Check that longer alt_locs are OK in mmCIF

The alternate location indicator used to be
truncated to a single character, as in legacy
PDB format. Check that multi-character indicators
are now handled correctly in mmCIF.

modules/atom/test/input/nonalttest.cif

@@ -0,0 +1,28 @@
+loop_
+_atom_site.group_PDB
+_atom_site.id
+_atom_site.type_symbol
+_atom_site.label_atom_id
+_atom_site.label_alt_id
+_atom_site.label_comp_id
+_atom_site.label_asym_id
+_atom_site.label_entity_id
+_atom_site.label_seq_id
+_atom_site.pdbx_PDB_ins_code
+_atom_site.Cartn_x
+_atom_site.Cartn_y
+_atom_site.Cartn_z
+_atom_site.occupancy
+_atom_site.B_iso_or_equiv
+_atom_site.pdbx_formal_charge
+_atom_site.auth_seq_id
+_atom_site.auth_comp_id
+_atom_site.auth_asym_id
+_atom_site.auth_atom_id
+_atom_site.pdbx_PDB_model_num
+ATOM 1      C CA  .  ALA A  1  1    ? 953.312  704.510 700.259 1.00 84.31  ? 1    ALA A CA  1
+ATOM 2      C CA  A  GLN A  1  2    ? 862.521  620.909 612.377 1.00 10.00  ? 2    GLN A CA  1 
+ATOM 3      C CA  B  GLN A  1  3    ? 862.521  620.909 612.377 1.00 10.00  ? 3    GLN A CA  1 
+ATOM 4      C CA  AA ALA A  1  4    ? 953.312  704.510 700.259 1.00 84.31  ? 4    ALA A CA  1
+ATOM 5      C CA  .  GLN A  1  5    ? 862.521  620.909 612.377 1.00 10.00  ? 5    GLN A CA  1 
+ATOM 6      C CA  .  GLN A  1  6    ? 862.521  620.909 612.377 1.00 10.00  ? 6    GLN A CA  1 

modules/atom/test/test_mmcif.py

@@ -175,6 +175,21 @@ def test_multiple_ligands_no_auth(self):
                           for x in residues],
                          ['LYS', 'CA', '7ZTVU', '7ZTVU'])
 
+    def test_non_alt_selector(self):
+        """Check NonAlternativePDBSelector when reading mmCIF files"""
+        m = IMP.Model()
+
+        mp = IMP.atom.read_mmcif(self.get_input_file_name('nonalttest.cif'), m,
+                                 IMP.atom.NonAlternativePDBSelector())
+        residues = IMP.atom.get_by_type(mp, IMP.atom.RESIDUE_TYPE)
+        # Residue #3 should be rejected because its alt_loc is "B" (only
+        # blank or "A" alt_loc should be accepted)
+        # Residue #4 should be rejected because alt_loc is "AA". Previous
+        # versions of IMP would pass this because it would be truncated to
+        # one character, "A".
+        self.assertEqual([IMP.atom.Residue(x).get_index() for x in residues],
+                         [1, 2, 5, 6])
+
     def test_chain_selector(self):
         """Check reading single chain from an mmCIF file"""
         m = IMP.Model()