Merge pull request #28 from openforcefield/map

remove identifiers field from qcschema molecule
openforcefield · May 27, 2019 · b41a8d8 · b41a8d8
2 parents 1b43757 + 78a8ace
commit b41a8d8
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Showing 4 changed files with 9 additions and 8 deletions.
diff --git a/cmiles/generator.py b/cmiles/generator.py
@@ -103,8 +103,9 @@ def get_molecule_ids(molecule_input, toolkit='openeye', strict=True, **kwargs):
 
     try:
         if kwargs['permute_xyz']:
-            permuted_json_mol = cmiles.utils.permute_qcschema(molecule_input, molecule_ids, toolkit=toolkit)
-            return permuted_json_mol
+            mapped_smiles = molecule_ids['canonical_isomeric_explicit_hydrogen_mapped_smiles']
+            permuted_json_mol = cmiles.utils.permute_qcschema(molecule_input, mapped_smiles, toolkit=toolkit)
+            return molecule_ids, permuted_json_mol
         else:
             return molecule_ids
 

diff --git a/cmiles/tests/test_cmiles.py b/cmiles/tests/test_cmiles.py
@@ -722,12 +722,12 @@ def test_permute_xyz(toolkit):
         'molecular_multiplicity': 1
     }
 
-    permuted_hooh = cmiles.get_molecule_ids(hooh, toolkit, permute_xyz=True)
+    mol_ids, permuted_hooh = cmiles.get_molecule_ids(hooh, toolkit, permute_xyz=True)
 
     assert hooh['geometry'] != permuted_hooh['geometry']
 
     mol = cmiles.utils.mol_from_json(hooh, toolkit=toolkit)
-    atom_map = cmiles.utils.get_atom_map(mol, permuted_hooh['identifiers']['canonical_isomeric_explicit_hydrogen_mapped_smiles'])
+    atom_map = cmiles.utils.get_atom_map(molecule=mol, mapped_smiles=mol_ids['canonical_isomeric_explicit_hydrogen_mapped_smiles'])
 
     json_geom = np.asarray(hooh['geometry']).reshape(int(len(hooh['geometry'])/3), 3)
     permuted_geom = np.asarray(permuted_hooh['geometry']).reshape(int(len(hooh['geometry'])/3), 3)

diff --git a/cmiles/tests/test_utils.py b/cmiles/tests/test_utils.py
@@ -334,9 +334,10 @@ def test_permute_json(toolkit):
         'connectivity': [[0, 1, 1], [1, 2, 1], [2, 3, 1]],
         'molecular_multiplicity': 1
     }
+    mapped_smiles = molecule_ids['canonical_isomeric_explicit_hydrogen_mapped_smiles']
     mol = utils.mol_from_json(hooh, toolkit=toolkit)
     atom_map = utils.get_atom_map(mol, '[H:3][O:1][O:2][H:4]')
-    permuted_hooh = utils.permute_qcschema(hooh, molecule_ids, toolkit=toolkit)
+    permuted_hooh = utils.permute_qcschema(hooh, mapped_smiles, toolkit=toolkit)
 
     json_geom = np.asarray(hooh['geometry']).reshape(int(len(hooh['geometry'])/3), 3)
     permuted_geom = np.asarray(permuted_hooh['geometry']).reshape(int(len(hooh['geometry'])/3), 3)

diff --git a/cmiles/utils.py b/cmiles/utils.py
@@ -237,7 +237,7 @@ def mol_to_hill_molecular_formula(molecule):
     return "".join(hill_sorted)
 
 
-def mol_to_map_ordered_qcschema(molecule, molecule_ids, multiplicity=1, **kwargs):
+def mol_to_map_ordered_qcschema(molecule, mapped_smiles, multiplicity=1, **kwargs):
     """
     Genereate JSON serialize following `QCSchema specs <https://molssi-qc-schema.readthedocs.io/en/latest/index.html#>`_
 
@@ -260,15 +260,14 @@ def mol_to_map_ordered_qcschema(molecule, molecule_ids, multiplicity=1, **kwargs
 
     """
     toolkit = _set_toolkit(molecule)
-    mapped_smiles = molecule_ids['canonical_isomeric_explicit_hydrogen_mapped_smiles']
     atom_map = toolkit.get_atom_map(molecule, mapped_smiles, **kwargs)
 
     connectivity = get_connectivity_table(molecule, atom_map)
     symbols, geometry = toolkit.get_map_ordered_geometry(molecule, atom_map)
     charge = get_charge(molecule)
 
     qcschema_mol = {'symbols': symbols, 'geometry': geometry, 'connectivity': connectivity,
-                    'molecular_charge': charge, 'molecular_multiplicity': multiplicity, 'identifiers': molecule_ids}
+                    'molecular_charge': charge, 'molecular_multiplicity': multiplicity}
 
     return qcschema_mol