correspondence

to the points in A)

Returns:

Rotation matrix (np.mat) and translation vector (np.array) to

optimally superpose A onto B

pyrosetta.toolbox.numpy_utils.rotate_pose(p, R)

Apply a rotation matrix to all of the coordinates in a Pose.

Args:

p (Pose): The Pose instance to manipulate R (np.mat): A rotation matrix to apply to the Pose coordinates

Returns:

None. The input Pose is manipulated.

pyrosetta.toolbox.numpy_utils.translate_pose(p, t)

Apply a translation to all of the coordinates in a Pose.

Args:

p (Pose): The Pose instance to manipulate t (np.array): A vector to add to the Pose coordinates

Returns:

None. The input Pose is manipulated.