sync internal updates

Author: OleinikovasV

docs/api.rst

@@ -113,7 +113,7 @@ Miscellaneous
     get_contact_residues
     find_atoms_by_pattern
     estimate_formal_charges
-    find_charged_atoms_in_resonance_structures
+    find_resonance_charges
     MatchWarning
     EvaluationWarning
     NoContactError

src/peppr/contacts.py

@@ -1,7 +1,7 @@
 __all__ = [
     "ContactMeasurement",
     "find_atoms_by_pattern",
-    "find_charged_atoms_in_resonance_structures",
+    "find_resonance_charges",
 ]
 
 from enum import IntEnum
@@ -284,13 +284,13 @@ def find_salt_bridges(
         When ``use_resonance=True``, Both oxygen atoms would be checked.
         """
         if use_resonance:
-            pos_mask, neg_mask, binding_site_conjugated_groups = (
-                find_charged_atoms_in_resonance_structures(self._binding_site_mol)
+            pos_mask, neg_mask, binding_site_conjugated_groups = find_resonance_charges(
+                self._binding_site_mol
             )
             binding_site_pos_indices = np.where(pos_mask)[0]
             binding_site_neg_indices = np.where(neg_mask)[0]
-            pos_mask, neg_mask, ligand_conjugated_groups = (
-                find_charged_atoms_in_resonance_structures(self._ligand_mol)
+            pos_mask, neg_mask, ligand_conjugated_groups = find_resonance_charges(
+                self._ligand_mol
             )
             ligand_pos_indices = np.where(pos_mask)[0]
             ligand_neg_indices = np.where(neg_mask)[0]
@@ -584,7 +584,7 @@ def _acceptable_angle(
     return abs(angle - ref_angle) <= tolerance
 
 
-def find_charged_atoms_in_resonance_structures(
+def find_resonance_charges(
     mol: Chem.Mol,
 ) -> tuple[NDArray[np.bool_], NDArray[np.bool_], NDArray[np.int_]]:
     """

tests/test_contacts.py

@@ -304,19 +304,13 @@ def test_no_bonds(contact_method):
     contact_method(contact_measurement)
 
 
-def test_find_charged_atoms_in_resonance_structures():
+def test_find_resonance_charges():
     """
     Test finding charged atoms in resonance structures using a real ligand from a PDB file.
     """
-    pdbx_file = pdbx.CIFFile.read(Path(__file__).parent / "data" / "pdb" / "3eca.cif")
-    structure = pdbx.get_structure(
-        pdbx_file,
-        model=1,
-        include_bonds=True,
-    )
-    structure = peppr.standardize(structure)
-    structure = structure[structure.chain_id == "A"]
-    ligand = structure[structure.hetero]
+    ligand = info.residue("ASP")
+    # standardize removes hydrogens - needed to estimate formal charges
+    ligand = peppr.standardize(ligand)
 
     # set annotations for the benefit of finding charged atoms
     ligand.set_annotation("charge", peppr.estimate_formal_charges(ligand, 7.4))
@@ -330,11 +324,11 @@ def test_find_charged_atoms_in_resonance_structures():
     assert np.equal(ligand_charged_atoms, [0, 7, 8]).all()
 
     # get charged atoms and their resonance groups
-    pos_mask, neg_mask, ligand_conjugated_groups = (
-        peppr.find_charged_atoms_in_resonance_structures(ligand_mol)
+    pos_mask, neg_mask, ligand_conjugated_groups = peppr.find_resonance_charges(
+        ligand_mol
     )
     assert len(set(ligand_conjugated_groups)) < len(ligand_conjugated_groups), (
-        "Some atoms are in the same conjugated group"
+        "Number of groups expected less than number of atoms as some are conjugated"
     )
     charged_atom_mask = pos_mask | neg_mask
     ligand_charged_in_resonance_atoms = np.where(charged_atom_mask)[0]