Add gromacs-2016 in the TPR test suite

Gromacs-2016 bumps the version of the TPR files. This commit adds the
files needed to test the support of that new TPR version, and include
the files in the test suite.

2lyz_gmx_2016.tpr was build from 2lyz_gmx_5.1.tpr using

    echo 0 | gmx convert-tpr -s 2lyz_gmx_5.1.tpr -o 2lyz_gmx_206.tpr

dummy_2016.tpr was build using gmx grompp on the source files in
data/tprs/all_bonded.

Author: jbarnoud

testsuite/MDAnalysisTests/data/tprs/2lyz_gmx_2016.tpr

@@ -58,8 +58,8 @@
     "PDB_xlserial",
     "TPR400", "TPR402", "TPR403", "TPR404", "TPR405", "TPR406", "TPR407",
     "TPR450", "TPR451", "TPR452", "TPR453", "TPR454", "TPR455", "TPR455Double",
-    "TPR460", "TPR461", "TPR502", "TPR504", "TPR505", "TPR510",
-    "TPR510_bonded",
+    "TPR460", "TPR461", "TPR502", "TPR504", "TPR505", "TPR510", "TPR2016",
+    "TPR510_bonded", "TPR2016_bonded",
     "PDB_sub_sol", "PDB_sub_dry",  # TRRReader sub selection
     "TRR_sub_sol",
     "XTC_sub_sol",
@@ -214,12 +214,14 @@
 TPR504 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.4.tpr')
 TPR505 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.0.5.tpr')
 TPR510 = resource_filename(__name__, 'data/tprs/2lyz_gmx_5.1.tpr')
+TPR2016 = resource_filename(__name__, 'data/tprs/2lyz_gmx_2016.tpr')
 # double precision
 TPR455Double = resource_filename(__name__, 'data/tprs/drew_gmx_4.5.5.double.tpr')
 TPR460 = resource_filename(__name__, 'data/tprs/ab42_gmx_4.6.tpr')
 TPR461 = resource_filename(__name__, 'data/tprs/ab42_gmx_4.6.1.tpr')
 # all bonded interactions
 TPR510_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_5.1.tpr')
+TPR2016_bonded = resource_filename(__name__, 'data/tprs/all_bonded/dummy_2016.tpr')
 
 XYZ_psf = resource_filename(__name__, 'data/2r9r-1b.psf')
 XYZ_bz2 = resource_filename(__name__, 'data/2r9r-1b.xyz.bz2')

testsuite/MDAnalysisTests/data/tprs/all_bonded/dummy_2016.tpr

@@ -13,10 +13,13 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-from MDAnalysis.tests.datafiles import TPR, \
-    TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407, \
-    TPR450, TPR451, TPR452, TPR453, TPR454, TPR455, TPR455Double, \
-    TPR460, TPR461, TPR502, TPR504, TPR505, TPR510, TPR510_bonded
+from MDAnalysis.tests.datafiles import (
+    TPR,
+    TPR400, TPR402, TPR403, TPR404, TPR405, TPR406, TPR407,
+    TPR450, TPR451, TPR452, TPR453, TPR454, TPR455, TPR455Double,
+    TPR460, TPR461, TPR502, TPR504, TPR505, TPR510, TPR2016,
+    TPR510_bonded, TPR2016_bonded,
+)
 
 from numpy.testing import TestCase, dec, assert_
 from test_topology import _TestTopology
@@ -240,7 +243,15 @@ class TestTPR510(_TestTopology, TPR510):
     """Testing TPR version 103"""
 
 
-def _test_is_in_topology(name, elements, topology_section, topology_path):
+class TPR2016(TPRBase):
+    topology = TPR2016
+
+
+class TestTPR2016(_TestTopology, TPR2016):
+    """Testing TPR version 110"""
+
+
+def _test_is_in_topology(name, elements, topology_path, topology_section):
     """
     Test if an interaction appears as expected in the topology
     """
@@ -252,51 +263,51 @@ def _test_is_in_topology(name, elements, topology_section, topology_path):
 
 def test_all_bonds():
     """Test that all bond types are parsed as expected"""
-    topology = TPR510_bonded
+    topologies = (TPR510_bonded, TPR2016_bonded)
     bonds = {'BONDS':[(0, 1)], 'G96BONDS':[(1, 2)], 'MORSE':[(2, 3)],
              'CUBICBONDS':[(3, 4)], 'CONNBONDS':[(4, 5)], 'HARMONIC':[(5, 6)],
              'FENEBONDS':[(6, 7)], 'RESTRAINTPOT':[(7, 8)],
              'TABBONDS':[(8, 9)], 'TABBONDSNC':[(9, 10)],
              'CONSTR':[(10, 11)], 'CONSTRNC':[(11, 12)],}
     bond_type_in_topology = functools.partial(_test_is_in_topology,
-                                              topology_section='bonds',
-                                              topology_path=topology)
-    for bond_type, elements in bonds.items():
-        yield (bond_type_in_topology, bond_type, elements)
+                                              topology_section='bonds')
+    for topology in topologies:
+        for bond_type, elements in bonds.items():
+            yield (bond_type_in_topology, bond_type, elements, topology)
 
 
 def test_all_angles():
-    topology = TPR510_bonded
+    topologies = (TPR510_bonded, TPR2016_bonded)
     angles = {'ANGLES':[(0, 1, 2)], 'G96ANGLES':[(1, 2, 3)],
               'CROSS_BOND_BOND':[(2, 3, 4)], 'CROSS_BOND_ANGLE':[(3, 4, 5)],
               'UREY_BRADLEY':[(4, 5, 6)], 'QANGLES':[(5, 6, 7)],
               'RESTRANGLES':[(6, 7, 8)], 'TABANGLES':[(7, 8, 9)],}
     angle_type_in_topology = functools.partial(_test_is_in_topology,
-                                               topology_section='angles',
-                                               topology_path=topology)
-    for angle_type, elements in angles.items():
-        yield (angle_type_in_topology, angle_type, elements)
+                                               topology_section='angles')
+    for topology in topologies:
+        for angle_type, elements in angles.items():
+            yield (angle_type_in_topology, angle_type, elements, topology)
 
 
 def test_all_dihedrals():
-    topology = TPR510_bonded
+    topologies = (TPR510_bonded, TPR2016_bonded)
     dihs = {'PDIHS':[(0, 1, 2, 3), (1, 2, 3, 4), (7, 8, 9, 10)],
             'RBDIHS':[(4, 5, 6, 7)], 'RESTRDIHS':[(8, 9, 10, 11)],
             'CBTDIHS':[(9, 10, 11, 12)], 'FOURDIHS':[(6, 7, 8, 9)],
             'TABDIHS':[(10, 11, 12, 13)],}
     dih_type_in_topology = functools.partial(_test_is_in_topology,
-                                             topology_section='dihedrals',
-                                             topology_path=topology)
-    for dih_type, elements in dihs.items():
-        yield (dih_type_in_topology, dih_type, elements)
+                                             topology_section='dihedrals')
+    for topology in topologies:
+        for dih_type, elements in dihs.items():
+            yield (dih_type_in_topology, dih_type, elements, topology)
 
 
 def test_all_impropers():
-    topology = TPR510_bonded
+    topologies = (TPR510_bonded, TPR2016_bonded)
     imprs = {'IDIHS':[(2, 3, 4, 5), (3, 4, 5, 6)], 'PIDIHS':[(5, 6, 7, 8)]}
     impr_type_in_topology = functools.partial(_test_is_in_topology,
-                                              topology_section='impropers',
-                                              topology_path=topology)
-    for impr_type, elements in imprs.items():
-        yield (impr_type_in_topology, impr_type, elements)
+                                              topology_section='impropers')
+    for topology in topologies:
+        for impr_type, elements in imprs.items():
+            yield (impr_type_in_topology, impr_type, elements, topology)