Resolving Truncation of resids for GRO file writing (Issue 886) (#887)

* Fixes #886. When .gro files are written their resids will now be properly truncated to 5 digits.
* Added a new unit test for Issue 886 -- dealing with residue number truncation when writing GRO files.


* The fix for Issue #886 has now been added to the CHANGELOG.

* Added a comment regarding usage of class-level fixtures for the unit test covering Issue 886.

* output file specification in unit test for Issue 886 has been fixed.

* Fixed the formatting of CHANGELOG following fixes to Issue 886.

package/CHANGELOG

@@ -13,11 +13,12 @@ The rules for this file:
   * release numbers follow "Semantic Versioning" http://semver.org
 
 ------------------------------------------------------------------------------
-??/??/16 kain88-de,jdetle, fiona-naughton, richardjgowers
+??/??/16 kain88-de, jdetle, fiona-naughton, richardjgowers, tyler.je.reddy
 
   * 0.15.1
 
 Fixes
+  * GROWriter resids now truncated properly (Issue #886)
   * reading/writing lambda value in trr files (Issue #859)
   * fix __iter__/next redundancy (Issue #869)
   * SingleFrameReader now raises StopIteration instead of IOError on calling

package/MDAnalysis/coordinates/GRO.py

@@ -297,9 +297,10 @@ def write(self, selection, frame=None):
             # Atom descriptions and coords
             for atom_index, atom in enumerate(atoms):
                 truncated_atom_index = int(str(atom_index + 1)[-5:])
+                truncated_resid = int(str(atom.resid)[:5])
                 if has_velocities:
                     output_gro.write(self.fmt['xyz_v'].format(
-                        resid=atom.resid,
+                        resid=truncated_resid,
                         resname=atom.resname,
                         index=truncated_atom_index,
                         name=atom.name,
@@ -308,7 +309,7 @@ def write(self, selection, frame=None):
                     ))
                 else:
                     output_gro.write(self.fmt['xyz'].format(
-                        resid=atom.resid,
+                        resid=truncated_resid,
                         resname=atom.resname,
                         index=truncated_atom_index,
                         name=atom.name,

testsuite/MDAnalysisTests/coordinates/test_gro.py

@@ -260,13 +260,18 @@ def test_check_coordinate_limits_max_noconversion(self):
 
 
 class TestGROWriterLarge(TestCase, tempdir.TempDir):
-    def setUp(self):
-        self.tmpdir = tempdir.TempDir()
-        self.large_universe = mda.Universe(GRO_large)
 
-    def tearDown(self):
-        del self.tmpdir
-        del self.large_universe
+    # not normally recommended to use class-level
+    # setup for universe (special case here)
+    @classmethod
+    def setUpClass(cls):
+        cls.tmpdir = tempdir.TempDir()
+        cls.large_universe = mda.Universe(GRO_large)
+
+    @classmethod
+    def tearDownClass(cls):
+        del cls.tmpdir
+        del cls.large_universe
 
     @dec.slow
     @attr('issue')
@@ -284,6 +289,28 @@ def test_writer_large(self):
                              err_msg="Writing GRO file with > 100 000 "
                                  "coords does not truncate properly.")
 
+    @dec.slow
+    @attr('issue')
+    def test_writer_large_residue_count(self):
+        """Ensure large residue number truncation for
+        GRO files (Issue 886)."""
+        outfile = os.path.join(self.tmpdir.name, 'outfile2.gro')
+        target_resname = self.large_universe.residues[-1].resname
+        resid_value = 999999999999999999999
+        self.large_universe.residues[-1].atoms.resids = resid_value
+        self.large_universe.atoms.write(outfile)
+        with open(outfile, 'rt') as mda_output:
+            output_lines = mda_output.readlines()
+            produced_resid = output_lines[-2].split(target_resname)[0]
+            expected_resid = str(resid_value)[:5]
+            assert_equal(produced_resid,
+                         expected_resid,
+                         err_msg="Writing GRO file with > 99 999 "
+                             "resids does not truncate properly.")
+
+
+
+
 class TestGROWriterVels(object):
     def setUp(self):
         self.tmpdir = tempdir.TempDir()