Merge branch 'master' into issue-2327-warn

package/CHANGELOG

@@ -33,6 +33,8 @@ Changes
 Deprecations
   * NCDFWriter `scale_factor` writing will change in version 2.0 to
     better match AMBER outputs (Issue #2327)
+  * Deprecated using the last letter of the segid as the
+    chainID when writing PDB files (Issue #3144)
   * Deprecated tempfactors and bfactors being separate
     TopologyAttrs, with a warning (PR #3161)
   * hbonds.WaterBridgeAnalysis will be removed in 2.0.0 and

package/MDAnalysis/coordinates/PDB.py

@@ -858,6 +858,10 @@ def write(self, obj):
             The :class:`~MDAnalysis.core.groups.AtomGroup` or
             :class:`~MDAnalysis.core.universe.Universe` to write.
         """
+        warnings.warn("Using the last letter of the segid for the chainID "
+                      "is now deprecated and will be changed in 2.0. "
+                      "In 2.0, the chainID attribute will be used if it "
+                      "exists, or a placeholder value.", DeprecationWarning)
 
         self._update_frame(obj)
         self._write_pdb_header()

testsuite/MDAnalysisTests/coordinates/test_pdb.py

@@ -1042,3 +1042,12 @@ def test_cryst_meaningless_select():
     u = mda.Universe(PDB_CRYOEM_BOX)
     cur_sele = u.select_atoms('around 0.1 (resid 4 and name CA and segid A)')
     assert cur_sele.n_atoms == 0
+
+
+def test_deprecated_chainid_from_segid(tmpdir):
+    u = mda.Universe(PDB)
+    err = ("Using the last letter of the segid for the chainID "
+           "is now deprecated and will be changed in 2.0. ")
+    with tmpdir.as_cwd():
+        with pytest.warns(DeprecationWarning, match=err):
+            u.atoms.write("test.pdb")