Make UnAssignedChemistryInPDBError hints clearer (#1926)

* Make UnAssignedChemistryInPDBError hints clearer * Update changelog * Simplify diff * Update pdb cookbook outputs
openforcefield · Aug 10, 2024 · d91b8f2 · d91b8f2
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diff --git a/docs/releasehistory.md b/docs/releasehistory.md
@@ -28,6 +28,7 @@ Releases follow the `major.minor.micro` scheme recommended by [PEP440](https://w
 ### Bugfixes
 
 - [PR #1923](https://github.com/openforcefield/openff-toolkit/pull/1923): `Topology.add_molecule` and `Topology.add_molecules` now return indices starting at 0. Previously, these indices started at 1, which does not match other indexing in the toolkit.
+- [PR #1926](https://github.com/openforcefield/openff-toolkit/pull/1926): Less noisy hints when the chemistry of a PDB file cannot be identified.
 
 ## 0.16.2
 

diff --git a/docs/users/pdb_cookbook/index.ipynb b/docs/users/pdb_cookbook/index.ipynb
@@ -240,10 +240,10 @@
    "outputs": [
     {
      "ename": "UnassignedChemistryInPDBError",
-     "evalue": "Some bonds or atoms in the input could not be identified.\n\nHint: The following residue names with unassigned atoms were not found in the substructure library. While the OpenFF Toolkit identifies residues by matching chemical substructures rather than by residue name, it currently only supports the 20 'canonical' amino acids.\n    JZ4\n\n\nHint: The following residues were assigned names that do not match the residue name in the input, or could not be assigned residue names at all. This may indicate that atoms are missing from the input or some other error. The OpenFF Toolkit requires all atoms, including hydrogens, to be explicit in the input to avoid ambiguities in protonation state or bond order:\n    Input residue X:JZ4#0001 contains atoms matching substructures {'No match'}\n\nError: The following 22 atoms exist in the input but could not be assigned chemical information from the substructure library:\n    Atom  2614 (C4) in residue X:JZ4#0001\n    Atom  2615 (C7) in residue X:JZ4#0001\n    Atom  2616 (C8) in residue X:JZ4#0001\n    Atom  2617 (C9) in residue X:JZ4#0001\n    Atom  2618 (C10) in residue X:JZ4#0001\n    Atom  2619 (C11) in residue X:JZ4#0001\n    Atom  2620 (C12) in residue X:JZ4#0001\n    Atom  2621 (C13) in residue X:JZ4#0001\n    Atom  2622 (C14) in residue X:JZ4#0001\n    Atom  2623 (OAB) in residue X:JZ4#0001\n    Atom  2624 (H1) in residue X:JZ4#0001\n    Atom  2625 (H2) in residue X:JZ4#0001\n    Atom  2626 (H3) in residue X:JZ4#0001\n    Atom  2627 (H4) in residue X:JZ4#0001\n    Atom  2628 (H5) in residue X:JZ4#0001\n    Atom  2629 (H6) in residue X:JZ4#0001\n    Atom  2630 (H7) in residue X:JZ4#0001\n    Atom  2631 (H8) in residue X:JZ4#0001\n    Atom  2632 (H9) in residue X:JZ4#0001\n    Atom  2633 (H10) in residue X:JZ4#0001\n    Atom  2634 (H11) in residue X:JZ4#0001\n    Atom  2635 (H12) in residue X:JZ4#0001\n",
+     "evalue": "Some bonds or atoms in the input could not be identified.\n\nHint: The following residue names with unassigned atoms were not found in the substructure library. While the OpenFF Toolkit identifies residues by matching chemical substructures rather than by residue name, it currently only supports the 20 'canonical' amino acids.\n    JZ4\n\n\nHint: The following residues were assigned names that do not match the residue name in the input, or could not be assigned residue names at all. This may indicate that atoms are missing from the input or some other error. The OpenFF Toolkit requires all atoms, including hydrogens, to be explicit in the input to avoid ambiguities in protonation state or bond order:\n    Input residue X:JZ4#0001 contains atoms matching substructures {'NO MATCH'}\n\nError: The following 22 atoms exist in the input but could not be assigned chemical information from the substructure library:\n    Atom  2614 (C4) in residue X:JZ4#0001\n    Atom  2615 (C7) in residue X:JZ4#0001\n    Atom  2616 (C8) in residue X:JZ4#0001\n    Atom  2617 (C9) in residue X:JZ4#0001\n    Atom  2618 (C10) in residue X:JZ4#0001\n    Atom  2619 (C11) in residue X:JZ4#0001\n    Atom  2620 (C12) in residue X:JZ4#0001\n    Atom  2621 (C13) in residue X:JZ4#0001\n    Atom  2622 (C14) in residue X:JZ4#0001\n    Atom  2623 (OAB) in residue X:JZ4#0001\n    Atom  2624 (H1) in residue X:JZ4#0001\n    Atom  2625 (H2) in residue X:JZ4#0001\n    Atom  2626 (H3) in residue X:JZ4#0001\n    Atom  2627 (H4) in residue X:JZ4#0001\n    Atom  2628 (H5) in residue X:JZ4#0001\n    Atom  2629 (H6) in residue X:JZ4#0001\n    Atom  2630 (H7) in residue X:JZ4#0001\n    Atom  2631 (H8) in residue X:JZ4#0001\n    Atom  2632 (H9) in residue X:JZ4#0001\n    Atom  2633 (H10) in residue X:JZ4#0001\n    Atom  2634 (H11) in residue X:JZ4#0001\n    Atom  2635 (H12) in residue X:JZ4#0001\n",
      "output_type": "error",
      "traceback": [
-      "\u001b[0;31mUnassignedChemistryInPDBError\u001b[0m\u001b[0;31m:\u001b[0m Some bonds or atoms in the input could not be identified.\n\nHint: The following residue names with unassigned atoms were not found in the substructure library. While the OpenFF Toolkit identifies residues by matching chemical substructures rather than by residue name, it currently only supports the 20 'canonical' amino acids.\n    JZ4\n\n\nHint: The following residues were assigned names that do not match the residue name in the input, or could not be assigned residue names at all. This may indicate that atoms are missing from the input or some other error. The OpenFF Toolkit requires all atoms, including hydrogens, to be explicit in the input to avoid ambiguities in protonation state or bond order:\n    Input residue X:JZ4#0001 contains atoms matching substructures {'No match'}\n\nError: The following 22 atoms exist in the input but could not be assigned chemical information from the substructure library:\n    Atom  2614 (C4) in residue X:JZ4#0001\n    Atom  2615 (C7) in residue X:JZ4#0001\n    Atom  2616 (C8) in residue X:JZ4#0001\n    Atom  2617 (C9) in residue X:JZ4#0001\n    Atom  2618 (C10) in residue X:JZ4#0001\n    Atom  2619 (C11) in residue X:JZ4#0001\n    Atom  2620 (C12) in residue X:JZ4#0001\n    Atom  2621 (C13) in residue X:JZ4#0001\n    Atom  2622 (C14) in residue X:JZ4#0001\n    Atom  2623 (OAB) in residue X:JZ4#0001\n    Atom  2624 (H1) in residue X:JZ4#0001\n    Atom  2625 (H2) in residue X:JZ4#0001\n    Atom  2626 (H3) in residue X:JZ4#0001\n    Atom  2627 (H4) in residue X:JZ4#0001\n    Atom  2628 (H5) in residue X:JZ4#0001\n    Atom  2629 (H6) in residue X:JZ4#0001\n    Atom  2630 (H7) in residue X:JZ4#0001\n    Atom  2631 (H8) in residue X:JZ4#0001\n    Atom  2632 (H9) in residue X:JZ4#0001\n    Atom  2633 (H10) in residue X:JZ4#0001\n    Atom  2634 (H11) in residue X:JZ4#0001\n    Atom  2635 (H12) in residue X:JZ4#0001\n\n"
+      "\u001b[0;31mUnassignedChemistryInPDBError\u001b[0m\u001b[0;31m:\u001b[0m Some bonds or atoms in the input could not be identified.\n\nHint: The following residue names with unassigned atoms were not found in the substructure library. While the OpenFF Toolkit identifies residues by matching chemical substructures rather than by residue name, it currently only supports the 20 'canonical' amino acids.\n    JZ4\n\n\nHint: The following residues were assigned names that do not match the residue name in the input, or could not be assigned residue names at all. This may indicate that atoms are missing from the input or some other error. The OpenFF Toolkit requires all atoms, including hydrogens, to be explicit in the input to avoid ambiguities in protonation state or bond order:\n    Input residue X:JZ4#0001 contains atoms matching substructures {'NO MATCH'}\n\nError: The following 22 atoms exist in the input but could not be assigned chemical information from the substructure library:\n    Atom  2614 (C4) in residue X:JZ4#0001\n    Atom  2615 (C7) in residue X:JZ4#0001\n    Atom  2616 (C8) in residue X:JZ4#0001\n    Atom  2617 (C9) in residue X:JZ4#0001\n    Atom  2618 (C10) in residue X:JZ4#0001\n    Atom  2619 (C11) in residue X:JZ4#0001\n    Atom  2620 (C12) in residue X:JZ4#0001\n    Atom  2621 (C13) in residue X:JZ4#0001\n    Atom  2622 (C14) in residue X:JZ4#0001\n    Atom  2623 (OAB) in residue X:JZ4#0001\n    Atom  2624 (H1) in residue X:JZ4#0001\n    Atom  2625 (H2) in residue X:JZ4#0001\n    Atom  2626 (H3) in residue X:JZ4#0001\n    Atom  2627 (H4) in residue X:JZ4#0001\n    Atom  2628 (H5) in residue X:JZ4#0001\n    Atom  2629 (H6) in residue X:JZ4#0001\n    Atom  2630 (H7) in residue X:JZ4#0001\n    Atom  2631 (H8) in residue X:JZ4#0001\n    Atom  2632 (H9) in residue X:JZ4#0001\n    Atom  2633 (H10) in residue X:JZ4#0001\n    Atom  2634 (H11) in residue X:JZ4#0001\n    Atom  2635 (H12) in residue X:JZ4#0001\n\n"
      ]
     }
    ],

diff --git a/openff/toolkit/utils/exceptions.py b/openff/toolkit/utils/exceptions.py
@@ -604,7 +604,7 @@ def assigned_residue_name_mismatch_hint(self) -> list[str]:
             input_chain: str = atom.residue.chain.id
             matched_resnames = self.matches[atom.index]
             # Only the first match is assigned, so throw out the others
-            assigned_resname = next(iter(matched_resnames), "No match")
+            assigned_resname = next(iter(matched_resnames), "No match").upper()
 
             residues[(input_resname, input_resnum, input_chain)].add(assigned_resname)