fixup! Fix remaining linter complaints

doc/bibliography.py

@@ -74,6 +74,6 @@ def format_article(self, param):
 
             return Text(*authors, title, journal, volume, pages, date, doi)
 
-        except Exception:
+        except:
             warnings.warn(f"Invalid BibTeX entry '{entry.key}'")
             return Text(entry.key)

doc/examples/scripts/structure/protein/peptide_assembly.py

@@ -40,84 +40,7 @@
 
 # Reference peptide bond atom coordinates taken from 1l2y:
 # CA, C, N, O, H
-peptide_coord = np.array(
-    [
-        [-8.608, 3.135, -1.618],
-        [-7.117, 2.964, -1.897],
-        [-6.379, 4.031, -2.228],
-        [-6.634, 1.849, -1.758],
-        [-6.821, 4.923, -2.394],
-    ]
-)
-
-
-def create_raw_backbone_coord(number_of_res):
-    """
-    Create coordinates for straight peptide chain in z-plane.
-    The peptide bonds are in trans configuration.
-    """
-    coord = np.zeros((number_of_res * 3, 3))
-    for i, angle, angle_direction, length in zip(
-        range(len(coord)),
-        itertools.cycle([CA_C_N_ANGLE, C_N_CA_ANGLE, N_CA_C_ANGLE]),
-        itertools.cycle([1, -1]),
-        itertools.cycle([C_N_LENGTH, N_CA_LENGTH, CA_C_LENGTH]),
-    ):
-        if i == 0:
-            coord[i] = [0, 0, 0]
-        elif i == 1:
-            coord[i] = [0, length, 0]
-        else:
-            # Rotate about z-axis -> backbone lies in z-plane
-            rot_axis = [0, 0, angle_direction]
-            # Calculate the coordinates of a new atoms by rotating the previous
-            # bond by the given angle
-            new_coord = struc.rotate_about_axis(
-                coord[i - 2],
-                axis=rot_axis,
-                angle=np.deg2rad(angle),
-                support=coord[i - 1],
-            )
-            # Scale bond to correct bond length
-            bond_vector = new_coord - coord[i - 1]
-            coord[i] = coord[i - 1] + bond_vector * length / norm(bond_vector)
-    return coord
-
-
-def append_residue(chain, residue):
-    """
-    Append a residue to an existing chain.
-    Modify annotation arrays and remove atoms as necessary.
-    The atom coordinates are not altered.
-    """
-    if chain.array_length() == 0:
-        # Chain is empty
-        residue.res_id[:] = 1
-        return residue
-
-    last_res_id = chain.res_id[-1]
-
-    # Remove atoms removed by peptide bond
-    chain = chain[
-        (chain.res_id != last_res_id) | ~np.isin(chain.atom_name, ["OXT", "HXT"])
-    ]
-    residue = residue[~np.isin(residue.atom_name, ["H2", "H3"])]
-
-    # Increment residue ID for attached residue
-    residue.res_id[:] = last_res_id + 1
-
-
-C_N_LENGTH = 1.34
-N_CA_LENGTH = 1.46
-CA_C_LENGTH = 1.54
-
-CA_C_N_ANGLE = 114
-C_N_CA_ANGLE = 123
-N_CA_C_ANGLE = 110
-
-# Reference peptide bond atom coordinates taken from 1l2y:
-# CA, C, N, O, H
-peptide_coord = np.array(
+PEPTIDE_COORD = np.array(
     [
         [-8.608, 3.135, -1.618],
         [-7.117, 2.964, -1.897],
@@ -221,9 +144,9 @@ def assemble_peptide(sequence):
                 for atom_name in ["N", "H"]
             ]
             _, transformation = struc.superimpose(
-                chain.coord[[ca_i, c_i, n_i]], peptide_coord[:3]
+                chain.coord[[ca_i, c_i, n_i]], PEPTIDE_COORD[:3]
             )
-            chain.coord[[o_i, h_i]] = transformation.apply(peptide_coord[3:])
+            chain.coord[[o_i, h_i]] = transformation.apply(PEPTIDE_COORD[3:])
     return chain
 
 

doc/scraper.py

@@ -63,8 +63,8 @@ def pymol_scraper(block, block_vars, gallery_conf):
         )
 
     try:
-        import ammolite
-        import pymol
+        import ammolite  # noqa: F401
+        import pymol  # noqa: F401
     except ImportError:
         # If Ammolite is not installed, fall back to the image file,
         # if already existing

doc/switcher.py

@@ -3,7 +3,7 @@
 # information.
 
 __author__ = "Patrick Kunzmann"
-__all__ = ["create_api_doc", "skip_non_methods"]
+__all__ = ["create_switcher_json"]
 
 import json
 import re

setup_ccd.py

@@ -1,8 +1,8 @@
 import gzip
 import logging
-from pathlib import Path
 from dataclasses import dataclass
 from io import StringIO
+from pathlib import Path
 import numpy as np
 import requests
 from biotite.structure.io.pdbx import *

src/biotite/__init__.py

@@ -14,5 +14,5 @@
 
 from .copyable import *
 from .file import *
-from .version import __version__, __version_tuple__
+from .version import __version__, __version_tuple__  # noqa: F401
 from .visualize import *

src/biotite/application/muscle/app3.py

@@ -10,6 +10,7 @@
 import re
 import subprocess
 import warnings
+from collections.abc import Sequence
 from tempfile import NamedTemporaryFile
 from biotite.application.application import AppState, VersionError, requires_state
 from biotite.application.localapp import cleanup_tempfile
@@ -136,7 +137,7 @@ def set_gap_penalty(self, gap_penalty):
                 raise ValueError("Gap penalty must be negative")
             self._gap_open = gap_penalty
             self._gap_ext = gap_penalty
-        elif type(gap_penalty) == tuple:
+        elif isinstance(gap_penalty, Sequence):
             if gap_penalty[0] > 0 or gap_penalty[1] > 0:
                 raise ValueError("Gap penalty must be negative")
             self._gap_open = gap_penalty[0]

src/biotite/sequence/align/alignment.py

@@ -7,6 +7,7 @@
 
 import numbers
 import textwrap
+from collections.abc import Sequence
 import numpy as np
 from biotite.sequence.alphabet import LetterAlphabet
 
@@ -519,10 +520,10 @@ def score(alignment, matrix, gap_penalty=-10, terminal_penalty=True):
                     score += matrix[code_i, code_j]
 
     # Sum gap penalties
-    if type(gap_penalty) == int:
+    if isinstance(gap_penalty, numbers.Real):
         gap_open = gap_penalty
         gap_ext = gap_penalty
-    elif type(gap_penalty) == tuple:
+    elif isinstance(gap_penalty, Sequence):
         gap_open = gap_penalty[0]
         gap_ext = gap_penalty[1]
     else:

src/biotite/sequence/codon.py

@@ -397,11 +397,11 @@ def load(table_name):
         for line in lines:
             if not line:
                 table_found = False
-            if type(table_name) == int and line.startswith("id"):
+            if isinstance(table_name, Integral) and line.startswith("id"):
                 # remove identifier 'id'
                 if table_name == int(line[2:]):
                     table_found = True
-            elif type(table_name) == str and line.startswith("name"):
+            elif isinstance(table_name, str) and line.startswith("name"):
                 # Get list of table names from lines
                 # (separated with ';')
                 # remove identifier 'name'

src/biotite/sequence/graphics/plasmid.py

@@ -252,7 +252,7 @@ def __init__(
                     bbox = Bbox.from_extents(0, 0, 0, 0)
                     # Draw features as curved arrows (feature indicator)
                     indicator = axes.add_artist(
-                        Feature_Indicator(
+                        FeatureIndicator(
                             axes,
                             self.zorder + 1,
                             feature,
@@ -340,7 +340,7 @@ def draw(self, renderer, *args, **kwargs):
                         )
                         indicator.set_bbox(bbox)
 
-    class Feature_Indicator(Artist):
+    class FeatureIndicator(Artist):
         def __init__(
             self,
             axes,

src/biotite/structure/__init__.py

@@ -129,4 +129,4 @@
 from .sse import *
 from .superimpose import *
 from .transform import *
-# util and resutil are used internally
+# util and segments are used internally

src/biotite/structure/chains.py

@@ -23,7 +23,14 @@
 ]
 
 import numpy as np
-from biotite.structure.resutil import *
+from biotite.structure.segments import (
+    apply_segment_wise,
+    get_segment_masks,
+    get_segment_positions,
+    get_segment_starts_for,
+    segment_iter,
+    spread_segment_wise,
+)
 
 
 def get_chain_starts(array, add_exclusive_stop=False):

src/biotite/structure/filter.py

@@ -491,7 +491,7 @@ def filter_first_altloc(atoms, altloc_ids):
     # And filter all atoms for each residue with the first altloc ID
     residue_starts = get_residue_starts(atoms, add_exclusive_stop=True)
     for start, stop in zip(residue_starts[:-1], residue_starts[1:]):
-        letter_altloc_ids = [l for l in altloc_ids[start:stop] if l.isalpha()]
+        letter_altloc_ids = [loc for loc in altloc_ids[start:stop] if loc.isalpha()]
         if len(letter_altloc_ids) > 0:
             first_id = letter_altloc_ids[0]
             altloc_filter[start:stop] |= altloc_ids[start:stop] == first_id
@@ -572,7 +572,7 @@ def filter_highest_occupancy_altloc(atoms, altloc_ids, occupancies):
         occupancies_in_res = occupancies[start:stop]
         altloc_ids_in_res = altloc_ids[start:stop]
 
-        letter_altloc_ids = [l for l in altloc_ids_in_res if l.isalpha()]
+        letter_altloc_ids = [loc for loc in altloc_ids_in_res if loc.isalpha()]
 
         if len(letter_altloc_ids) > 0:
             highest = -1.0

src/biotite/structure/io/pdbx/convert.py

@@ -895,7 +895,7 @@ def _determine_entity_id(chain_id):
     for i in range(len(chain_id)):
         try:
             entity_id[i] = id_translation[chain_id[i]]
-        except:
+        except KeyError:
             # chain_id is not in dictionary -> new entry
             id_translation[chain_id[i]] = id
             entity_id[i] = id_translation[chain_id[i]]

src/biotite/structure/residues.py

@@ -22,7 +22,14 @@
 ]
 
 import numpy as np
-from biotite.structure.resutil import *
+from biotite.structure.segments import (
+    apply_segment_wise,
+    get_segment_masks,
+    get_segment_positions,
+    get_segment_starts_for,
+    segment_iter,
+    spread_segment_wise,
+)
 
 
 def get_residue_starts(array, add_exclusive_stop=False):

src/biotite/visualize.py

@@ -85,7 +85,7 @@ def __init__(self, text, width, height, mode):
             self._width = width
             self._height = height
 
-        def draw_path(self, renderer, gc, tpath, affine, rgbFace=None):
+        def draw_path(self, renderer, gc, tpath, affine, rgbFace=None):  # noqa: N803
             ax = self._text.axes
             try:
                 renderer = ax.get_figure().canvas.get_renderer()

tests/structure/test_basepairs.py

@@ -100,8 +100,8 @@ def test_base_pairs_reverse(nuc_sample_array, basepairs, unique_bool):
 
     # Reverse sequence of residues in nuc_sample_array
     reversed_nuc_sample_array = struc.AtomArray(0)
-    for residue in reversed_iterator(struc.residue_iter(nuc_sample_array)):
-        reversed_nuc_sample_array = reversed_nuc_sample_array + residue
+    for res in reversed_iterator(struc.residue_iter(nuc_sample_array)):
+        reversed_nuc_sample_array = reversed_nuc_sample_array + res
 
     computed_basepairs = struc.base_pairs(reversed_nuc_sample_array, unique=unique_bool)
     check_residue_starts(computed_basepairs, reversed_nuc_sample_array)
@@ -117,8 +117,8 @@ def test_base_pairs_reverse_no_hydrogen(nuc_sample_array, basepairs):
     nuc_sample_array = nuc_sample_array[nuc_sample_array.element != "H"]
     # Reverse sequence of residues in nuc_sample_array
     reversed_nuc_sample_array = struc.AtomArray(0)
-    for residue in reversed_iterator(struc.residue_iter(nuc_sample_array)):
-        reversed_nuc_sample_array = reversed_nuc_sample_array + residue
+    for res in reversed_iterator(struc.residue_iter(nuc_sample_array)):
+        reversed_nuc_sample_array = reversed_nuc_sample_array + res
 
     computed_basepairs = struc.base_pairs(reversed_nuc_sample_array)
     check_residue_starts(computed_basepairs, reversed_nuc_sample_array)
@@ -154,10 +154,10 @@ def test_base_pairs_reordered(nuc_sample_array, seed):
     nuc_sample_array_reordered = struc.AtomArray(0)
     np.random.seed(seed)
 
-    for residue in struc.residue_iter(nuc_sample_array):
-        bound = residue.array_length()
+    for res in struc.residue_iter(nuc_sample_array):
+        bound = res.array_length()
         indices = np.random.choice(np.arange(bound), bound, replace=False)
-        nuc_sample_array_reordered += residue[..., indices]
+        nuc_sample_array_reordered += res[..., indices]
 
     assert np.all(
         struc.base_pairs(nuc_sample_array)

tests/structure/test_info.py

@@ -58,7 +58,7 @@ def test_mass():
     assert np.all(np.round(multiple_of_h_masses, decimals=2) % 1 == 0)
 
 
-def test_protOr_radii():
+def test_protor_radii():
     """
     Assert that ProtOr VdW radii (except hydrogen) can be calculated for
     all atoms in the given structure, since the structure (1GYA)

tests/structure/test_mol.py

@@ -84,7 +84,11 @@ def test_header_conversion():
     ),
 )
 def test_structure_conversion(
-    FileClass, path, version, omit_charge, use_charge_property
+    FileClass,  # noqa: N803
+    path,
+    version,
+    omit_charge,
+    use_charge_property,
 ):
     """
     After reading a file, writing the structure back to a new file

tests/structure/test_sasa.py

@@ -24,10 +24,12 @@ def test_single(pdb_id):
     sasa = struc.sasa(array, vdw_radii="Single", point_number=5000)
 
     import mdtraj
-    from biotite.structure.info.radii import _SINGLE_RADII as radii
+    from biotite.structure.info.radii import _SINGLE_RADII as SINGLE_RADII
 
     # Use the same atom radii
-    radii = {element.capitalize(): radius / 10 for element, radius in radii.items()}
+    radii = {
+        element.capitalize(): radius / 10 for element, radius in SINGLE_RADII.items()
+    }
     traj = mdtraj.load(file_name)
     # Conversion from nm^2 to A^2
     sasa_exp = (