chore: formatting and linting

prolif/ifp.py

@@ -2,6 +2,7 @@
 Storing interactions --- :mod:`prolif.ifp`
 ==========================================
 """
+
 from collections import UserDict
 
 from prolif.residue import ResidueId

prolif/interactions/base.py

@@ -4,6 +4,7 @@
 
 This module contains the base classes used to build most of the interactions.
 """
+
 import warnings
 from itertools import product
 from math import degrees, radians

prolif/interactions/interactions.py

@@ -64,9 +64,7 @@ class Hydrophobic(Distance):
 
     def __init__(
         self,
-        hydrophobic=(
-            "[c,s,Br,I,S&H0&v2," "$([D3,D4;#6])&!$([#6]~[#7,#8,#9])&!$([#6X4H0]);+0]"
-        ),
+        hydrophobic="[c,s,Br,I,S&H0&v2,$([D3,D4;#6])&!$([#6]~[#7,#8,#9])&!$([#6X4H0]);+0]",
         distance=4.5,
     ):
         super().__init__(
@@ -99,11 +97,7 @@ class HBAcceptor(SingleAngle):
 
     def __init__(
         self,
-        acceptor=(
-            "[#7&!$([nX3])&!$([NX3]-*=[O,N,P,S])&!$([NX3]-[a])&!$([Nv4&+1]),"
-            "O&!$([OX2](C)C=O)&!$(O(~a)~a)&!$(O=N-*)&!$([O-]-N=O),o+0,"
-            "F&$(F-[#6])&!$(F-[#6][F,Cl,Br,I])]"
-        ),
+        acceptor="[#7&!$([nX3])&!$([NX3]-*=[O,N,P,S])&!$([NX3]-[a])&!$([Nv4&+1]),O&!$([OX2](C)C=O)&!$(O(~a)~a)&!$(O=N-*)&!$([O-]-N=O),o+0,F&$(F-[#6])&!$(F-[#6][F,Cl,Br,I])]",
         donor="[$([O,S;+0]),$([N;v3,v4&+1]),n+0]-[H]",
         distance=3.5,
         DHA_angle=(130, 180),

prolif/molecule.py

@@ -2,6 +2,7 @@
 Reading proteins and ligands --- :mod:`prolif.molecule`
 =======================================================
 """
+
 import copy
 from collections import defaultdict
 from collections.abc import Sequence
@@ -116,7 +117,7 @@ def from_mda(cls, obj, selection=None, **kwargs):
         """
         ag = obj.select_atoms(selection) if selection else obj.atoms
         if ag.n_atoms == 0:
-            raise mda.SelectionError(f"AtomGroup is empty, please check your selection")
+            raise mda.SelectionError("AtomGroup is empty, please check your selection")
         mol = ag.convert_to.rdkit(**kwargs)
         return cls(mol)
 

prolif/parallel.py

@@ -7,6 +7,7 @@
 in :meth:`~prolif.fingerprint.Fingerprint.run` and
 :meth:`~prolif.fingerprint.Fingerprint.run_from_iterable` respectively.
 """
+
 from ctypes import c_uint32
 from threading import Event, Thread
 from time import sleep

prolif/pickling.py

@@ -9,6 +9,7 @@
 behavior upon importing the `prolif` package to ensure that the parallelization code
 works as on other platforms.
 """
+
 import sys
 from typing import Optional
 

prolif/plotting/barcode.py

@@ -8,6 +8,7 @@
    :members:
 
 """
+
 from __future__ import annotations
 
 from typing import TYPE_CHECKING, ClassVar, Dict, List, Literal, Optional, Tuple
@@ -73,9 +74,9 @@ def _bit_to_color_value(s: pd.Series) -> pd.Series:
             """Replaces a bit value with it's corresponding color value"""
             interaction = s.name[-1]
             return s.apply(
-                lambda v: self.color_mapper[interaction]
-                if v
-                else self.color_mapper[None]
+                lambda v: (
+                    self.color_mapper[interaction] if v else self.color_mapper[None]
+                )
             )
 
         self.df = df.astype(np.uint8).T.apply(_bit_to_color_value, axis=1)
@@ -85,7 +86,8 @@ def from_fingerprint(cls, fp: Fingerprint) -> Barcode:
         """Creates a barcode object from a fingerprint."""
         if not hasattr(fp, "ifp"):
             raise RunRequiredError(
-                "Please run the fingerprint analysis before attempting to display results."
+                "Please run the fingerprint analysis before attempting to display"
+                " results."
             )
         return cls(fp.to_dataframe())
 

prolif/plotting/complex3d.py

@@ -8,6 +8,7 @@
    :members:
 
 """
+
 from __future__ import annotations
 
 from copy import deepcopy
@@ -101,7 +102,8 @@ class Complex3D:
     PROTEIN_RING_INTERACTIONS: ClassVar[Set[str]] = {*RING_SYSTEMS, "CationPi"}
     RESIDUE_HOVER_CALLBACK: ClassVar[
         str
-    ] = """function(atom,viewer) {
+    ] = """
+    function(atom,viewer) {
         if(!atom.label) {
             atom.label = viewer.addLabel('%s:'+atom.atom+atom.serial,
                 {position: atom, backgroundColor: 'mintcream', fontColor:'black'});
@@ -157,7 +159,8 @@ def from_fingerprint(
         """
         if not hasattr(fp, "ifp"):
             raise RunRequiredError(
-                "Please run the fingerprint analysis before attempting to display results."
+                "Please run the fingerprint analysis before attempting to display"
+                " results."
             )
         ifp = fp.ifp[frame]
         return cls(ifp, lig_mol, prot_mol)

prolif/plotting/network.py

@@ -317,7 +317,8 @@ def from_fingerprint(
         """
         if not hasattr(fp, "ifp"):
             raise RunRequiredError(
-                "Please run the fingerprint analysis before attempting to display results."
+                "Please run the fingerprint analysis before attempting to display"
+                " results."
             )
         if kind == "frame":
             df = cls._make_frame_df_from_fp(fp, frame=frame, display_all=display_all)
@@ -790,9 +791,7 @@ def _get_legend(self, height="90px"):
         });
         legend.appendChild(div_residues);
         legend.appendChild(div_interactions);
-        """ % dict(
-            div_id="networklegend", buttons=json.dumps(buttons)
-        )
+        """ % dict(div_id="networklegend", buttons=json.dumps(buttons))
 
     @requires("IPython.display")
     def display(self, **kwargs):

prolif/plotting/residues.py

@@ -7,6 +7,7 @@
 .. autofunction:: display_residues
 
 """
+
 from typing import Any, Optional, Tuple
 
 from rdkit import Chem

prolif/rdkitmol.py

@@ -2,6 +2,7 @@
 Reading RDKit molecules --- :mod:`prolif.rdkitmol`
 ==================================================
 """
+
 from rdkit import Chem
 from rdkit.Chem.rdMolTransforms import ComputeCentroid
 

prolif/residue.py

@@ -2,6 +2,7 @@
 Residue-related classes --- :mod:`prolif.residue`
 =================================================
 """
+
 import re
 from collections import UserDict
 from typing import List, Optional
@@ -182,8 +183,7 @@ def __getitem__(self, key):
         # bool is a subclass of int but shouldn't be used here
         if isinstance(key, bool):
             raise KeyError(
-                "Expected a ResidueId, int, or str, "
-                f"got {type(key).__name__!r} instead"
+                f"Expected a ResidueId, int, or str, got {type(key).__name__!r} instead"
             )
         if isinstance(key, int):
             return self._residues[key]
@@ -193,7 +193,7 @@ def __getitem__(self, key):
         elif isinstance(key, ResidueId):
             return self.data[key]
         raise KeyError(
-            "Expected a ResidueId, int, or str, " f"got {type(key).__name__!r} instead"
+            f"Expected a ResidueId, int, or str, got {type(key).__name__!r} instead"
         )
 
     def select(self, mask):

prolif/utils.py

@@ -2,6 +2,7 @@
 Helper functions --- :mod:`prolif.utils`
 ========================================
 """
+
 import warnings
 from collections import defaultdict
 from contextlib import contextmanager