linting

biopandas/mol2/__init__.py

@@ -9,7 +9,7 @@
 files in pandas DataFrames.
 """
 
-from .pandas_mol2 import PandasMol2
 from .mol2_io import split_multimol2
+from .pandas_mol2 import PandasMol2
 
 __all__ = ["PandasMol2", "split_multimol2"]

biopandas/mol2/pandas_mol2.py

@@ -1,14 +1,15 @@
 """ Class for working with Tripos MOL2 files"""
+
 # BioPandas
 # Author: Sebastian Raschka <[email protected]>
 # License: BSD 3 clause
 # Project Website: http://rasbt.github.io/biopandas/
 # Code Repository: https://github.com/rasbt/biopandas
 
-import pandas as pd
 import numpy as np
-from .mol2_io import split_multimol2
+import pandas as pd
 
+from .mol2_io import split_multimol2
 
 COLUMN_NAMES = (
     "atom_id",
@@ -167,7 +168,9 @@ def read_mol2_from_list(self, mol2_lines, mol2_code, columns=None):
     def _construct_df(self, mol2_lines, col_names, col_types):
         """Construct DataFrames from list of PDB lines."""
         return self._atomsection_to_pandas(
-            self._get_atomsection(mol2_lines), col_names=col_names, col_types=col_types
+            self._get_atomsection(mol2_lines),
+            col_names=col_names,
+            col_types=col_types,
         )
 
     @staticmethod
@@ -195,7 +198,9 @@ def _get_atomsection(mol2_lst):
     @staticmethod
     def _atomsection_to_pandas(mol2_atom_lst, col_names, col_types):
 
-        df = pd.DataFrame([lst.split() for lst in mol2_atom_lst], columns=col_names)
+        df = pd.DataFrame(
+            [lst.split() for lst in mol2_atom_lst], columns=col_names
+        )
 
         for i in range(df.shape[1]):
             df[col_names[i]] = df[col_names[i]].astype(col_types[i])
@@ -281,4 +286,6 @@ def distance_df(df, xyz=(0.00, 0.00, 0.00)):
 
         """
 
-        return np.sqrt(np.sum(df[["x", "y", "z"]].subtract(xyz, axis=1) ** 2, axis=1))
+        return np.sqrt(
+            np.sum(df[["x", "y", "z"]].subtract(xyz, axis=1) ** 2, axis=1)
+        )

biopandas/mol2/tests/test_mol2_io.py

@@ -5,6 +5,7 @@
 # Code Repository: https://github.com/rasbt/biopandas
 
 import os
+
 from biopandas.mol2.mol2_io import split_multimol2
 from biopandas.testutils import assert_raises
 
@@ -13,15 +14,19 @@
 
 def test_split_multimol2():
     all_mol2 = []
-    for i in split_multimol2(os.path.join(this_dir, "data", "40_mol2_files.mol2")):
+    for i in split_multimol2(
+        os.path.join(this_dir, "data", "40_mol2_files.mol2")
+    ):
         all_mol2.append(i[0])
     assert all_mol2[1] == "ZINC04084113"
     assert len(all_mol2) == 40
 
 
 def test_split_multimol2_wrong_format():
 
-    expect = "Wrong file format;" "allowed file formats are .mol2 and .mol2.gz."
+    expect = (
+        "Wrong file format;" "allowed file formats are .mol2 and .mol2.gz."
+    )
 
     def run_code():
         next(split_multimol2("40_mol2_files.pdb"))
@@ -31,7 +36,9 @@ def run_code():
 
 def test_split_multimol2_gz():
     all_mol2 = []
-    for i in split_multimol2(os.path.join(this_dir, "data", "40_mol2_files.mol2.gz")):
+    for i in split_multimol2(
+        os.path.join(this_dir, "data", "40_mol2_files.mol2.gz")
+    ):
         all_mol2.append(i[0])
     assert all_mol2[1].decode() == "ZINC04084113"
     assert len(all_mol2) == 40

biopandas/mol2/tests/test_pandas_mol2.py

@@ -1,11 +1,13 @@
 """ Utility function for reading Tripos MOL2 files from files"""
+
 # BioPandas
 # Author: Sebastian Raschka <[email protected]>
 # License: BSD 3 clause
 # Project Website: http://rasbt.github.io/biopandas/
 # Code Repository: https://github.com/rasbt/biopandas
 
 import os
+
 from biopandas.mol2 import PandasMol2
 from biopandas.mol2.mol2_io import split_multimol2
 from biopandas.testutils import assert_raises
@@ -48,7 +50,9 @@ def test_read_mol2_from_list():
     data_path = os.path.join(this_dir, "data", "40_mol2_files.mol2")
     mol2 = next(split_multimol2(data_path))
 
-    pdmol = PandasMol2().read_mol2_from_list(mol2_lines=mol2[1], mol2_code=mol2[0])
+    pdmol = PandasMol2().read_mol2_from_list(
+        mol2_lines=mol2[1], mol2_code=mol2[0]
+    )
     assert pdmol.df.shape == (65, 9)
     assert pdmol.code == "ZINC38611810"