diff --git a/package/MDAnalysis/core/topologyobjects.py b/package/MDAnalysis/core/topologyobjects.py index b7818d9a143..8dcd96dc580 100644 --- a/package/MDAnalysis/core/topologyobjects.py +++ b/package/MDAnalysis/core/topologyobjects.py @@ -899,22 +899,6 @@ def values(self, **kwargs): elif self.btype == 'improper': return self.dihedrals(**kwargs) - def _bondsSlow(self, pbc=False): # pragma: no cover - """Slow version of bond (numpy implementation)""" - if not self.btype == 'bond': - return TypeError("TopologyGroup is not of type 'bond'") - else: - bond_dist = self._ags[0].positions - self._ags[1].positions - if pbc: - box = self._ags[0].dimensions - # orthogonal and divide by zero check - if (box[6:9] == 90.).all() and not (box[0:3] == 0).any(): - bond_dist -= np.rint(bond_dist / box[0:3]) * box[0:3] - else: - raise ValueError("Only orthogonal boxes supported") - - return np.array([mdamath.norm(a) for a in bond_dist]) - def _calc_connection_values(self, func, *btypes, result=None, pbc=False): if not any(self.btype == btype for btype in btypes): strbtype = "' or '".join(btypes) @@ -941,17 +925,6 @@ def bonds(self, pbc=False, result=None): return self._calc_connection_values(distances.calc_bonds, "bond", pbc=pbc, result=result) - def _anglesSlow(self): # pragma: no cover - """Slow version of angle (numpy implementation)""" - if not self.btype == 'angle': - raise TypeError("TopologyGroup is not of type 'angle'") - - vec1 = self._ags[0].positions - self._ags[1].positions - vec2 = self._ags[2].positions - self._ags[1].positions - - angles = np.array([mdamath.angle(a, b) for a, b in zip(vec1, vec2)]) - return angles - def angles(self, result=None, pbc=False): """Calculates the angle in radians formed between a bond between atoms 1 and 2 and a bond between atoms 2 & 3 @@ -977,19 +950,6 @@ def angles(self, result=None, pbc=False): return self._calc_connection_values(distances.calc_angles, "angle", pbc=pbc, result=result) - def _dihedralsSlow(self): # pragma: no cover - """Slow version of dihedral (numpy implementation)""" - if self.btype not in ['dihedral', 'improper']: - raise TypeError("TopologyGroup is not of type 'dihedral' or " - "'improper'") - - ab = self._ags[0].positions - self._ags[1].positions - bc = self._ags[1].positions - self._ags[2].positions - cd = self._ags[2].positions - self._ags[3].positions - - return np.array([mdamath.dihedral(a, b, c) - for a, b, c in zip(ab, bc, cd)]) - def dihedrals(self, result=None, pbc=False): """Calculate the dihedral angle in radians for this topology group.