Merge pull request #1 from Yoshanuikabundi/abandon-aa-variants

Abandon aa variants

.gitignore

@@ -112,3 +112,5 @@ poetry.lock
 
 # ruff
 .ruff_cache
+
+.ccd_cache

openff/pablo/_pdb.py

@@ -88,7 +88,7 @@ def _load_unknown_residue(
 
 
 def topology_from_pdb(
-    path: PathLike[str],
+    path: PathLike[str] | str,
     unknown_molecules: Iterable[Molecule] = [],
     residue_database: Mapping[
         str,
@@ -284,7 +284,8 @@ def topology_from_pdb(
 
         prev_chain_id = data.chain_id[prototype_index]
         prev_model = data.model[prototype_index]
-    molecules.append(this_molecule)
+    if this_molecule.n_atoms != 0:
+        molecules.append(this_molecule)
 
     for offmol in molecules:
         offmol._invalidate_cached_properties()

openff/pablo/_tests/test_pdb.py

@@ -0,0 +1,62 @@
+import pytest
+from openff.toolkit import Molecule, Topology
+from pkg_resources import resource_filename
+
+from openff.pablo._pdb import topology_from_pdb
+from openff.pablo._utils import sort_tuple
+
+
+@pytest.mark.parametrize(
+    ("pdbfile", "unknown_smiles"),
+    [
+        (
+            "data/5ap1_prepared.pdb",
+            ["O=C([O-])Cn1cc(cn1)c2ccc(cc2OCC#N)Nc3ccc(c(n3)NC4CCCCC4)C#N"],
+        ),
+    ],
+)
+def test_connectivity_and_atom_order_and_net_residue_charge_and_metadata_matches_legacy(
+    pdbfile: str,
+    unknown_smiles: list[str],
+):
+    unknown_molecules = [Molecule.from_smiles(s) for s in unknown_smiles]
+    filename = resource_filename(__name__, pdbfile)
+
+    pablo_top = topology_from_pdb(
+        filename,
+        unknown_molecules=unknown_molecules,
+    )
+    legacy_top: Topology = Topology.from_pdb(
+        filename,
+        unique_molecules=unknown_molecules,
+    )
+
+    assert pablo_top.n_molecules == legacy_top.n_molecules
+    for pablo_mol, legacy_mol in zip(pablo_top.molecules, legacy_top.molecules):
+        assert pablo_mol.n_atoms == legacy_mol.n_atoms
+        for pablo_atom, legacy_atom in zip(pablo_mol.atoms, legacy_mol.atoms):
+            assert pablo_atom.name == legacy_atom.name
+            assert pablo_atom.symbol == legacy_atom.symbol
+            for key in [
+                "residue_name",
+                "chain_id",
+                "residue_number",
+                "insertion_code",
+            ]:
+                assert pablo_atom.metadata[key] == legacy_atom.metadata[key]
+
+        pablo_bonds = {
+            sort_tuple((bond.atom1_index, bond.atom2_index)) for bond in pablo_mol.bonds
+        }
+        legacy_bonds = {
+            sort_tuple((bond.atom1_index, bond.atom2_index))
+            for bond in legacy_mol.bonds
+        }
+        assert pablo_bonds == legacy_bonds
+
+    for pablo_res, legacy_res in zip(pablo_top.residues, legacy_top.residues):
+        pablo_res_charge, legacy_res_charge = 0, 0
+        for pablo_atom, legacy_atom in zip(pablo_res.atoms, legacy_res.atoms):
+            pablo_res_charge += pablo_atom.formal_charge
+            legacy_res_charge += legacy_atom.formal_charge
+        assert pablo_res_charge == legacy_res_charge