def compute_dihedrals(trajectory, indices, opt=True):
"""Compute the dihedral angles between the supplied quartets of atoms in each frame in a trajectory.
Parameters
----------
trajectory : Trajectory
An mtraj trajectory.
indices : np.ndarray, shape=(n_dihedrals, 4), dtype=int
Each row gives the indices of four atoms which together make a
dihedral angle. The angle is between the planes spanned by the first
three atoms and the last three atoms, a torsion around the bond
between the middle two atoms.
opt : bool, default=True
Use an optimized native library to calculate angles.
Returns
-------
dihedrals : np.ndarray, shape=(n_frames, n_dihedrals), dtype=float
The output array gives, in each frame from the trajectory, each of the
`n_dihedrals` torsion angles. The angles are measured in **radians**.
"""
xyz = ensure_type(trajectory.xyz, dtype=np.float32, ndim=3, name='traj.xyz', shape=(None, None, 3), warn_on_cast=False)
quartets = ensure_type(np.asarray(indices), dtype=np.int32, ndim=2, name='indices', shape=(None, 4), warn_on_cast=False)
if not np.all(np.logical_and(quartets < trajectory.n_atoms, quartets >= 0)):
raise ValueError('indices must be between 0 and %d' % trajectory.n_atoms)
out = np.zeros((xyz.shape[0], quartets.shape[0]), dtype=np.float32)
if opt:
_geometry._dihedral(xyz, quartets, out)
else:
_dihedral(xyz, quartets, out)
return out
def compute_dihedrals(traj, indices, periodic=True, opt=True):
"""Compute the dihedral angles between the supplied quartets of atoms in each frame in a trajectory.
Parameters
----------
traj : Trajectory
An mtraj trajectory.
indices : np.ndarray, shape=(n_dihedrals, 4), dtype=int
Each row gives the indices of four atoms which together make a
dihedral angle. The angle is between the planes spanned by the first
three atoms and the last three atoms, a torsion around the bond
between the middle two atoms.
periodic : bool, default=True
If `periodic` is True and the trajectory contains unitcell
information, we will treat dihedrals that cross periodic images
using the minimum image convention.
opt : bool, default=True
Use an optimized native library to calculate angles.
Returns
-------
dihedrals : np.ndarray, shape=(n_frames, n_dihedrals), dtype=float
The output array gives, in each frame from the trajectory, each of the
`n_dihedrals` torsion angles. The angles are measured in **radians**.
"""
xyz = ensure_type(traj.xyz,
dtype=np.float32,
ndim=3,
name='traj.xyz',
shape=(None, None, 3),
warn_on_cast=False)
quartets = ensure_type(np.asarray(indices),
dtype=np.int32,
ndim=2,
name='indices',
shape=(None, 4),
warn_on_cast=False)
if not np.all(np.logical_and(quartets < traj.n_atoms, quartets >= 0)):
raise ValueError('indices must be between 0 and %d' % traj.n_atoms)
out = np.zeros((xyz.shape[0], quartets.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._dihedral_mic(xyz, quartets, box, out)
return out
else:
_dihedral(traj, quartets, periodic, out)
return out
if opt and _geometry._processor_supports_sse41():
_geometry._dihedral(xyz, quartets, out)
else:
_dihedral(traj, quartets, periodic, out)
return out
def compute_dihedrals(traj, indices, periodic=True, opt=True):
"""Compute the dihedral angles between the supplied quartets of atoms in each frame in a trajectory.
Parameters
----------
traj : Trajectory
An mtraj trajectory.
indices : np.ndarray, shape=(n_dihedrals, 4), dtype=int
Each row gives the indices of four atoms which together make a
dihedral angle. The angle is between the planes spanned by the first
three atoms and the last three atoms, a torsion around the bond
between the middle two atoms.
periodic : bool, default=True
If `periodic` is True and the trajectory contains unitcell
information, we will treat dihedrals that cross periodic images
using the minimum image convention.
opt : bool, default=True
Use an optimized native library to calculate angles.
Returns
-------
dihedrals : np.ndarray, shape=(n_frames, n_dihedrals), dtype=float
The output array gives, in each frame from the trajectory, each of the
`n_dihedrals` torsion angles. The angles are measured in **radians**.
"""
xyz = ensure_type(traj.xyz, dtype=np.float32, ndim=3, name='traj.xyz', shape=(None, None, 3), warn_on_cast=False)
quartets = ensure_type(indices, dtype=np.int32, ndim=2, name='indices', shape=(None, 4), warn_on_cast=False)
if not np.all(np.logical_and(quartets < traj.n_atoms, quartets >= 0)):
raise ValueError('indices must be between 0 and %d' % traj.n_atoms)
if len(quartets) == 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 dihedral 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], quartets.shape[0]), dtype=np.float32)
if periodic 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._dihedral_mic(xyz, quartets, box, out)
return out
else:
_dihedral(traj, quartets, periodic, out)
return out
if opt:
_geometry._dihedral(xyz, quartets, out)
else:
_dihedral(traj, quartets, periodic, out)
return out