Fix #2692

package/CHANGELOG

@@ -23,6 +23,7 @@ mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira
   * 0.21.0
 
 Fixes
+  * Use user-provided `remark` in `XYZWriter` (Issue #2692)
   * Added more informative error messages about topology attributes
     (Issue #2565)
   * Made NoDataError a subclass of ValueError *and* AttributeError

package/MDAnalysis/coordinates/XYZ.py

@@ -54,7 +54,7 @@
 XYZ File format
 ---------------
 
-Definiton used by the :class:`XYZReader` and :class:`XYZWriter` (and
+Definition used by the :class:`XYZReader` and :class:`XYZWriter` (and
 the `VMD xyzplugin`_ from whence the definition was taken)::
 
     [ comment line            ] !! NOT IMPLEMENTED !! DO NOT INCLUDE
@@ -146,16 +146,18 @@ def __init__(self, filename, n_atoms=None, atoms=None, convert_units=True,
             writing  [``True``]
         remark: str (optional)
             single line of text ("molecule name"). By default writes MDAnalysis
-            version
+            version and frame
+
+        .. versionchanged:: 1.0.0
+           Removed :code:`default_remark` variable (Issue #2692).
         """
         self.filename = filename
+        self.remark = remark
         self.n_atoms = n_atoms
         self.convert_units = convert_units
 
         self.atomnames = self._get_atoms_elements_or_names(atoms)
-        default_remark = "Written by {0} (release {1})".format(
-            self.__class__.__name__, __version__)
-        self.remark = default_remark if remark is None else remark
+
         # can also be gz, bz2
         self._xyz = util.anyopen(self.filename, 'wt')
 
@@ -190,8 +192,8 @@ def close(self):
     def write(self, obj):
         """Write object `obj` at current trajectory frame to file.
 
-        Atom elements (or names) in the output are taken from the `obj` or default
-        to the value of the `atoms` keyword supplied to the
+        Atom elements (or names) in the output are taken from the `obj` or
+        default to the value of the `atoms` keyword supplied to the
         :class:`XYZWriter` constructor.
 
         Parameters
@@ -229,7 +231,13 @@ def write(self, obj):
         self.write_next_timestep(ts)
 
     def write_next_timestep(self, ts=None):
-        """Write coordinate information in *ts* to the trajectory"""
+        """
+        Write coordinate information in *ts* to the trajectory
+
+        .. versionchanged:: 1.0.0
+           Print out :code:`remark` if present, otherwise use generic one 
+           (Issue #2692).
+        """
         if ts is None:
             if not hasattr(self, 'ts'):
                 raise NoDataError('XYZWriter: no coordinate data to write to '
@@ -259,8 +267,19 @@ def write_next_timestep(self, ts=None):
         else:
             coordinates = ts.positions
 
+        # Write number of atoms
         self._xyz.write("{0:d}\n".format(ts.n_atoms))
-        self._xyz.write("frame {0}\n".format(ts.frame))
+
+        # Write remark
+        if self.remark is None:
+            remark = "frame {} | Written by MDAnalysis {} (release {})\n".format(
+                ts.frame, self.__class__.__name__, __version__)
+
+            self._xyz.write(remark)
+        else:
+            self._xyz.write(self.remark.strip() + "\n")
+
+        # Write content
         for atom, (x, y, z) in zip(self.atomnames, coordinates):
             self._xyz.write("{0!s:>8}  {1:10.5f} {2:10.5f} {3:10.5f}\n"
                             "".format(atom, x, y, z))

testsuite/MDAnalysisTests/coordinates/test_xyz.py

@@ -38,6 +38,7 @@
                                               BaseWriterTest)
 from MDAnalysisTests import make_Universe
 
+from MDAnalysis import __version__
 
 class XYZReference(BaseReference):
     def __init__(self):
@@ -106,6 +107,25 @@ def test_no_conversion(self, ref, reader, tmpdir):
                     w.write(ts)
             self._check_copy(outfile, ref, reader)
 
+    @pytest.mark.parametrize("remarkout, remarkin", 
+        [   
+            2 * ["Curstom Remark"],
+            2 * [""],
+            [None, "frame 0 | Written by MDAnalysis XYZWriter (release {0})".format(__version__)],
+        ]
+    )
+    def test_remark(self, remarkout, remarkin, ref, tmpdir):
+        u = mda.Universe(ref.topology, ref.trajectory)
+        outfile = "write-remark.xyz"
+
+        with tmpdir.as_cwd():
+            u.atoms.write(outfile, remark=remarkout)
+
+            with open(outfile, "r") as xyzout:
+                lines = xyzout.readlines()
+
+                assert lines[1].strip() == remarkin
+
 
 class XYZ_BZ_Reference(XYZReference):
     def __init__(self):