Add q1q2 analysis wrapper

package/MDAnalysis/analysis/contacts.py

@@ -33,6 +33,8 @@
 Classes are available for two somewhat different ways to perform a contact
 analysis:
 
+
+
 1. Contacts between two groups of atoms are defined with
    :class:`ContactAnalysis1`), which allows one to calculate *q(t)* over
    time. This is especially useful in order to look at native contacts during
@@ -359,17 +361,18 @@ def _single_frame(self):
         # compute distance array for a frame
         d = distance_array(self.grA.positions, self.grB.positions)
 
-        y = np.empty(len(self.r0))
+        y = np.empty(len(self.r0) + 1)
+        y[0] = self._ts.frame
         for i, (initial_contacts, r0) in enumerate(zip(self.initial_contacts,
                                                        self.r0)):
         # select only the contacts that were formed in the reference state
             r = d[initial_contacts]
             r0 = r0[initial_contacts]
-            y[i] = self.fraction_contacts(r, r0, **self.fraction_kwargs)
+            y[i + 1] = self.fraction_contacts(r, r0, **self.fraction_kwargs)
 
         if len(y) == 1:
             y = y[0]
-        self.timeseries.append((self._ts.frame, y))
+        self.timeseries.append(y)
 
     def save(self, outfile):
         """save contacts timeseries
@@ -387,6 +390,24 @@ def save(self, outfile):
                 f.write("{frame:4d}  {q1:8.6f}\n".format(**vars()))
 
 
+def _new_selections(u_orig, selections, frame):
+    """create stand alone AGs from selections at frame"""
+    u = MDAnalysis.Universe(u_orig.filename, u_orig.trajectory.filename)
+    u.trajectory[frame]
+    return (u.select_atoms(s) for s in selections)
+
+
+def q1q2(u, selection=('all', 'all'), radius=4.5, method='cutoff',
+         start=None, stop=None, step=None, **kwargs):
+    """Helper function to create q1q2 contact analysis"""
+    first_frame_refs = _new_selections(u, selection, 0)
+    last_frame_refs = _new_selections(u, selection, -1)
+    return Contacts(u, selection,
+                    (first_frame_refs, last_frame_refs),
+                    radius=radius, method=method,
+                    start=start, stop=stop, step=step,
+                    **kwargs)
+
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