Get dictionary connecting label_asym_id with auth_asym_id

iotbx/pdb/__init__.py

@@ -801,6 +801,11 @@ def input(
 
 class pdb_input_mixin(object):
 
+  def label_to_auth_asym_id_dictionary(self):
+    """ Only avaliable for cif_input
+    """
+    return None
+
   def deposition_date(self, us_style=True):
     """
     Placeholder to match mmCIF functionality. Probably could parse

iotbx/pdb/mmcif.py

@@ -397,9 +397,14 @@ def construct_hierarchy(self, set_atom_i_seq=True, sort_atoms=True):
       if (set_atom_i_seq):
         self.hierarchy.reset_atom_i_seqs()
       self.hierarchy.atoms_reset_serial()
-
     return self.hierarchy
 
+  def label_to_auth_asym_id_dictionary(self):
+    auth_asym = self.cif_block.get('_atom_site.auth_asym_id')
+    label_asym = self.cif_block.get('_atom_site.label_asym_id')
+    assert len(label_asym) == len(auth_asym)
+    return dict(zip(label_asym, auth_asym))
+
   def source_info(self):
     return self._source_info
 

iotbx/regression/tst_mmcif_input.py

@@ -37,8 +37,8 @@
 _atom_site.pdbx_PDB_model_num
 ATOM   1  N N   . GLY A 1 1 ? -9.009  4.612  6.102  1.00 16.77 ? 1  GLY A N   1
 ATOM   2  C CA  . GLY A 1 1 ? -9.052  4.207  4.651  1.00 16.57 ? 1  GLY A CA  1
-ATOM   3  C C   . GLY A 1 1 ? -8.015  3.140  4.419  1.00 16.16 ? 1  GLY A C   1
-ATOM   4  O O   . GLY A 1 1 ? -7.523  2.521  5.381  1.00 16.78 ? 1  GLY A O   1
+ATOM   3  C C   . GLY C 1 1 ? -8.015  3.140  4.419  1.00 16.16 ? 1  GLY CC C   1
+ATOM   4  O O   . GLY D 1 1 ? -7.523  2.521  5.381  1.00 16.78 ? 1  GLY DDDD O   1
 """
 
 
@@ -58,5 +58,12 @@ def exercise_extract_header_year(prefix="iotbx_tst_mmcif_segids"):
   assert cif_inp_2.deposition_date() == '?'
   assert cif_inp_2.extract_header_year() == None
 
+def exercise_label_to_auth_asym_id_dictionary():
+  cif_inp = iotbx.pdb.input(lines=cif_str, source_info=None)
+  res = cif_inp.label_to_auth_asym_id_dictionary()
+  # print(res)
+  assert res == {'A': 'A', 'C': 'CC', 'D': 'DDDD'}, res
+
 if __name__ == "__main__":
   exercise_extract_header_year()
+  exercise_label_to_auth_asym_id_dictionary()