chore: fix formatting with black

opencadd/structure/superposition/cli.py

@@ -1,6 +1,7 @@
 """
 Command Line Interface for opencadd
 """
+
 import argparse
 import logging
 

opencadd/structure/superposition/engines/base.py

@@ -1,6 +1,7 @@
 """
 Base class for all the superposition engines.
 """
+
 import logging
 
 _logger = logging.getLogger(__name__)

opencadd/structure/superposition/engines/mda.py

@@ -19,7 +19,6 @@
 
 
 class MDAnalysisAligner(BaseAligner):
-
     """
     Factory to configure an aligner based on
     MDAnalysis' superposition algorithms.

opencadd/structure/superposition/engines/theseus.py

@@ -18,6 +18,7 @@
 * Accurate structural correlations from maximum likelihood superpositions.
   Theobald, Douglas L. & Wuttke, Deborah S. (2008) PLOS Computational Biology 4(2):e43
 """
+
 import os
 import subprocess
 import logging
@@ -33,7 +34,6 @@
 
 
 class TheseusAligner(BaseAligner):
-
     """
     Superpose structures with different sequences but similar structures
 

opencadd/structure/superposition/sequences.py

@@ -1,6 +1,7 @@
 """
 Utilities for sequence alignment
 """
+
 import logging
 
 import numpy as np
@@ -89,13 +90,13 @@ def find_gap_character(seq):
         gap character if found: str
         None else
     """
-    if '-' in seq:
-        return '-'
-    elif '=' in seq:
-        return '='
+    if "-" in seq:
+        return "-"
+    elif "=" in seq:
+        return "="
     else:
-        return ''
-    #raise ValueError("No standard gap character found!")
+        return ""
+    # raise ValueError("No standard gap character found!")
 
 
 def fasta2select(
@@ -225,4 +226,4 @@ def resid(nseq, ipos, t=t, s=s):
 
     ref_selection = " or ".join(sel[0])
     target_selection = " or ".join(sel[1])
-    return {"reference": ref_selection, "mobile": target_selection}
+    return {"reference": ref_selection, "mobile": target_selection}