Merge pull request #35 from radifar/add-ruff

style: add ruff
radifar · Jan 18, 2025 · 5ee46e9 · 5ee46e9
2 parents 53191bc + c064992
commit 5ee46e9
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diff --git a/docs/conf.py b/docs/conf.py
@@ -6,9 +6,9 @@
 
 # -- Project information -----------------------------------------------------
 
-project = u"pilah"
-copyright = u"2024, Muhammad Radifar & Enade Perdana Istyastono"
-author = u"Muhammad Radifar"
+project = "pilah"
+copyright = "2024, Muhammad Radifar & Enade Perdana Istyastono"
+author = "Muhammad Radifar"
 
 # -- General configuration ---------------------------------------------------
 
@@ -38,4 +38,3 @@
     "light_logo": "PiLAH_web.png",
     "dark_logo": "PiLAH_web.png",
 }
-
diff --git a/pyi_rth_obdata.py b/pyi_rth_obdata.py
@@ -5,6 +5,6 @@
 pyinstaller_temp_dir = sys._MEIPASS
 ob_temp_dir = os.path.join(pyinstaller_temp_dir, "Openbabel")
 
-os.environ["BABEL_DATADIR"] = os.path.join(ob_temp_dir, 'data')
+os.environ["BABEL_DATADIR"] = os.path.join(ob_temp_dir, "data")
 os.environ["BABEL_LIBDIR"] = ob_temp_dir
-os.environ["PATH"] = ob_temp_dir + ";" + os.environ["PATH"]
+os.environ["PATH"] = ob_temp_dir + ";" + os.environ["PATH"]
diff --git a/src/pilah/__init__.py b/src/pilah/__init__.py
@@ -1,3 +1,4 @@
 # read version from installed package
 from importlib.metadata import version
-__version__ = version("pilah")
+
+__version__ = version("pilah")
diff --git a/src/pilah/atom_names.py b/src/pilah/atom_names.py
@@ -17,6 +17,21 @@
     "SER": {"C", "O", "CA", "N", "CB", "OG"},
     "THR": {"C", "O", "CA", "N", "CB", "CG2", "OG1"},
     "VAL": {"C", "O", "CA", "N", "CB", "CG1", "CG2"},
-    "TRP": {"C", "O", "CA", "N", "CB", "CG", "CD1", "NE1", "CE2", "CD2", "CE3", "CZ3", "CH2", "CZ2"},
+    "TRP": {
+        "C",
+        "O",
+        "CA",
+        "N",
+        "CB",
+        "CG",
+        "CD1",
+        "NE1",
+        "CE2",
+        "CD2",
+        "CE3",
+        "CZ3",
+        "CH2",
+        "CZ2",
+    },
     "TYR": {"C", "O", "CA", "N", "CB", "CG", "CD1", "CE1", "CZ", "OH", "CE2", "CD2"},
-}
+}
diff --git a/src/pilah/dimorphite_dl/dimorphite_dl.py b/src/pilah/dimorphite_dl/dimorphite_dl.py
@@ -30,6 +30,7 @@
 
 RDLogger.DisableLog("rdApp.*")
 
+
 def print_header():
     """Prints out header information."""
     # Always let the user know a help file is available.
@@ -292,7 +293,7 @@ def neutralize_mol(mol):
             [
                 "[H]-[N:1]-[N:2]#[N:3]",
                 "[N:1]=[N+1:2]=[N:3]-[H]",
-            ]  # To handle bad azide. R-N-N#N should
+            ],  # To handle bad azide. R-N-N#N should
             # be R-N=[N+]=N
         ]
 
@@ -897,7 +898,10 @@ def set_protonation_charge(mols, idx, charges, prot_site_name):
                 try:
                     mol_copy = Chem.RemoveHs(mol_copy)
                 except:
-                    if "silent" in ProtSubstructFuncs.args and not ProtSubstructFuncs.args["silent"]:
+                    if (
+                        "silent" in ProtSubstructFuncs.args
+                        and not ProtSubstructFuncs.args["silent"]
+                    ):
                         UtilFuncs.eprint(
                             "WARNING: Skipping poorly formed SMILES string: "
                             + Chem.MolToSmiles(mol_copy)
@@ -1108,7 +1112,7 @@ def test():
             "pka_precision": 0.5,
             "smiles": "",
             "label_states": True,
-            "silent": True
+            "silent": True,
         }
 
         for smi, protonated, deprotonated, category in smis:
@@ -1252,7 +1256,7 @@ def test():
                             "min_ph": ph,
                             "max_ph": ph,
                             "pka_precision": 0,
-                            "silent": True
+                            "silent": True,
                         }
                     )
                 )

diff --git a/src/pilah/element.py b/src/pilah/element.py
@@ -1,16 +1,68 @@
-metal_list = ["CA", "CO", "CU", "FE", "K", "MG", "MN", "NA", "NI",
-              "ZN", "AG", "AL", "AU", "BA", "BE", "CD", "CR", "CS",
-              "GA", "GD", "HG", "IR", "LI", "MO", "PB", "PD", "PR",
-              "PT", "RB", "RE", "RH", "RU", "SR", "TB", "TL", "U",
-              "V", "W", "Y", "YB"]
+metal_list = [
+    "CA",
+    "CO",
+    "CU",
+    "FE",
+    "K",
+    "MG",
+    "MN",
+    "NA",
+    "NI",
+    "ZN",
+    "AG",
+    "AL",
+    "AU",
+    "BA",
+    "BE",
+    "CD",
+    "CR",
+    "CS",
+    "GA",
+    "GD",
+    "HG",
+    "IR",
+    "LI",
+    "MO",
+    "PB",
+    "PD",
+    "PR",
+    "PT",
+    "RB",
+    "RE",
+    "RH",
+    "RU",
+    "SR",
+    "TB",
+    "TL",
+    "U",
+    "V",
+    "W",
+    "Y",
+    "YB",
+]
 
 # These charges are based on the ion charge in RCSB PDB page for
 # each corresponding ion.
 
 positive_one = ["LI", "NA", "K", "RB", "CS", "AU", "TL"]
 
-positive_two = ["BE", "MG", "CA", "SR", "BA", "MN", "ZN", "CO", "NI",
-                "PD", "PT", "CU", "CD", "HG", "PB"]
+positive_two = [
+    "BE",
+    "MG",
+    "CA",
+    "SR",
+    "BA",
+    "MN",
+    "ZN",
+    "CO",
+    "NI",
+    "PD",
+    "PT",
+    "CU",
+    "CD",
+    "HG",
+    "PB",
+]
 
 positive_three = ["V", "CR", "FE", "RU", "SB", "SM", "Y"]