Update NCDF Reader to read .ncrst Restart Files

package/AUTHORS

@@ -258,8 +258,10 @@ Chronological list of authors
   - Abdulrahman Elbanna
   - Tulga-Erdene Sodjargal
   - Gareth Elliott
+  - Marc Schuh
   - Jeremy M.G. Leung
 
+
 External code
 -------------
 

package/CHANGELOG

@@ -16,7 +16,7 @@ The rules for this file:
 -------------------------------------------------------------------------------
 ??/??/?? IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev,
          yuxuanzhuang, yuyuan871111, tanishy7777, jpkrowe, tulga-rdn,
-         Gareth-elliott, hmacdope, jeremyleung521
+         Gareth-elliott, hmacdope, tylerjereddy, cbouy, jeremyleung521
 
  * 2.10.0
 
@@ -41,6 +41,9 @@ Fixes
 Enhancements
  * Allow NCDF reader to read Amber Restart Files with extension `.ncrst`
    (Issue #5030, PR #5031)
+ * Added `TemplateInferrer` and `RDKitInferrer` dataclasses to the
+   `RDKitInferring` module to be used by the RDKit converter. (PR #4305)
+ * Improve speed of GROMOS11 (TRC) reader (Issue #5079, PR #5080)
  * Improve parsing of topology information from LAMMPS dump files to allow
    reading of mass, charge and element attributes. (Issue #3449, PR #4995)
  * Added timestep support for XDR writers and readers (Issue #4905, PR #4908)

package/MDAnalysis/coordinates/INPCRD.py

@@ -22,7 +22,7 @@
 #
 
 
-"""AMBER restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`
+"""AMBER coordinate/restart files in MDAnalysis --- :mod:`MDAnalysis.coordinates.INPCRD`
 ================================================================================
 
 AMBER_ can write :ref:`ASCII restart<ascii-restart>` ("inpcrd") and
@@ -76,7 +76,7 @@
 .. Links
 
 .. _AMBER: http://ambermd.org
-.. _AMBER INPCRD FORMAT: http://ambermd.org/formats.html#restart
+.. _AMBER INPCRD FORMAT: https://ambermd.org/FileFormats.php#restart
 .. _AMBER netcdf: http://ambermd.org/netcdf/nctraj.xhtml
 .. _NetCDF: http://www.unidata.ucar.edu/software/netcdf
 
@@ -102,7 +102,7 @@ class INPReader(base.SingleFrameReaderBase):
     * Box information is not read (or checked for).
     * Velocities are currently *not supported*.
 
-    .. versionchanged: 0.20.0
+    .. versionchanged: 2.10.0
        Now automatically detects files with .rst7 extension.
 
     """
@@ -158,7 +158,7 @@ class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin):
     """Reader for `AMBER NETCDF format`_ (version 1.0 rev C) restart files.
 
     This reader is a :class:`SingleFrameReaderBase` adaptation of the
-    :class:`NCDFReader` AMBER NETCDF trajectory reader.
+    :class:`~MDAnalysis.coordinates.TRJ.NCDFReader` AMBER NETCDF trajectory reader.
 
     AMBER binary restart files are automatically recognised by the file
     extensions ".ncrst", ".ncrestrt", and ".ncrst7".
@@ -181,7 +181,8 @@ class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin):
     ``[0,0,0,0,0,0]``).
 
     Support for the *mmap* keyword is available as detailed
-    in :class:`NCDFReader` and :mod:`scipy.io.netcdf.netcdf_file`. The use of
+    in :class:`~MDAnalysis.coordinates.TRJ.NCDFReader` and
+    :mod:`scipy.io.netcdf.netcdf_file`. The use of
     ``mmap=True`` leads to around a 2x read speed improvement in a ~ 1 million
     atom system (AMBER STMV benchmark). As per the :class:`NCDFReader`, the
     default behaviour is ``mmap=None``, which means that the default behaviour
@@ -201,8 +202,8 @@ class NCRSTReader(base.SingleFrameReaderBase, NCDFMixin):
 
     See Also
     --------
-    :class:`NCDFReader`
-    :class:`NCDFWriter`
+    :class:`~MDAnalysis.coordinates.TRJ.NCDFReader`
+    :class:`~MDAnalysis.coordinates.TRJ.NCDFWriter`
 
 
     .. versionadded: 2.10.0

package/MDAnalysis/coordinates/TRJ.py

@@ -435,23 +435,6 @@ def _check_conventions(self, n_atoms=None):
                       "information".format(file_format, self.filename))
             raise ValueError(errmsg) from None
 
-        # try:
-        #     self.n_frames = self.trjfile.dimensions['frame']
-        #     # example trajectory when read with scipy.io.netcdf has
-        #     # dimensions['frame'] == None (indicating a record dimension that
-        #     # can grow) whereas if read with netCDF4 I get
-        #     # len(dimensions['frame']) ==  10: in any case, we need to get
-        #     # the number of frames from somewhere such as the time variable:
-        #     if self.n_frames is None:
-        #         self.n_frames = self.trjfile.variables['coordinates'].shape[0]
-        # except KeyError:
-        #     if self.is_restart:
-        #          self.n_frames = 1
-        #     else:
-        #         errmsg = ("NCDF {file_format} {self.filename} does not contain "
-        #                   "frame information").format
-        #         raise ValueError(errmsg) from None
-
         try:
             self.remarks = self.trjfile.title
         except AttributeError:

package/MDAnalysis/coordinates/__init__.py

@@ -215,7 +215,7 @@ class can choose an appropriate reader automatically.
    |               |           |       | velocities). Module :mod:`MDAnalysis.coordinates.TRJ`|
    +---------------+-----------+-------+------------------------------------------------------+
    | AMBER         | ncrst,    |  r    | binary (NetCDF) restart file                         |
-   |               | ncrestrt, |       | Module :mod:`MDAnalysis.coordinates.INPCRD           |
+   |               | ncrestrt, |       | Module :mod:`MDAnalysis.coordinates.INPCRD`          |
    |               | ncrst7    |       |                                                      |
    +---------------+-----------+-------+------------------------------------------------------+
    | Brookhaven    | pdb/ent   |  r/w  | a relaxed PDB format (as used in MD simulations)     |

testsuite/MDAnalysisTests/coordinates/test_ncrst.py

@@ -147,16 +147,6 @@ def test_positions_resid42(self, universe):
         assert_almost_equal(expected, ag.positions, self.prec)
 
 
-#    def test_velocities(self, universe, selstr, expected):
-#        ag = universe.select_atoms(selstr)
-#        assert_almost_equal(expected, ag.velocities, self.prec)
-#
-#    def test_forces(self, universe, selstr, expected):
-#        ag = universe.select_atoms(selstr)
-#        # We convert from kj back to the original kcal value
-#        assert_almost_equal(expected, ag.forces * 4.184, self.prec)
-
-
 class _NCRSTGenerator(object):
     """A basic modular ncrst writer based on :class:`NCDFWriter`"""
 
@@ -293,17 +283,6 @@ def test_not_implemented_errors(self, tmpdir, key, value):
             with pytest.raises(NotImplementedError):
                 NCRSTReader(params["filename"])
 
-    # @pytest.mark.parametrize('value', [
-    #     'time', 'coordinates', 'spatial',
-    #     'velocities', 'forces'
-    # ])
-    # def test_scale_factor(self, tmpdir, value):
-    #     params = self.gen_params(key='scale_factor', value=value)
-    #     with tmpdir.as_cwd():
-    #         self.create_ncrst(params)
-    #         with pytest.raises(NotImplementedError):
-    #             NCRSTReader(params['filename'])
-
     def test_conventionversion_warn(self, tmpdir):
         params = self.gen_params(key="ConventionVersion", value="2.0")
         with tmpdir.as_cwd():

testsuite/MDAnalysisTests/coordinates/test_netcdf.py

@@ -390,70 +390,70 @@ def test_warn_user_no_time_information(self, u):
             u2 = mda.Universe(CPPTRAJ_TRAJ_TOP, CPPTRAJ_TRAJ)
 
 
-# class TestNCDFReader5(object):
-#    """NCRST Restart File with positions and forces, exported by CPPTRAJ.
-#
-#    Contributed by Jeremy M. G. Leung
-#    """
-#
-#    prec = 6
-#
-#    @pytest.fixture(scope="class")
-#    def u(self):
-#        return mda.Universe(PRMNCRST, TRJNCRST)
-#
-#    def test_positions(self, u):
-#        """Check positions on first frame"""
-#        u.trajectory[0]
-#        ref_1 = np.array(
-#            [
-#                [-1.1455358, -2.0177484, -0.55771565],
-#                [-0.19042611, -2.2511053, -1.0282656],
-#                [0.53238064, -1.5778863, -0.56737846],
-#            ],
-#            dtype=np.float64,
-#        )
-#        assert_almost_equal(ref_1, u.atoms.positions[:3], self.prec)
-#
-#    def test_velocities(self, u):
-#        """Check forces on first frame"""
-#        u.trajectory[0]
-#        ref_1 = np.array(
-#            [
-#                [11.86471367, 31.22108269, -4.03538418],
-#                [7.36676359, -4.68035316, 1.78124952],
-#                [12.86675262, 1.39324546, -14.97190762],
-#            ],
-#            dtype=np.float64,
-#        )
-#        assert_almost_equal(ref_1, u.atoms.velocities[:3], self.prec)
-#
-#    def test_forces(self, u):
-#        """Check forces on first frame"""
-#        u.trajectory[0]
-#        ref_1 = np.array(
-#            [
-#                [-9.7262249, -0.37627634, -24.79876137],
-#                [-32.43384552, 37.47783279, -12.45422745],
-#                [24.10939026, -19.80618095, -17.09523582],
-#            ],
-#            dtype=np.float64,
-#        )
-#        assert_almost_equal(ref_1, u.atoms.forces[:3], self.prec)
-#
-#    def test_time(self, u):
-#        """Check time on first frame"""
-#        ref = 5.0
-#        assert_almost_equal(ref, u.trajectory[0].time, self.prec)
-#
-#    def test_dt(self, u):
-#        """Default 1.0 fs"""
-#        ref = 1.0
-#        assert_almost_equal(ref, u.trajectory.dt, self.prec)
-#        assert_almost_equal(ref, u.trajectory.ts.dt, self.prec)
-#
-#    def test_box(self, u):
-#        assert u.trajectory[0].dimensions is None
+class TestNCDFReader5(object):
+    """NCRST Restart File with positions and forces, exported by CPPTRAJ.
+
+    Contributed by Jeremy M. G. Leung
+    """
+
+    prec = 6
+
+    @pytest.fixture(scope="class")
+    def u(self):
+        return mda.Universe(PRMNCRST, TRJNCRST)
+
+    def test_positions(self, u):
+        """Check positions on first frame"""
+        u.trajectory[0]
+        ref_1 = np.array(
+            [
+                [-1.1455358, -2.0177484, -0.55771565],
+                [-0.19042611, -2.2511053, -1.0282656],
+                [0.53238064, -1.5778863, -0.56737846],
+            ],
+            dtype=np.float64,
+        )
+        assert_almost_equal(ref_1, u.atoms.positions[:3], self.prec)
+
+    def test_velocities(self, u):
+        """Check forces on first frame"""
+        u.trajectory[0]
+        ref_1 = np.array(
+            [
+                [11.86471367, 31.22108269, -4.03538418],
+                [7.36676359, -4.68035316, 1.78124952],
+                [12.86675262, 1.39324546, -14.97190762],
+            ],
+            dtype=np.float64,
+        )
+        assert_almost_equal(ref_1, u.atoms.velocities[:3], self.prec)
+
+    def test_forces(self, u):
+        """Check forces on first frame"""
+        u.trajectory[0]
+        ref_1 = np.array(
+            [
+                [ -2.32462358,  -0.0899322 ,  -5.9270463 ],
+                [ -7.7518754 ,   8.95741653,  -2.97663188],
+                [  5.76228237,  -4.73379087,  -4.0858593 ],
+            ],
+            dtype=np.float64,
+        )
+        assert_almost_equal(ref_1, u.atoms.forces[:3], self.prec)
+
+    def test_time(self, u):
+        """Check time on first frame"""
+        ref = 5.0
+        assert_almost_equal(ref, u.trajectory[0].time, self.prec)
+
+    def test_dt(self, u):
+        """Default 1.0 fs"""
+        ref = 1.0
+        assert_almost_equal(ref, u.trajectory.dt, self.prec)
+        assert_almost_equal(ref, u.trajectory.ts.dt, self.prec)
+
+    def test_box(self, u):
+        assert u.trajectory[0].dimensions is None
 
 
 class _NCDFGenerator(object):
@@ -853,20 +853,20 @@ def _test_write_trajectory(self, universe, outfile):
         #       See http://docs.scipy.org/doc/numpy-1.10.0/reference/arrays.dtypes.html
         #       and https://github.com/MDAnalysis/mdanalysis/pull/503
         with netcdf_file(outfile, "r") as dataset:
-            coords = dataset.variables["coordinates"][...]
-            time = dataset.variables["time"][...]
-        assert_equal(
-            coords[:].dtype.name,
-            np.dtype(np.float32).name,
-            err_msg="ncdf coord output not float32 "
-            "but {}".format(coords[:].dtype),
-        )
-        assert_equal(
-            time[:].dtype.name,
-            np.dtype(np.float32).name,
-            err_msg="ncdf time output not float32 "
-            "but {}".format(time[:].dtype),
-        )
+            coords = dataset.variables["coordinates"]
+            time = dataset.variables["time"]
+            assert_equal(
+                coords[:].dtype.name,
+                np.dtype(np.float32).name,
+                err_msg="ncdf coord output not float32 "
+                "but {}".format(coords[:].dtype),
+            )
+            assert_equal(
+                time[:].dtype.name,
+                np.dtype(np.float32).name,
+                err_msg="ncdf time output not float32 "
+                "but {}".format(time[:].dtype),
+            )
 
     def test_write_trajectory_netCDF4(self, universe, outfile):
         pytest.importorskip("netCDF4")