better iotbx.pdb fix - preserves the ANISOUs

src/qfit/structure/pdbfile.py

@@ -1,5 +1,5 @@
 from collections import defaultdict, namedtuple
-import itertools as itl
+import itertools
 from math import inf
 import logging
 
@@ -156,10 +156,10 @@ def load_combined_atoms(*atom_lists):
 
 
 def load_atoms_from_labels(atom_labels):
-    atom_lines = [atom.format_atom_record_group().split('\n')[0]
-                  for atom in atom_labels]
+    atom_lines = itertools.chain(*[atom.format_atom_record_group().split('\n')
+                                   for atom in atom_labels])
     return iotbx.pdb.pdb_input(source_info="qfit_structure",
-                               lines=atom_lines)
+                               lines=list(atom_lines))
 
 
 def write_mmcif(fname, structure):
@@ -250,7 +250,7 @@ def format_line(cls, values):
         )
 
         # Intersperse formatted values with spaces
-        line = itl.zip_longest(formatted_values, spaces, fillvalue="")
+        line = itertools.zip_longest(formatted_values, spaces, fillvalue="")
         line = "".join(flatten(line)) + "\n"
         return line
 

tests/unit/test_structure.py

@@ -127,6 +127,11 @@ def test_structure_extract_io_recycling(self):
         s2.tofile(pdb_tmp)
         s3 = Structure.fromfile(pdb_tmp)
         assert len(list(s3.single_conformer_residues)) == 2
+        # sanity check for presence of ANISOUs
+        PDB2 = op.join(self.DATA, "..", "qfit_ligand_test", "5AGK.pdb")
+        s4 = Structure.fromfile(PDB2)
+        s5 = s4.combine(s3)
+        xrs = s5.to_xray_structure()
 
     def test_structure_pickle(self):
         PDB = op.join(self.DATA, "4ms6_tiny.pdb.gz")