def __init__(self,
topology,
selstr=None,
deg=False,
cossin=False,
periodic=True):
indices = indices_phi(topology)
if not selstr:
self._phi_inds = indices
else:
self._phi_inds = indices[np.in1d(indices[:, 1],
topology.select(selstr),
assume_unique=True)]
indices = indices_psi(topology)
if not selstr:
self._psi_inds = indices
else:
self._psi_inds = indices[np.in1d(indices[:, 1],
topology.select(selstr),
assume_unique=True)]
# alternate phi, psi pairs (phi_1, psi_1, ..., phi_n, psi_n)
dih_indexes = np.array(
list(phi_psi
for phi_psi in zip(self._phi_inds, self._psi_inds))).reshape(
-1, 4)
super(BackboneTorsionFeature, self).__init__(topology,
dih_indexes,
deg=deg,
cossin=cossin,
periodic=periodic)
def _dihedral_indices(top: md.Topology, which: str) -> np.ndarray:
indices = [indices_phi(top),
indices_psi(top)]
if which == 'all':
indices.extend([indices_chi1(top),
indices_chi2(top),
indices_chi3(top),
indices_chi4(top),
indices_chi5(top)])
indices = np.vstack(indices)
assert indices.shape[1] == 4
return indices