Fix PDBWriter with StringIO for invalid coordinates (#2518)

* failing test

* check if file is StringIO

* changelog

* small change

* fix typos

* actually check exception message

* fix problem with exception catch

* use pytest match

package/CHANGELOG

@@ -20,6 +20,8 @@ mm/dd/yy richardjgowers, kain88-de, lilyminium, p-j-smith, bdice, joaomcteixeira
   * 0.21.0
 
 Fixes
+  * Handle exception when PDBWriter is trying to remove an invalid StringIO
+    (Issue #2512)
   * Clarifies density_from_Universe docs and adds user warning (Issue #2372)
   * Fix upstream deprecation of `matplotlib.axis.Tick` attributes in 
     `MDAnalysis.analysis.psa`

package/MDAnalysis/coordinates/PDB.py

@@ -653,6 +653,10 @@ def _check_pdb_coordinates(self):
         coordinates and closes the file.
 
         Raises :exc:`ValueError` if the coordinates fail the check.
+
+        .. versionchanged: 1.0.0
+            Check if :attr:`filename` is `StringIO` when attempting to remove
+            a PDB file with invalid coordinates (Issue #2512)
         """
         atoms = self.obj.atoms  # make sure to use atoms (Issue 46)
         # can write from selection == Universe (Issue 49)
@@ -678,6 +682,14 @@ def _check_pdb_coordinates(self):
             except OSError as err:
                 if err.errno == errno.ENOENT:
                     pass
+                else:
+                    raise
+            except TypeError:
+                if isinstance(self.filename, StringIO):
+                    pass
+                else:
+                    raise
+
         raise ValueError("PDB files must have coordinate values between "
                          "{0:.3f} and {1:.3f} Angstroem: file writing was "
                          "aborted.".format(self.pdb_coor_limits["min"],

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -185,6 +185,10 @@ def universe(self):
     def universe2(self):
         return mda.Universe(PSF, DCD)
 
+    @pytest.fixture
+    def universe3(self):
+        return mda.Universe(PDB)
+
     @pytest.fixture
     def outfile(self, tmpdir):
         return str(tmpdir.mkdir("PDBWriter").join('primitive-pdb-writer' + self.ext))
@@ -362,6 +366,26 @@ def test_segid_chainid(self, universe2, outfile):
         u_pdb = mda.Universe(outfile)
         assert u_pdb.segments.chainIDs[0][0] == ref_id
 
+    def test_stringio_outofrange(self, universe3):
+        """
+        Check that when StringIO is used, the correct out-of-range error for
+        coordinates is raised (instead of failing trying to remove StringIO
+        as a file).
+        """
+
+        u = universe3
+
+        u.atoms.translate([-9999, -9999, -9999])
+
+        outstring = StringIO()
+
+        errmsg = "PDB files must have coordinate values between"
+
+        with pytest.raises(ValueError, match=errmsg):
+            with mda.coordinates.PDB.PDBWriter(outstring) as writer:
+                writer.write(u.atoms)
+
+
 class TestMultiPDBReader(object):
     @staticmethod
     @pytest.fixture(scope='class')