noncontig passthrough

qcelemental/models/molecule.py

@@ -341,14 +341,22 @@ def __init__(self, orient: bool = False, validate: Optional[bool] = None, **kwar
  # original_keys = set(kwargs.keys()) # revive when ready to revisit sparsity
 
  nonphysical = kwargs.pop("nonphysical", False)
+ throw_reorder = not (kwargs.pop("allow_noncontiguous_but_reorder", False)) # experimental
  schema = to_schema(
- from_schema(kwargs, nonphysical=nonphysical), dtype=kwargs["schema_version"], copy=False, np_out=True
+ from_schema(kwargs, nonphysical=nonphysical, throw_reorder=throw_reorder),
+ dtype=kwargs["schema_version"],
+ copy=False,
+ np_out=True,
  )
  schema = _filter_defaults(schema)
 
  kwargs["validated"] = True
  kwargs = {**kwargs, **schema} # Allow any extra fields
  validate = True
+ else:
+ # these kwargs only relevant for validation
+ kwargs.pop("nonphysical", None)
+ kwargs.pop("allow_noncontiguous_but_reorder", None)
 
  super().__init__(**kwargs)
 

qcelemental/molparse/from_schema.py

@@ -7,7 +7,7 @@
 from .from_arrays import from_arrays
 
 
-def from_schema(molschema: Dict, *, nonphysical: bool = False, verbose: int = 1) -> Dict:
+def from_schema(molschema: Dict, *, nonphysical: bool = False, throw_reorder: bool = True, verbose: int = 1) -> Dict:
  r"""Construct molecule dictionary representation from non-Psi4 schema.
 
  Parameters
@@ -16,6 +16,10 @@ def from_schema(molschema: Dict, *, nonphysical: bool = False, verbose: int = 1)
  Dictionary form of Molecule following known schema.
  nonphysical
  Do allow masses outside an element's natural range to pass validation?
+ throw_reorder
+ Do, when non-contiguous fragments detected, raise
+ ValidationError (``True``) or to proceed to reorder atoms to
+ contiguize fragments (``False``).
  verbose
  Amount of printing.
 
@@ -54,7 +58,7 @@ def from_schema(molschema: Dict, *, nonphysical: bool = False, verbose: int = 1)
  mass=ms.get("masses", None),
  real=ms.get("real", None),
  elbl=ms.get("atom_labels", None),
- throw_reorder=True,
+ throw_reorder=throw_reorder,
  )
 
  molrec = from_arrays(

qcelemental/tests/test_molecule.py

@@ -436,6 +436,38 @@ def test_charged_fragment():
 # })
 
 
+@pytest.mark.parametrize(
+ "validate, allow_noncontiguous_but_reorder", [(True, True), (True, False), (False, True), (False, False)]
+)
+def test_noncontig(validate, allow_noncontiguous_but_reorder):
+ mol = {
+ "fragments": [[2, 0], [1]],
+ "geometry": np.array([[0.0, 0.0, 1.0], [0.0, 0.0, 2.0], [0.0, 0.0, 0.0]]),
+ "symbols": np.array(["Li", "H", "He"]),
+ "fragment_multiplicities": [4, 2],
+ }
+
+ if validate:
+ if allow_noncontiguous_but_reorder:
+ mol = Molecule(**mol, validate=validate, allow_noncontiguous_but_reorder=allow_noncontiguous_but_reorder)
+ assert compare(["He", "Li", "H"], mol.symbols)
+ assert compare([2, 3, 1], mol.atomic_numbers)
+ assert compare_values([[0, 0, 0], [0, 0, 1], [0, 0, 2]], mol.geometry)
+ assert compare([4, 2], mol.fragment_multiplicities)
+
+ else:
+ with pytest.raises(qcel.ValidationError) as e:
+ Molecule(**mol, validate=validate, allow_noncontiguous_but_reorder=allow_noncontiguous_but_reorder)
+ assert "QCElemental would need to reorder atoms to accommodate non-contiguous fragments" in str(e.value)
+
+ else:
+ mol = Molecule(**mol, validate=validate, allow_noncontiguous_but_reorder=allow_noncontiguous_but_reorder)
+ assert compare(["Li", "H", "He"], mol.symbols)
+ assert compare([3, 1, 2], mol.atomic_numbers)
+ assert compare_values([[0, 0, 1], [0, 0, 2], [0, 0, 0]], mol.geometry)
+ assert compare([4, 2], mol.fragment_multiplicities)
+
+
 @pytest.mark.parametrize("group_fragments, orient", [(True, True), (False, False)]) # original # Psi4-like
 def test_get_fragment(group_fragments, orient):
  mol = Molecule(