Merge pull request #12 from mattwthompson/new-qcarhive

Use new QCArchive APIs

devtools/conda-envs/dev.yaml

@@ -1,21 +1,21 @@
 name: ib-dev
 channels:
-  - conda-forge
   - openeye
+  - conda-forge
 dependencies:
   - python
 
   - openff-toolkit =0.14.3
-  - openff-qcsubmit
+  - openff-qcsubmit =0.50.1
   - openmmforcefields
   - smirnoff-plugins =2023.08.0
-  - espaloma
+  # espaloma =0.3
 
   - ipython
   - ipdb
   - pre-commit
 
-  - openeye-toolkits
+  - openeye::openeye-toolkits
   - rich
 
   - pytest

ibstore/_db.py

@@ -20,7 +20,7 @@ class DBQMConformerRecord(DBBase):
     id = Column(Integer, primary_key=True, index=True)
     parent_id = Column(Integer, ForeignKey("molecules.id"), nullable=False, index=True)
 
-    qcarchive_id = Column(String(20), nullable=False)
+    qcarchive_id = Column(Integer, nullable=False)
 
     mapped_smiles = Column(String, nullable=False)
     coordinates = Column(PickleType, nullable=False)
@@ -33,7 +33,7 @@ class DBMMConformerRecord(DBBase):
     id = Column(Integer, primary_key=True, index=True)
     parent_id = Column(Integer, ForeignKey("molecules.id"), nullable=False, index=True)
 
-    qcarchive_id = Column(String(20), nullable=False)
+    qcarchive_id = Column(Integer, nullable=False)
     force_field = Column(String, nullable=False)
 
     mapped_smiles = Column(String, nullable=False)

ibstore/_forcefields.py

@@ -73,7 +73,7 @@ def _espaloma(molecule: Molecule, force_field_name: str) -> openmm.System:
     espaloma.graphs.deploy.openmm_system_from_graph, where it will be appended
     with .offxml. Raises a ValueError if there is no dash in force_field_name.
     """
-    import espaloma as esp
+    import espaloma
 
     if not force_field_name.startswith("espaloma"):
         raise NotImplementedError(f"Force field {force_field_name} not implemented.")
@@ -85,8 +85,8 @@ def _espaloma(molecule: Molecule, force_field_name: str) -> openmm.System:
     else:
         ff = ff[0]
 
-    mol_graph = esp.Graph(molecule)
-    model = esp.get_model("latest")
+    mol_graph = espaloma.Graph(molecule)
+    model = espaloma.get_model("latest")
     model(mol_graph.heterograph)
 
-    return esp.graphs.deploy.openmm_system_from_graph(mol_graph, forcefield=ff)
+    return espaloma.graphs.deploy.openmm_system_from_graph(mol_graph, forcefield=ff)

ibstore/_session.py

@@ -187,7 +187,7 @@ def store_qm_conformer_record(
 
     def _qm_conformer_already_exists(
         self,
-        qcarchive_id: str,
+        qcarchive_id: int,
     ) -> bool:
         records = self.db.query(
             DBQMConformerRecord.qcarchive_id,
@@ -214,7 +214,7 @@ def store_mm_conformer_record(
 
     def _mm_conformer_already_exists(
         self,
-        qcarchive_id: str,
+        qcarchive_id: int,
         force_field: str,
     ) -> bool:
         records = (

ibstore/_tests/unit_tests/test_forcefields.py

@@ -30,12 +30,16 @@ def test_gaff_unsupported(molecule):
 
 
 def test_espaloma_basic(molecule):
+    pytest.importorskip("espaloma")
+
     system = _espaloma(molecule, "espaloma-openff_unconstrained-2.1.0")
 
     assert isinstance(system, openmm.System)
     assert system.getNumParticles() == molecule.n_atoms
 
 
 def test_espaloma_unsupported(molecule):
+    pytest.importorskip("espaloma")
+
     with pytest.raises(NotImplementedError):
         _espaloma(molecule, "foo")

ibstore/_tests/unit_tests/test_models.py

@@ -26,7 +26,7 @@ def test_load_from_qcsubmit(small_collection):
         assert molecule_record.inchi_key == ichi_key
 
         assert isinstance(qm_conformer, QMConformerRecord)
-        assert qm_conformer.energy == qc_record.get_final_energy() * hartree2kcalmol
+        assert qm_conformer.energy == qc_record.energies[-1] * hartree2kcalmol
         assert qm_conformer.qcarchive_id == qc_record.id
         assert numpy.allclose(
             qm_conformer.coordinates,

ibstore/analysis.py

@@ -7,7 +7,7 @@
 
 
 class DDE(ImmutableModel):
-    qcarchive_id: str
+    qcarchive_id: int
     force_field: str
     difference: float
 
@@ -25,7 +25,7 @@ def to_csv(self, path: str):
 
 
 class RMSD(ImmutableModel):
-    qcarchive_id: str
+    qcarchive_id: int
     force_field: str
     rmsd: float
 
@@ -43,7 +43,7 @@ def to_csv(self, path: str):
 
 
 class TFD(ImmutableModel):
-    qcarchive_id: str
+    qcarchive_id: int
     force_field: str
     tfd: float
 

ibstore/models.py

@@ -1,9 +1,8 @@
-from typing import TypeVar
+from typing import Any, TypeVar
 
 import qcelemental
 from openff.toolkit import Molecule
 from pydantic import Field
-from qcportal.models.records import OptimizationRecord
 
 from ibstore._base.array import Array
 from ibstore._base.base import ImmutableModel
@@ -26,7 +25,7 @@ class QMConformerRecord(Record):
         ...,
         description="The ID of the molecule in the database",
     )
-    qcarchive_id: str = Field(
+    qcarchive_id: int = Field(
         ...,
         description="The ID of the molecule in the QCArchive database",
     )
@@ -50,15 +49,15 @@ def from_qcarchive_record(
         cls,
         molecule_id: int,
         mapped_smiles: str,
-        qc_record: OptimizationRecord,
+        qc_record: Any,  # qcportal.optimization.OptimizationRecord ?
         coordinates,
     ):
         return cls(
             molecule_id=molecule_id,
             qcarchive_id=qc_record.id,
             mapped_smiles=mapped_smiles,
             coordinates=coordinates,
-            energy=qc_record.get_final_energy() * hartree2kcalmol,
+            energy=qc_record.energies[-1] * hartree2kcalmol,
         )
 
 
@@ -67,7 +66,7 @@ class MMConformerRecord(Record):
         ...,
         description="The ID of the molecule in the database",
     )
-    qcarchive_id: str = Field(
+    qcarchive_id: int = Field(
         ...,
         description="The ID of the molecule in the QCArchive database that this conformer corresponds to",
     )