def test_asa_0():
conf = get("native.pdb")
n_atoms = conf["XYZList"].shape[1]
angle_indices = np.array(list(itertools.combinations(range(n_atoms), 3)))
a1 = bond_angles(conf["XYZList"], angle_indices)
a2 = __bond_angles(conf["XYZList"], angle_indices)
eq(a1, a2)
def get_redundant_internal_coordinates(trajectory, **kwargs):
"""Compute internal coordinates from the cartesian coordinates
This extracts all of the bond lengths, bond angles and dihedral angles
from every frame in a trajectory.
Parameters
----------
trajectory : msmbuilder.Trajectory
Trajectory object containing the internal coordinates
Additional Parameters
---------------------
ibonds : np.ndarray, optional, shape[n_bonds, 2], dtype=int
Each row gives the indices of two atoms involved in a bond
iangles : np.ndarray, optional shape[n_angles, 3], dtype=int
Each row gives the indices of three atoms which together make an angle
idihedrals : np.ndarray, optional, shape[n_dihedrals, 4], dtype=int
Each row gives the indices of the four atoms which together make a
dihedral
Notes
-----
ibonds, iangles, and idihedrals will be computed usig the first
frame in the trajectory, if not supplied
Returns
-------
internal_coords : np.ndarray, shape=[n_frames, n_bonds+n_angles+n_dihedrals]
All of the internal coordinates collected into a big array, such that
internal_coords[i,j] gives the jth coordinate for the ith frame.
"""
if 'ibonds' in kwargs and 'iangles' in kwargs and 'idihedrals' in kwargs:
ibonds = kwargs['ibonds']
iangles = kwargs['iangles']
idihedrals = kwargs['idihedrals']
else:
ibonds, iangles, idihedrals = get_connectivity(trajectory)
# convert everything to the right shape and C ordering, since
# all of these methods are in C and are going to need things to be
# the right type. The methods will all do a copy for things that
# aren't the right type, but hopefully we can only do the copy once
# instead of three times if xyzlist really does need to be reordered
# in memory
xyzlist = np.array(trajectory['XYZList'], dtype=np.float32, order='c')
ibonds = np.array(ibonds, dtype=np.int32, order='c')
iangles = np.array(iangles, dtype=np.int32, order='c')
idihedrals = np.array(idihedrals, dtype=np.int32, order='c')
b = atom_distances(xyzlist, ibonds)
a = bond_angles(xyzlist, iangles)
d = compute_dihedrals(xyzlist, idihedrals, degrees=False)
return np.hstack((b, a, d))