Fixing some doctests. (#4118)

Towards #3925 
* Solved failing doctests in `core/universe.py`, `lib/util.py`, and `lib/transformations.py`

package/MDAnalysis/core/universe.py

@@ -806,9 +806,12 @@ def add_TopologyAttr(self, topologyattr, values=None):
         -------
         For example to add bfactors to a Universe:
 
-        >>> u.add_TopologyAttr('bfactors')
-        >>> u.atoms.bfactors
-        array([ 0.,  0.,  0., ...,  0.,  0.,  0.])
+        >>> import MDAnalysis as mda
+        >>> from MDAnalysis.tests.datafiles import PSF, DCD
+        >>> u = mda.Universe(PSF, DCD)
+        >>> u.add_TopologyAttr('tempfactors')
+        >>> u.atoms.tempfactors
+        array([0., 0., 0., ..., 0., 0., 0.])
 
         .. versionchanged:: 0.17.0
            Can now also add TopologyAttrs with a string of the name of the
@@ -863,8 +866,15 @@ def del_TopologyAttr(self, topologyattr):
         -------
         For example to remove bfactors to a Universe:
 
-        >>> u.del_TopologyAttr('bfactors')
-        >>> hasattr(u.atoms[:3], 'bfactors')
+        >>> import MDAnalysis as mda
+        >>> from MDAnalysis.tests.datafiles import PSF, DCD
+        >>> u = mda.Universe(PSF, DCD)
+        >>> u.add_TopologyAttr('tempfactors')
+        >>> hasattr(u.atoms[:3], 'tempfactors')
+        True
+        >>>
+        >>> u.del_TopologyAttr('tempfactors')
+        >>> hasattr(u.atoms[:3], 'tempfactors')
         False
 
 
@@ -987,9 +997,12 @@ def add_Residue(self, segment=None, **attrs):
 
         Adding a new GLY residue, then placing atoms within it:
 
-        >>> newres = u.add_Residue(segment=u.segments[0], resid=42, resname='GLY')
+        >>> import MDAnalysis as mda
+        >>> from MDAnalysis.tests.datafiles import PSF, DCD
+        >>> u = mda.Universe(PSF, DCD)
+        >>> newres = u.add_Residue(segment=u.segments[0], resid=42, resname='GLY', resnum=0)
         >>> u.atoms[[1, 2, 3]].residues = newres
-        >>> u.select_atoms('resname GLY and resid 42')
+        >>> u.select_atoms('resname GLY and resid 42 and resnum 0')
         <AtomGroup with 3 atoms>
 
         """
@@ -1407,6 +1420,7 @@ def from_smiles(cls, smiles, sanitize=True, addHs=True,
         --------
         To create a Universe with 10 conformers of ethanol:
 
+        >>> from rdkit.Chem import AllChem
         >>> u = mda.Universe.from_smiles('CCO', numConfs=10)
         >>> u
         <Universe with 9 atoms>
@@ -1416,7 +1430,7 @@ def from_smiles(cls, smiles, sanitize=True, addHs=True,
         To use a different conformer generation algorithm, like ETKDGv3:
 
         >>> u = mda.Universe.from_smiles('CCO', rdkit_kwargs=dict(
-                                         params=AllChem.ETKDGv3()))
+        ...      params=AllChem.ETKDGv3()))
         >>> u.trajectory
         <RDKitReader with 1 frames of 9 atoms>