allow pickling xdr trajectory readers

the low level __reduce__ function is used by the pickle protocol as a recipe
to reconstruct this class.

package/CHANGELOG

@@ -27,6 +27,7 @@ Enhancements
     the `moltype` selection keyword is added (Issue #1555)
   * about 20% speed improvements for GNM analysis. (PR #1579)
   * added support for Tinker TXYZ and ARC files
+  * libmdaxdr classes can now be pickled (PR #1680)
 
 Deprecations
 

package/MDAnalysis/lib/formats/libmdaxdr.pyx

@@ -274,6 +274,39 @@ cdef class _XDRFile:
             raise IOError('No file currently opened')
         return self.offsets.size
 
+    def __reduce__(self):
+        """low level pickle function. It gives instructions for unpickling which class
+        should be created with arguments to `__cinit__` and the current state
+
+        """
+        return (self.__class__, (self.fname.decode(), self.mode),
+                self.__getstate__())
+
+    def __getstate__(self):
+        """
+        current state
+        """
+        return (self.is_open, self.current_frame, self._offsets,
+                self._has_offsets)
+
+    def __setstate__(self, state):
+        """
+        reset state offsets and current frame
+        """
+        is_open = state[0]
+        # by default the file is open
+        if not is_open:
+            self.close()
+            return
+
+        # set them now to avoid recalculation
+        self._offsets = state[2]
+        self._has_offsets = state[3]
+
+        # where was I
+        current_frame = state[1]
+        self.seek(current_frame)
+
     def seek(self, frame):
         """Seek to Frame.
 
@@ -402,6 +435,11 @@ cdef class TRRFile(_XDRFile):
     >>> with TRRFile('foo.trr') as f:
     >>>     for frame in f:
     >>>         print(frame.x)
+
+    Notes
+    -----
+    This class can be pickled. The pickle will store filename, mode, current
+    frame and offsets
     """
 
     def _calc_natoms(self, fname):
@@ -614,6 +652,11 @@ cdef class XTCFile(_XDRFile):
     >>> with XTCFile('foo.trr') as f:
     >>>     for frame in f:
     >>>         print(frame.x)
+
+    Notes
+    -----
+    This class can be pickled. The pickle will store filename, mode, current
+    frame and offsets
     """
     cdef float precision
 

testsuite/MDAnalysisTests/formats/test_libmdaxdr.py

@@ -20,6 +20,7 @@
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
 from __future__ import print_function, absolute_import
+from six.moves import cPickle as pickle
 
 import numpy as np
 
@@ -115,6 +116,25 @@ def test_read_write_mode_file(self, xdr, tmpdir, fname):
             with pytest.raises(IOError):
                 f.read()
 
+    def test_pickle(self, reader):
+        reader.seek(len(reader) - 1)
+        dump = pickle.dumps(reader)
+        new_reader = pickle.loads(dump)
+
+        assert reader.fname == new_reader.fname
+        assert reader.tell() == new_reader.tell()
+        assert_almost_equal(reader.offsets, new_reader.offsets)
+
+    def test_pickle_closed(self, reader):
+        reader.seek(len(reader) - 1)
+        reader.close()
+        dump = pickle.dumps(reader)
+        new_reader = pickle.loads(dump)
+
+        assert reader.fname == new_reader.fname
+        assert reader.tell() != new_reader.tell()
+
+
 
 @pytest.mark.parametrize("xdrfile, fname, offsets",
                          ((XTCFile, XTC_multi_frame, XTC_OFFSETS),