Restore doc pages for XTC and TRR

Fixes #855

Also delete obsolete doc files for xdrfile.

package/MDAnalysis/coordinates/TRR.py

@@ -13,6 +13,17 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
+"""
+TRR trajectory files --- :mod:`MDAnalysis.coordinates.TRR`
+==========================================================
+
+Read and write GROMACS TRR trajectories.
+
+See Also
+--------
+MDAnalysis.coordinates.XTC: Read and write GROMACS XTC trajectory files.
+"""
+
 from .XDR import XDRBaseReader, XDRBaseWriter
 from ..lib.formats.libmdaxdr import TRRFile
 from ..lib.mdamath import triclinic_vectors, triclinic_box
@@ -28,8 +39,8 @@ class TRRWriter(XDRBaseWriter):
     corresponding value will be used as the lambda value for written TRR file.
     If None is found the lambda is set to 0.
 
-    Parameter
-    ---------
+    Parameters
+    ----------
     filename : str
         filename of the trajectory
     n_atoms : int
@@ -100,8 +111,8 @@ class TRRReader(XDRBaseReader):
 
     The lambda value is written in the data dictionary of the returned TimeStep
 
-    Parameter
-    ---------
+    Parameters
+    ----------
     filename : str
         filename of the trajectory
     convert_units : bool (optional)

package/MDAnalysis/coordinates/XTC.py

@@ -13,6 +13,17 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
+"""
+XTC trajectory files --- :mod:`MDAnalysis.coordinates.XTC`
+==========================================================
+
+Read and write GROMACS XTC trajectories.
+
+See Also
+--------
+MDAnalysis.coordinates.TRR: Read and write GROMACS TRR trajectory files.
+"""
+
 from .XDR import XDRBaseReader, XDRBaseWriter
 from ..lib.formats.libmdaxdr import XTCFile
 from ..lib.mdamath import triclinic_vectors, triclinic_box
@@ -26,15 +37,15 @@ class XTCWriter(XDRBaseWriter):
     they require significantly less disk space and the loss of precision is
     usually not a problem.
 
-    Parameter
-    ---------
-    filename : str
+    Parameters
+    ----------
+    filename: str
         filename of the trajectory
-    n_atoms : int
+    n_atoms: int
         number of atoms to write
-    convert_units : bool (optional)
+    convert_units: bool (optional)
         convert into MDAnalysis units
-    precision : float (optional)
+    precision: float (optional)
         set precision of saved trjactory to this number of decimal places.
     """
     format = 'XTC'
@@ -52,7 +63,7 @@ def write_next_timestep(self, ts):
 
         Parameters
         ----------
-        ts : TimeStep
+        ts: TimeStep
 
         See Also
         --------
@@ -83,15 +94,15 @@ class XTCReader(XDRBaseReader):
     require significantly less disk space and the loss of precision is usually
     not a problem.
 
-    Parameter
-    ---------
-    filename : str
+    Parameters
+    ----------
+    filename: str
         filename of the trajectory
-    convert_units : bool (optional)
+    convert_units: bool (optional)
         convert into MDAnalysis units
-    sub : atomgroup (optional)
+    sub: atomgroup (optional)
         Yeah what is that exactly
-    refresh_offsets : bool (optional)
+    refresh_offsets: bool (optional)
         Recalculate offsets for random access from file. If ``False`` try to
         retrieve offsets from hidden offsets file.
 

package/doc/sphinx/source/documentation_pages/coordinates/TRR.rst

@@ -1 +1,2 @@
 .. automodule:: MDAnalysis.coordinates.TRR
+   :members:

package/doc/sphinx/source/documentation_pages/coordinates/XTC.rst

@@ -1 +1,2 @@
 .. automodule:: MDAnalysis.coordinates.XTC
+   :members:

package/doc/sphinx/source/documentation_pages/coordinates_modules.rst

@@ -49,6 +49,5 @@ functionality should first read the :ref:`Trajectory API`.
 
    coordinates/base
    coordinates/core
-   coordinates/xdrfile
    coordinates/pdbextensions