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ISISNeutronMuon · Apr 29, 2024 · 17aa08e · 17aa08e
1 parent f7e6512
commit 17aa08e
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/MDANSE/Src/MDANSE/IO/PDB.py b/MDANSE/Src/MDANSE/IO/PDB.py
@@ -489,7 +489,11 @@ def nextResidue(self, name, number=None, terminus=None):
         name = name.upper()
         if self.export_filter is not None:
             name, number = self.export_filter.processResidue(name, number, terminus)
-        self.het_flag = not (name in RESIDUES_DATABASE or name in RESIDUE_ALT_NAMES or name in NUCLEOTIDES_DATABASE)
+        self.het_flag = not (
+            name in RESIDUES_DATABASE
+            or name in RESIDUE_ALT_NAMES
+            or name in NUCLEOTIDES_DATABASE
+        )
         self.data["residue_name"] = name
         self.data["residue_number"] = (self.data["residue_number"] + 1) % 10000
         self.data["insertion_code"] = ""
@@ -1051,8 +1055,10 @@ def isCompatible(self, chain_data, residue_data):
         return (
             chain_data["chain_id"] == self.chain_id
             and chain_data["segment_id"] == self.segment_id
-            and (residue_data["residue_name"] in RESIDUES_DATABASE
-            or residue_data["residue_name"] in RESIDUE_ALT_NAMES)
+            and (
+                residue_data["residue_name"] in RESIDUES_DATABASE
+                or residue_data["residue_name"] in RESIDUE_ALT_NAMES
+            )
         )
 
 

diff --git a/MDANSE/Src/MDANSE/IO/PDBReader.py b/MDANSE/Src/MDANSE/IO/PDBReader.py
@@ -37,7 +37,7 @@
     MOLECULES_DATABASE,
     NUCLEOTIDES_DATABASE,
     RESIDUES_DATABASE,
-    RESIDUE_ALT_NAMES
+    RESIDUE_ALT_NAMES,
 )
 from MDANSE.MolecularDynamics.Configuration import RealConfiguration
 from MDANSE.IO.PDB import PDBMolecule, PDBNucleotideChain, PDBPeptideChain, Structure
@@ -484,7 +484,9 @@ def _process_residue(self, residue):
                 # go through each name that code could be
                 atoms_found = [None] * len(pdb_atoms)
                 for comp, pdb_atom in enumerate(pdb_atoms):
-                    if len(atoms_found) != len(RESIDUES_DATABASE[new_code]["atoms"].items()):
+                    if len(atoms_found) != len(
+                        RESIDUES_DATABASE[new_code]["atoms"].items()
+                    ):
                         # different number of atoms break and try the next name
                         break
                     for at, info in RESIDUES_DATABASE[new_code]["atoms"].items():
@@ -518,7 +520,9 @@ def _process_residue(self, residue):
                         break
                 else:
                     raise PDBReaderError(
-                        "The atom {}{}:{} is unknown".format(code, residue.number, pdb_atom)
+                        "The atom {}{}:{} is unknown".format(
+                            code, residue.number, pdb_atom
+                        )
                     )
 
         resname = "{}{}".format(code, residue.number)