def compute_angles(traj, angle_indices, opt=True):
"""Compute the bond angles between the supplied triplets of indices in each frame of a trajectory.
Parameters
----------
traj : Trajectory
An mtraj trajectory.
angle_indices : np.ndarray, shape=(num_pairs, 2), dtype=int
Each row gives the indices of three atoms which together make an angle.
opt : bool, default=True
Use an optimized native library to calculate distances. Our optimized
SSE angle calculation implementation is 10-20x faster than the
(itself optimized) numpy implementation.
Returns
-------
angles : np.ndarray, shape=[n_frames, n_angles], dtype=float
The angles are in radians
"""
xyz = ensure_type(traj.xyz, dtype=np.float32, ndim=3, name='traj.xyz', shape=(None, None, 3), warn_on_cast=False)
triplets = ensure_type(np.asarray(angle_indices), dtype=np.int32, ndim=2, name='angle_indices', shape=(None, 3), warn_on_cast=False)
if not np.all(np.logical_and(triplets < traj.n_atoms, triplets >= 0)):
raise ValueError('angle_indices must be between 0 and %d' % traj.n_atoms)
out = np.zeros((xyz.shape[0], triplets.shape[0]), dtype=np.float32)
if opt:
_geometry._angle(xyz, triplets, out)
else:
_angle(xyz, triplets, out)
return out
def compute_angles(traj, angle_indices, periodic=True, opt=True):
"""Compute the bond angles between the supplied triplets of indices in each frame of a trajectory.
Parameters
----------
traj : Trajectory
An mdtraj trajectory.
angle_indices : np.ndarray, shape=(num_angles, 3), dtype=int
Each row gives the indices of three atoms which together make an angle.
periodic : bool, default=True
If `periodic` is True and the trajectory contains unitcell
information, we will treat angles that cross periodic images using
the minimum image convention.
opt : bool, default=True
Use an optimized native library to calculate distances. Our optimized
SSE angle calculation implementation is 10-20x faster than the
(itself optimized) numpy implementation.
Returns
-------
angles : np.ndarray, shape=[n_frames, n_angles], dtype=float
The angles are in radians
"""
xyz = ensure_type(traj.xyz, dtype=np.float32, ndim=3, name='traj.xyz', shape=(None, None, 3), warn_on_cast=False)
triplets = ensure_type(angle_indices, dtype=np.int32, ndim=2, name='angle_indices', shape=(None, 3), warn_on_cast=False)
if not np.all(np.logical_and(triplets < traj.n_atoms, triplets >= 0)):
raise ValueError('angle_indices must be between 0 and %d' % traj.n_atoms)
if len(triplets) == 0:
return np.zeros((len(xyz), 0), dtype=np.float32)
if periodic and traj._have_unitcell:
if opt and not np.allclose(traj.unitcell_angles, 90):
warnings.warn('Optimized angle calculation does not work for non-orthorhombic '
'unit cells and periodic boundary conditions. Falling back to much '
'slower pure-Python implementation. Set periodic=False or opt=False '
'to disable this message.')
opt = False
out = np.zeros((xyz.shape[0], triplets.shape[0]), dtype=np.float32)
if periodic is True and traj._have_unitcell:
box = ensure_type(traj.unitcell_vectors, dtype=np.float32, ndim=3, name='unitcell_vectors', shape=(len(xyz), 3, 3))
if opt:
_geometry._angle_mic(xyz, triplets, box, out)
return out
else:
_angle(traj, triplets, periodic, out)
return out
if opt:
_geometry._angle(xyz, triplets, out)
else:
_angle(traj, triplets, periodic, out)
return out
def compute_angles(traj, angle_indices, periodic=True, opt=True):
"""Compute the bond angles between the supplied triplets of indices in each frame of a trajectory.
Parameters
----------
traj : Trajectory
An mdtraj trajectory.
angle_indices : np.ndarray, shape=(num_angles, 3), dtype=int
Each row gives the indices of three atoms which together make an angle.
periodic : bool, default=True
If `periodic` is True and the trajectory contains unitcell
information, we will treat angles that cross periodic images using
the minimum image convention.
opt : bool, default=True
Use an optimized native library to calculate distances. Our optimized
SSE angle calculation implementation is 10-20x faster than the
(itself optimized) numpy implementation.
Returns
-------
angles : np.ndarray, shape=[n_frames, n_angles], dtype=float
The angles are in radians
"""
xyz = ensure_type(traj.xyz, dtype=np.float32, ndim=3, name="traj.xyz", shape=(None, None, 3), warn_on_cast=False)
triplets = ensure_type(
angle_indices, dtype=np.int32, ndim=2, name="angle_indices", shape=(None, 3), warn_on_cast=False
)
if not np.all(np.logical_and(triplets < traj.n_atoms, triplets >= 0)):
raise ValueError("angle_indices must be between 0 and %d" % traj.n_atoms)
if len(triplets) == 0:
return np.zeros((len(xyz), 0), dtype=np.float32)
out = np.zeros((xyz.shape[0], triplets.shape[0]), dtype=np.float32)
if periodic is True and traj._have_unitcell:
box = ensure_type(
traj.unitcell_vectors, dtype=np.float32, ndim=3, name="unitcell_vectors", shape=(len(xyz), 3, 3)
)
if opt:
orthogonal = np.allclose(traj.unitcell_angles, 90)
_geometry._angle_mic(xyz, triplets, box.transpose(0, 2, 1).copy(), out, orthogonal)
return out
else:
_angle(traj, triplets, periodic, out)
return out
if opt:
_geometry._angle(xyz, triplets, out)
else:
_angle(traj, triplets, periodic, out)
return out
def _compute_angles_chunk(xyz,
triplets,
box=None,
periodic=True,
opt=True,
orthogonal=False):
"""Compute the angles for a single chunk
Parameters
----------
xyz : ndarray of shape (any, any, 3)
The xyz coordinates of the chunk
triplets : array of shape (any, 3)
The indices for which to compute an angle
box : ndarray of shape (any, 3, 3)
The box vectors of the chunk
periodic : bool
Wether to use the periodc boundary during the calculation.
opt : bool, default=True
Use an optimized native library to calculate distances. MDTraj's
optimized SSE angle calculation implementation is 10-20x faster than
the (itself optimized) numpy implementation.
orthogonal : bool or da.bool
Wether all angles are close to 90 degrees
"""
# Cast dask.bool to a true bool
orthogonal = bool(orthogonal)
xyz = ensure_type(
xyz,
dtype=np.float32,
ndim=3,
name="xyz",
shape=(None, None, 3),
warn_on_cast=False,
cast_da_to_np=True,
)
out = np.empty((xyz.shape[0], triplets.shape[0]), dtype=np.float32)
if opt:
if periodic and box is not None:
_geometry._angle_mic(xyz, triplets,
box.transpose(0, 2, 1).copy(), out,
orthogonal)
else:
_geometry._angle(xyz, triplets, out)
else:
out = _angle(xyz, triplets, periodic, out).compute()
return out
def compute_angles(traj, angle_indices, periodic=True, opt=True):
"""Compute the bond angles between the supplied triplets of indices in each frame of a trajectory.
Parameters
----------
traj : Trajectory
An mtraj trajectory.
angle_indices : np.ndarray, shape=(num_pairs, 2), dtype=int
Each row gives the indices of three atoms which together make an angle.
periodic : bool, default=True
If `periodic` is True and the trajectory contains unitcell
information, we will treat angles that cross periodic images using
the minimum image convention.
opt : bool, default=True
Use an optimized native library to calculate distances. Our optimized
SSE angle calculation implementation is 10-20x faster than the
(itself optimized) numpy implementation.
Returns
-------
angles : np.ndarray, shape=[n_frames, n_angles], dtype=float
The angles are in radians
"""
xyz = ensure_type(traj.xyz, dtype=np.float32, ndim=3, name='traj.xyz', shape=(None, None, 3), warn_on_cast=False)
triplets = ensure_type(np.asarray(angle_indices), dtype=np.int32, ndim=2, name='angle_indices', shape=(None, 3), warn_on_cast=False)
if not np.all(np.logical_and(triplets < traj.n_atoms, triplets >= 0)):
raise ValueError('angle_indices must be between 0 and %d' % traj.n_atoms)
out = np.zeros((xyz.shape[0], triplets.shape[0]), dtype=np.float32)
if periodic is True and traj._have_unitcell:
box = ensure_type(traj.unitcell_vectors, dtype=np.float32, ndim=3, name='unitcell_vectors', shape=(len(xyz), 3, 3))
if opt and _geometry._processor_supports_sse41():
_geometry._angle_mic(xyz, triplets, box, out)
return out
else:
_angle(traj, triplets, periodic, out)
return out
if opt and _geometry._processor_supports_sse41():
_geometry._angle(xyz, triplets, out)
else:
_angle(traj, triplets, periodic, out)
return out