Fill in formula_weight from CCD info if requested

Author: benmwebb

ihm/util/make_mmcif.py

@@ -305,8 +305,9 @@ class _ChemCompHandler:
     """Read the _chem_comp table from a CCD entry"""
     not_in_file = omitted = unknown = None
 
-    def __call__(self, name, type, formula):
+    def __call__(self, name, type, formula, formula_weight: float):
         self.name, self.type, self.formula = name, type, formula
+        self.formula_weight = formula_weight
 
 
 def _fix_incomplete_chem_comps(s):
@@ -329,6 +330,7 @@ def _fix_chem_comp(cc, typmap):
     if hasattr(h, 'name') and h.name is not None:
         cc.name = h.name
         cc.formula = h.formula
+        cc.formula_weight = h.formula_weight
         cc.__class__ = typmap.get(h.type.lower(), ihm.ChemComp)
 
 

test/mock/non_canon_atom/urllib/request.py

@@ -3,12 +3,15 @@
 
 zinc_atoms = b'_chem_comp_atom.comp_id ZN\n_chem_comp_atom.atom_id ZN\n'
 
+# The weight for MG here is deliberately wrong to ensure that we use
+# this CCD info and not the element mass
 mg = b"""
 _chem_comp.id                                   MG
 _chem_comp.name                                 "MAGNESIUM ION"
 _chem_comp.type                                 NON-POLYMER
 _chem_comp.pdbx_type                            HETAI
 _chem_comp.formula                              Mg
+_chem_comp.formula_weight                       26.305
 """
 
 uniprot_fasta = b""">tr|Q90VU7|Q90VU7_HV1 Protein Nef

test/test_make_mmcif.py

@@ -377,10 +377,12 @@ def test_missing_chem_comp(self):
         with open('output.cif') as fh:
             contents = fh.readlines()
         ind = contents.index('_chem_comp.formula_weight\n')
+        # Note that the mass for MG in our mock CCD is deliberately wrong
+        # (26, not 24) to ensure that we use it instead of the element mass
         self.assertEqual(
             contents[ind + 1:ind + 5],
             ["ALA 'L-peptide linking' ALANINE 'C3 H7 N O2' 89.094\n",
-             "MG non-polymer 'MAGNESIUM ION' Mg 24.305\n",
+             "MG non-polymer 'MAGNESIUM ION' Mg 26.305\n",
              'ZN other . . .\n',
              'invalid-chem-comp other . . .\n'])
         os.unlink('output.cif')