From d950a309c6767dca6df934f9f9f1cbfdcad40ced Mon Sep 17 00:00:00 2001
From: Jan Domanski <jan.domanski@nih.gov>
Date: Thu, 25 Feb 2016 12:20:23 -0500
Subject: [PATCH] Upated CHANGELOG, brought back the old ContactAnalysis class

---
 package/MDAnalysis/analysis/contacts.py | 50 ++-----------------------
 1 file changed, 4 insertions(+), 46 deletions(-)

diff --git a/package/MDAnalysis/analysis/contacts.py b/package/MDAnalysis/analysis/contacts.py
index 23c92c04b98..559c7b429a1 100644
--- a/package/MDAnalysis/analysis/contacts.py
+++ b/package/MDAnalysis/analysis/contacts.py
@@ -1070,7 +1070,6 @@ 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.
 
@@ -1093,31 +1092,6 @@ 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)
@@ -1128,7 +1102,6 @@ def qarray(self, d, out=None):
     def fraction_native(q, out=None):
         """Calculate native contacts relative to reference state.
 
-<<<<<<< 0b318502a33fc222a7621937cfc96541788ce84d
         Parameters
         ----------
         q: array
@@ -1168,9 +1141,11 @@ def fraction_native(q, out=None):
         contacts : integer
            total number of contacts
         fraction : float
-           fraction of contacts relative to the reference state
+           Fraction of native contacts (Q) calculated from a contact matrix
 
->>>>>>> doc string upgrades in analysis.contacts
+        Note
+        ----
+        This method is typically only used internally.
         """
         if out:
             np.logical_and(q, self.mask, out)
@@ -1180,7 +1155,6 @@ def fraction_native(q, out=None):
         return contacts, float(contacts) / self.mask.sum()
 
     def plot(self, filename=None, **kwargs):
-<<<<<<< 0b318502a33fc222a7621937cfc96541788ce84d
         """Plot q(t).
 
         Parameters
@@ -1212,7 +1186,6 @@ 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
@@ -1223,21 +1196,6 @@ 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.")