Lint utilities/ subdirectory (#1891)

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 ci:
   autoupdate_schedule: "quarterly"
-files: ^openff|(^examples/((?!deprecated).)*$)|^docs
+files: ^openff|(^examples/((?!deprecated).)*$)|^docs|(^utilities/((?!deprecated).)*$)
 repos:
 - repo: https://github.com/psf/black
   rev: 24.3.0
@@ -15,7 +15,7 @@ repos:
   rev: 7.0.0
   hooks:
   - id: flake8
-    files: ^openff
+    files: ^openff|(^utilities/((?!deprecated).)*$)
     additional_dependencies: [
         'flake8-absolute-import',
         'flake8-no-pep420',

utilities/make_substructure_dict/_cif_to_substructure_dict.py

@@ -5,20 +5,21 @@
 """
 
 import copy
-from copy import deepcopy
 import json
-from collections import defaultdict, OrderedDict
+from collections import OrderedDict, defaultdict
+from copy import deepcopy
 
 import rdkit
-from rdkit import Chem
 from CifFile import ReadCif
 from openff.units.elements import SYMBOLS
+from rdkit import Chem
 
 from openff.toolkit import Molecule
 from openff.toolkit.utils.rdkit_wrapper import RDKitToolkitWrapper
 
 _SYMBOL_TO_ATOMIC_NUMBER = {v: k for k, v in SYMBOLS.items()}
 
+
 # Amber ff porting functions
 def remove_charge_and_bond_order_from_guanidinium(rdmol):
     """
@@ -677,7 +678,7 @@ def _patch_known_problems(self):
         }
         # Fix PRO smarts substructure
         for aa_name, replacement_list in substructures_to_fix.items():
-            for (old_smarts, new_smarts) in replacement_list:
+            for old_smarts, new_smarts in replacement_list:
                 self.data[aa_name][new_smarts] = self.data[aa_name][old_smarts]
                 self.data[aa_name].pop(old_smarts)
 
@@ -719,7 +720,13 @@ def _reformat_substructs(self):
         Implemented 7/7/23: add-on to existing substructure library to reformat amino acids
             to a new format. Self contained for now to the following function:
         """
-        def add_atom(rdmol, begin_atom_idx, new_atom_smarts, bond_order=Chem.rdchem.BondType.SINGLE):
+
+        def add_atom(
+            rdmol,
+            begin_atom_idx,
+            new_atom_smarts,
+            bond_order=Chem.rdchem.BondType.SINGLE,
+        ):
             # adds atom with single bond, returns new mol
             emol = Chem.RWMol(deepcopy(rdmol))
             new_atom = Chem.AtomFromSmarts(new_atom_smarts)
@@ -735,10 +742,29 @@ def _fill_out_query(rdmol):
             params = Chem.SmilesParserParams()
             params.removeHs = False
             params.sanitize = True
-            rdmol = Chem.MolFromSmiles(Chem.MolToSmiles(deepcopy(rdmol), isomericSmiles=False, kekuleSmiles=True, canonical=False), params) # create non-query version of substruct
-            Chem.Kekulize(rdmol, clearAromaticFlags=True) # kekulize using molops (regular molecule required here)
-            rdmol = Chem.MolFromSmarts(Chem.MolToSmiles(deepcopy(rdmol), isomericSmiles=False, kekuleSmiles=True, canonical=False)) # remake into query mol
-            current_map_num = 1 + _get_maximum_map_num(rdmol) # do not change existing atom map numbers! 
+            rdmol = Chem.MolFromSmiles(
+                Chem.MolToSmiles(
+                    deepcopy(rdmol),
+                    isomericSmiles=False,
+                    kekuleSmiles=True,
+                    canonical=False,
+                ),
+                params,
+            )  # create non-query version of substruct
+            Chem.Kekulize(
+                rdmol, clearAromaticFlags=True
+            )  # kekulize using molops (regular molecule required here)
+            rdmol = Chem.MolFromSmarts(
+                Chem.MolToSmiles(
+                    deepcopy(rdmol),
+                    isomericSmiles=False,
+                    kekuleSmiles=True,
+                    canonical=False,
+                )
+            )  # remake into query mol
+            current_map_num = 1 + _get_maximum_map_num(
+                rdmol
+            )  # do not change existing atom map numbers!
             for atom in rdmol.GetAtoms():
                 if atom.GetAtomicNum() > 0:
                     if atom.GetAtomMapNum() == 0:
@@ -760,13 +786,12 @@ def _fill_out_query(rdmol):
                 else:
                     raise Exception
             for bond in rdmol.GetBonds():
-                if bond.GetBondType() == Chem.rdchem.BondType.AROMATIC: 
-                    raise Exception # there should be no aromatic bonds unless kekulization has failed 
+                if bond.GetBondType() == Chem.rdchem.BondType.AROMATIC:
+                    raise Exception  # there should be no aromatic bonds unless kekulization has failed
                 elif bond.GetBondType() == Chem.rdchem.BondType.SINGLE:
                     query = Chem.BondFromSmarts("-")
                     bond.SetQuery(query)
-
-
+
             return rdmol
 
         def get_atom_with_map_num(rdmol, map_num):
@@ -786,32 +811,156 @@ def clear_query(rdmol):
 
         new_subs_dict = OrderedDict()
         #               = [(Smarts without terminal groups   , [ids to add port to],       [ids to add H to],            [id of amide bond carbon])]
-        amino_acid_subs = [(Chem.MolFromSmarts("[N+:1](-[H])(-[H])1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"), [], [], 4),
-                        (Chem.MolFromSmarts("[N+0:1](-[H])1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"), [], [], 3),
-                        (Chem.MolFromSmarts("[N+1:1](-[H])1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"), [0], [], 3),
-                        (Chem.MolFromSmarts("[N+0:1]1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"), [0], [], 2),
-                        (Chem.MolFromSmarts("[N+](-[H])(-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"), [], [], 5),
-                        (Chem.MolFromSmarts("[N+](-[H])(-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"), [8], [], 5),
-                        (Chem.MolFromSmarts("[N+](-[H])(-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"), [], [], 5),
-                        (Chem.MolFromSmarts("[N](-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"), [], [], 4),
-                        (Chem.MolFromSmarts("[N](-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"), [7], [], 4),
-                        (Chem.MolFromSmarts("[N](-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"), [], [], 4),
-                        (Chem.MolFromSmarts("[N](-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"), [0], [], 3),
-                        (Chem.MolFromSmarts("[N](-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"), [0, 6], [], 3),
-                        (Chem.MolFromSmarts("[N](-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"), [0], [], 3),
-                        (Chem.MolFromSmarts("[N:1][C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"), [0,0], [], 2),
-                        (Chem.MolFromSmarts("[N:1][C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"), [0,0, 5], [], 2),
-                        (Chem.MolFromSmarts("[N:1][C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"), [0,0], [], 2),
-                        (Chem.MolFromSmarts("[N+](-[H])(-[H])(-[H])-[C@](-[H])(-[*])-[C](=[O])"), [], [], 7),
-                        (Chem.MolFromSmarts("[N](-[H])(-[H])-[C@](-[H])(-[*])-[C](=[O])"), [], [], 6),
-                        (Chem.MolFromSmarts("[N](-[H])-[C@](-[H])(-[*])-[C](=[O])"), [0], [], 5),
-                        ]
-        special_cases = {'[C:1](=[O:2])[C:3]([H:4])([H:5])[H:6]': '[*]-[C:1](=[O:2])[C:3]([H:4])([H:5])[H:6]',
-                        '[N:1]([C:2]([H:4])([H:5])[H:6])[H:3]': '[*]-[N:1]([C:2]([H:4])([H:5])[H:6])[H:3]',
-                        '[N:1]([H:2])[H:3]': '[*]-C(=O)[N:1]([H:2])[H:3]',
-                        '[C:1](=[O:2])[N:3]': '[*]-[C:1](=[O:2])[N:3](-[H])[C:4](-[*])(-[*])(-[*])',
-                        '[S:1][S:2]': '[*]-[S:1]-[S:2]-[*]',
-                        }
+        amino_acid_subs = [
+            (
+                Chem.MolFromSmarts(
+                    "[N+:1](-[H])(-[H])1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"
+                ),
+                [],
+                [],
+                4,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N+0:1](-[H])1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"
+                ),
+                [],
+                [],
+                3,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N+1:1](-[H])1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"
+                ),
+                [0],
+                [],
+                3,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N+0:1]1[C@@:2]([C:3](=[O:4]))([H:9])[C:5]([H:10])([H:11])[C:6]([H:12])([H:13])[C:7]1([H:14])[H:15]"
+                ),
+                [0],
+                [],
+                2,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N+](-[H])(-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"
+                ),
+                [],
+                [],
+                5,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N+](-[H])(-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"
+                ),
+                [8],
+                [],
+                5,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N+](-[H])(-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"
+                ),
+                [],
+                [],
+                5,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N](-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"
+                ),
+                [],
+                [],
+                4,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N](-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"
+                ),
+                [7],
+                [],
+                4,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N](-[H])(-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"
+                ),
+                [],
+                [],
+                4,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N](-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"
+                ),
+                [0],
+                [],
+                3,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N](-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"
+                ),
+                [0, 6],
+                [],
+                3,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N](-[H])-[C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"
+                ),
+                [0],
+                [],
+                3,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N:1][C@:2]([C:3](=[O:4]))([C:5]([S+0:6]([H]))([H:9])[H:10])[H:8]"
+                ),
+                [0, 0],
+                [],
+                2,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N:1][C@:2]([C:3](=[O:4]))([C:5]([S+0:6])([H:9])[H:10])[H:8]"
+                ),
+                [0, 0, 5],
+                [],
+                2,
+            ),
+            (
+                Chem.MolFromSmarts(
+                    "[N:1][C@:2]([C:3](=[O:4]))([C:5]([S-1:6])([H:9])[H:10])[H:8]"
+                ),
+                [0, 0],
+                [],
+                2,
+            ),
+            (
+                Chem.MolFromSmarts("[N+](-[H])(-[H])(-[H])-[C@](-[H])(-[*])-[C](=[O])"),
+                [],
+                [],
+                7,
+            ),
+            (
+                Chem.MolFromSmarts("[N](-[H])(-[H])-[C@](-[H])(-[*])-[C](=[O])"),
+                [],
+                [],
+                6,
+            ),
+            (Chem.MolFromSmarts("[N](-[H])-[C@](-[H])(-[*])-[C](=[O])"), [0], [], 5),
+        ]
+        special_cases = {
+            "[C:1](=[O:2])[C:3]([H:4])([H:5])[H:6]": "[*]-[C:1](=[O:2])[C:3]([H:4])([H:5])[H:6]",
+            "[N:1]([C:2]([H:4])([H:5])[H:6])[H:3]": "[*]-[N:1]([C:2]([H:4])([H:5])[H:6])[H:3]",
+            "[N:1]([H:2])[H:3]": "[*]-C(=O)[N:1]([H:2])[H:3]",
+            "[C:1](=[O:2])[N:3]": "[*]-[C:1](=[O:2])[N:3](-[H])[C:4](-[*])(-[*])(-[*])",
+            "[S:1][S:2]": "[*]-[S:1]-[S:2]-[*]",
+        }
         for res_name, subs in self.data.items():
             res_dict = OrderedDict()
             res_num = 0
@@ -831,7 +980,7 @@ def clear_query(rdmol):
                 if substruct in special_cases.keys():
                     if special_cases[substruct]:
                         rdmol = Chem.MolFromSmarts(special_cases[substruct])
-                    else: # empty, discard
+                    else:  # empty, discard
                         continue
                 else:
                     # add * where appropriate
@@ -844,14 +993,14 @@ def clear_query(rdmol):
                     carb = rdmol.GetAtomWithIdx(aa_match[carboxyl_C])
                     if carb.GetDegree() == 2:
                         rdmol = add_atom(rdmol, aa_match[carboxyl_C], "[*]")
-                formated_rdmol= _fill_out_query(rdmol)
+                formated_rdmol = _fill_out_query(rdmol)
                 # In this document, the only new atoms I add are *, so edit the atom names
                 num_new_atoms = formated_rdmol.GetNumAtoms() - len(atom_names)
-                atom_names = atom_names + ["*"]*num_new_atoms
+                atom_names = atom_names + ["*"] * num_new_atoms
                 sub_smarts = Chem.MolToSmarts(formated_rdmol)
                 res_num += 1
 
-                sub_smarts = sub_smarts.replace('&', '')
+                sub_smarts = sub_smarts.replace("&", "")
                 res_dict[sub_smarts] = atom_names
 
             new_subs_dict[res_name] = res_dict
@@ -861,7 +1010,9 @@ def clear_query(rdmol):
         for res_name, subs in new_subs_dict.items():
             res_num = 0
             for substruct, atom_names in subs.items():
-                check_dict[f"{res_name}_{res_num}"] = [ substruct ]
+                check_dict[f"{res_name}_{res_num}"] = [substruct]
                 res_num += 1
-        RDKitToolkitWrapper()._validate_custom_substructures(custom_substructures=check_dict, forbidden_keys=[]) # errors if any are invalid
+        RDKitToolkitWrapper()._validate_custom_substructures(
+            custom_substructures=check_dict, forbidden_keys=[]
+        )  # errors if any are invalid
         self.data = new_subs_dict

utilities/make_substructure_dict/_make_chemical_substructures.py

@@ -1,8 +1,10 @@
+# noqa: INP001
 import os
 
-from openff.toolkit.utils.utils import get_data_file_path
 from _cif_to_substructure_dict import CifSubstructures
 
+from openff.toolkit.utils.utils import get_data_file_path
+
 if not os.path.exists("aa-variants-v1.cif"):
     import requests
 
@@ -39,6 +41,7 @@
 cif_object._reformat_substructs()
 
 output_file = get_data_file_path("proteins/T4-protein.sdf").replace(
-    "T4-protein.sdf", "aa_residues_substructures_explicit_bond_orders_with_caps_explicit_connectivity.json"
+    "T4-protein.sdf",
+    "aa_residues_substructures_explicit_bond_orders_with_caps_explicit_connectivity.json",
 )
-cif_object.to_json_file(output_file)
+cif_object.to_json_file(output_file)

utilities/make_substructure_dict/_make_metadata_assignment_substructures.py

@@ -1,8 +1,10 @@
+# noqa: INP001
 import os
 
-from openff.toolkit.utils import get_data_file_path
 from _cif_to_substructure_dict import CifSubstructures
 
+from openff.toolkit.utils import get_data_file_path
+
 if not os.path.exists("aa-variants-v1.cif"):
     import requests
 

utilities/test_plugins/custom_plugins/handler_plugins.py

@@ -1,3 +1,4 @@
+# noqa: INP001
 from openff.toolkit.typing.engines.smirnoff import ParameterHandler, ParameterIOHandler
 from openff.toolkit.typing.engines.smirnoff.parameters import ParameterAttribute, ParameterType, _NonbondedHandler
 from openff.toolkit import unit

utilities/test_plugins/setup.py

@@ -1,7 +1,9 @@
+# noqa: INP001
 """
 openff-test-parameter-plugins
 A test package used to ensure that parameterhandler plugins are handled correctly
 """
+
 from setuptools import setup
 
 setup(