angles.py 文件源码

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)