in-class mol formation, req'd kwargs for core

docs/changelog.md

@@ -26,6 +26,8 @@
  * [\#28](https://github.com/MolSSI/QCManyBody/pull/28) Intf -- low-level "core" interface renamed from
    `ManyBodyCalculator` to `ManyBodyCore`. The old name will continue to work for a few months. Also, its file changed
    from `manybody.py` to `core.py` but it was already a top-level import. @loriab
+ * [\#30](https://github.com/MolSSI/QCManyBody/pull/30) Intf -- low-level "core" interface now requires named arguments
+   beyond the first recognizable ones (mol, bsse_type, levels). @loriab
 
 #### New Features
 
@@ -35,6 +37,8 @@
    module. @loriab
  * [\#29](https://github.com/MolSSI/QCManyBody/pull/29) Maint -- QCEngine is needed only for the continuous running
    function of the high-level interface, so making it an optional dependency. @loriab
+ * [\#30](https://github.com/MolSSI/QCManyBody/pull/30) Intf -- low-level "core" interface now accepts a molecule in
+   partial schema dictionary format rather than requiring a constructed `qcelemental.Molecule` object.
 
 #### Bug Fixes
 

qcmanybody/__init__.py

@@ -1,7 +1,7 @@
 from importlib.metadata import version
 
 from .core import ManyBodyCore
-from .core import ManyBodyCore as ManyBodyCalculator  # legacy alias
+from .core import ManyBodyCalculator  # legacy near-alias to ManyBodyCore
 from .computer import ManyBodyComputer
 from .models import BsseEnum
 from .utils import labeler, delabeler, resize_gradient, resize_hessian

qcmanybody/computer.py

@@ -402,15 +402,20 @@ def from_manybodyinput(cls, input_model: ManyBodyInput, build_tasks: bool = True
             computer_model.molecule,
             computer_model.bsse_type,
             comp_levels,
-            computer_model.return_total_data,
-            computer_model.supersystem_ie_only,
-            computer_model.embedding_charges,
+            return_total_data=computer_model.return_total_data,
+            supersystem_ie_only=computer_model.supersystem_ie_only,
+            embedding_charges=computer_model.embedding_charges,
         )
 
         if not build_tasks:
             return computer_model
 
-        import qcengine as qcng
+        try:
+            import qcengine as qcng
+        except ModuleNotFoundError:
+            raise ModuleNotFoundError(
+                "Python module qcengine not found. Solve by installing it: "
+                "`conda install qcengine -c conda-forge` or `pip install qcengine`")
 
         component_properties = {}
         component_results = {}

qcmanybody/core.py

@@ -33,16 +33,23 @@ def __init__(
         molecule: Molecule,
         bsse_type: Sequence[BsseEnum],
         levels: Mapping[Union[int, Literal["supersystem"]], str],
+        *,
         return_total_data: bool,
         supersystem_ie_only: bool,
         embedding_charges: Mapping[int, Sequence[float]],
     ):
         self.embedding_charges = embedding_charges
-        self.molecule = molecule
+        if isinstance(molecule, dict):
+            mol = Molecule(**molecule)
+        elif isinstance(molecule, Molecule):
+            mol = molecule.copy()
+        else:
+            raise ValueError(f"Molecule input type of {type(molecule)} not understood.")
+        self.molecule = mol
         self.bsse_type = [BsseEnum(x) for x in bsse_type]
         self.return_total_data = return_total_data
         self.supersystem_ie_only = supersystem_ie_only
-        self.nfragments = len(molecule.fragments)
+        self.nfragments = len(self.molecule.fragments)
 
         self.levels = levels
 
@@ -561,3 +568,21 @@ def analyze(
         all_results["stdout"] = stdout
 
         return all_results
+
+
+class ManyBodyCalculator(ManyBodyCore):
+    # retire after a grace period
+    def __init__(
+        self,
+        molecule: Molecule,
+        bsse_type: Sequence[BsseEnum],
+        levels: Mapping[Union[int, Literal["supersystem"]], str],
+        return_total_data: bool,
+        supersystem_ie_only: bool,
+        embedding_charges: Mapping[int, Sequence[float]],
+    ):
+        super().__init__(molecule, bsse_type, levels,
+            return_total_data=return_total_data,
+            supersystem_ie_only=supersystem_ie_only,
+            embedding_charges=embedding_charges,
+        )

qcmanybody/tests/common.py

@@ -21,6 +21,8 @@
 """
 )
 
+mol_h2o_3_dict = {k: v for k, v in mol_h2o_3.dict().items() if k in ["symbols", "geometry", "fragments"]}
+
 specifications = {
     "e_scf": {
         "program": "psi4",

qcmanybody/tests/test_multi_ss.py

@@ -28,6 +28,7 @@ def test_h2o_trimer_multi_ss(levels, component_file, ref_file):
     component_results = load_component_data(component_file)
     ref_data = load_ref_data(ref_file)
 
-    mc = ManyBodyCore(mol_h2o_3, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels, True, False, None)
+    mc = ManyBodyCore(mol_h2o_3, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels,
+        return_total_data=True, supersystem_ie_only=False, embedding_charges=None)
     nbody_results = mc.analyze(component_results)
     compare_results(nbody_results, ref_data, levels)

qcmanybody/tests/test_single.py

@@ -1,8 +1,9 @@
 import pytest
 
+import qcelemental
 from qcmanybody import ManyBodyCore
 from qcmanybody.models import BsseEnum
-from .common import mol_h2o_3
+from .common import mol_h2o_3_dict
 from .utils import load_ref_data, compare_results, load_component_data
 
 
@@ -25,6 +26,16 @@ def test_h2o_trimer_single(levels, component_file, ref_file):
     component_results = load_component_data(component_file)
     ref_data = load_ref_data(ref_file)
 
-    mc = ManyBodyCore(mol_h2o_3, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels, True, False, None)
+    mc = ManyBodyCore(mol_h2o_3_dict, [BsseEnum.cp, BsseEnum.nocp, BsseEnum.vmfc], levels,
+        return_total_data=True, supersystem_ie_only=False, embedding_charges=None)
     nbody_results = mc.analyze(component_results)
     compare_results(nbody_results, ref_data, levels)
+
+
+def test_core_mol_error():
+    # check sensible error from internal Molecule construction
+    odd_mol = mol_h2o_3_dict.copy()
+    odd_mol["symbols"][0] = "A"
+    with pytest.raises(qcelemental.exceptions.NotAnElementError):
+        ManyBodyCore(odd_mol, [BsseEnum.nocp], {1: "asdf"},
+            return_total_data=False, supersystem_ie_only=False, embedding_charges=None)