add tests for ccd and prd readers

Author: roshkjr

pdbeccdutils/tests/test_ccd_reader.py

@@ -26,3 +26,68 @@ def test_read_pdb_components_file_parses_all_for_empty_include(tmp_path):
         assert list(result) == ["00O", "007"]
 
 
+def test_read_pdb_components_file_uses_include_order_and_skips_missing(
+    tmp_path, caplog
+):
+    path = _components_cif(tmp_path)
+
+    with caplog.at_level(logging.WARNING):
+        result = ccd_reader.read_pdb_components_file(
+            str(path), sanitize=False, include=["007", "MISSING", "00O", "007"]
+        )
+
+    assert list(result) == ["007", "00O"]
+    assert "Data block MISSING not found" in caplog.text
+
+
+def test_parse_pdb_bonds_uses_atom_id_lookup():
+    block = cif.read_string(
+        """
+        data_TST
+        loop_
+        _chem_comp_atom.atom_id
+        A
+        B
+        loop_
+        _chem_comp_bond.atom_id_1
+        _chem_comp_bond.atom_id_2
+        _chem_comp_bond.value_order
+        A B SING
+        """
+    ).sole_block()
+    mol = Chem.RWMol()
+    mol.AddAtom(Chem.Atom("C"))
+    mol.AddAtom(Chem.Atom("O"))
+    errors = []
+
+    ccd_reader._parse_pdb_bonds(mol, block, errors)
+
+    assert errors == []
+    assert mol.GetNumBonds() == 1
+    assert mol.GetBondBetweenAtoms(0, 1) is not None
+
+
+def test_parse_pdb_bonds_missing_atom_1_does_not_mask_error():
+    block = cif.read_string(
+        """
+        data_TST
+        loop_
+        _chem_comp_atom.atom_id
+        A
+        loop_
+        _chem_comp_bond.atom_id_1
+        _chem_comp_bond.atom_id_2
+        _chem_comp_bond.value_order
+        ? A SING
+        """
+    ).sole_block()
+    mol = Chem.RWMol()
+    mol.AddAtom(Chem.Atom("C"))
+    errors = []
+
+    ccd_reader._parse_pdb_bonds(mol, block, errors)
+
+    assert errors == [
+        f"Missing atom in 0 entry in _chem_comp_bond"
+    ]
+    assert mol.GetNumBonds() == 0

pdbeccdutils/tests/test_prd_reader.py

@@ -13,3 +13,16 @@ def test_read_prd_components_file_parses_all_for_empty_include():
         )
 
         assert list(result) == ["PRD_000103"]
+
+def test_read_prd_components_file_uses_include_order_and_skips_missing(caplog):
+    path = prd_cif_filename("PRDCC_000103")
+
+    with caplog.at_level(logging.WARNING):
+        result = prd_reader.read_pdb_components_file(
+            path,
+            sanitize=False,
+            include=["PRD_000103", "MISSING", "PRD_000103"],
+        )
+
+    assert list(result) == ["PRD_000103"]
+    assert "Data block MISSING not found" in caplog.text