doc string upgrades in analysis.contacts

package/MDAnalysis/analysis/contacts.py

@@ -573,8 +573,6 @@ def __init__(self, *args, **kwargs):
         # - select contact pairs to write out as a timecourse
         # - make this selection based on qavg
         from os.path import splitext
-
-        warnings.warn("ContactAnalysis1 is deprecated and will be removed in 1.0/. Use Contacts instead.", DeprecationWarning)
 
         warnings.warn("ContactAnalysis1 is deprecated and will be removed in 1.0. "
                       "Use Contacts instead.", category=DeprecationWarning)
@@ -1072,6 +1070,7 @@ def _conclude(self):
             for frame, q1, n1 in self.timeseries:
                 f.write("{frame:4d}  {q1:8.6f} {n1:5d}\n".format(**vars()))
 
+<<<<<<< 0b318502a33fc222a7621937cfc96541788ce84d
     def contact_matrix(self, d, out=None):
         """Return distance array with True for contacts.
 
@@ -1094,6 +1093,31 @@ def contact_matrix(self, d, out=None):
         Note
         ----
         This method is typically only used internally.
+=======
+    def qarray(self, d, out=None):
+        """Return array with ``True`` for contacts.
+
+        Note
+        ----
+        This method is typically only used internally.
+
+        Arguments
+        ---------
+        d : array
+          2D array of distances. The method uses the value of
+          :attr:`radius` to determine if a ``distance < radius``
+          is considered a contact.
+        out : array, optional
+          If `out` is supplied as a pre-allocated array of the correct
+          shape then it is filled instead of allocating a new one in
+          order to increase performance.
+
+        Returns
+        -------
+        array
+           contact matrix
+
+>>>>>>> doc string upgrades in analysis.contacts
         """
         if out:
             out[:] = (d <= self.radius)
@@ -1104,6 +1128,7 @@ def contact_matrix(self, d, out=None):
     def fraction_native(q, out=None):
         """Calculate native contacts relative to reference state.
 
+<<<<<<< 0b318502a33fc222a7621937cfc96541788ce84d
         Parameters
         ----------
         q: array
@@ -1123,6 +1148,29 @@ def fraction_native(q, out=None):
         Note
         ----
         This method is typically only used internally.
+=======
+        Note
+        ----
+        This method is typically only used internally.
+
+        Arguments
+        ---------
+        q : array
+          contact matrix (see :meth:`Contacts.qarray`)
+        out : array, optional
+          If `out` is supplied as a pre-allocated array of the correct
+          shape then it will contain the contact matrix relative
+          to the reference state, i.e. only those contacts that
+          are also seen in the reference state.
+
+        Returns
+        -------
+        contacts : integer
+           total number of contacts
+        fraction : float
+           fraction of contacts relative to the reference state
+
+>>>>>>> doc string upgrades in analysis.contacts
         """
         if out:
             np.logical_and(q, self.mask, out)
@@ -1132,6 +1180,7 @@ def fraction_native(q, out=None):
         return contacts, float(contacts) / self.mask.sum()
 
     def plot(self, filename=None, **kwargs):
+<<<<<<< 0b318502a33fc222a7621937cfc96541788ce84d
         """Plot q(t).
 
         Parameters
@@ -1163,6 +1212,7 @@ def plot(self, filename=None, **kwargs):
             fig.show()
 
     def plot_qavg(self, filename=None, **kwargs):
+<<<<<<< 0b318502a33fc222a7621937cfc96541788ce84d
         """Plot `Contacts.qavg`, the matrix of average contacts.
 
         Parameters
@@ -1173,6 +1223,21 @@ def plot_qavg(self, filename=None, **kwargs):
             keyword arguments are passed on to `pylab.imshow`.
         **kwargs
             Arbitrary keyword arguments for the plotting function
+=======
+        """Plot the matrix of average contacts.
+
+        Convenience function to plot :attr:`qavg`.
+
+        Arguments
+        ---------
+        filename : string, optional
+           If `filename` is supplied then the figure is also written
+           to file (the suffix determines the file type, e.g. pdf,
+           png, eps, ...).
+        **kwargs
+           All other keyword arguments are passed on to
+           :func:`matplotlib.pyplot.imshow`.
+>>>>>>> doc string upgrades in analysis.contacts
         """
         if not self.contact_matrix :
             raise ValueError("No timeseries data; do 'Contacts.run()' first.")