Merge pull request #411 from kiyoon/refactor/ruff-lint-rules

refactor: fix lint and some type issues

pdb2pqr/__main__.py

@@ -7,15 +7,11 @@
 """
 
 import logging
-from sys import version_info
 
 from pdb2pqr.main import main
 
-assert version_info >= (3, 5)
-
-
 _LOGGER = logging.getLogger(__name__)
-logging.captureWarnings(True)
+logging.captureWarnings(capture=True)
 
 
 if __name__ == "__main__":

pdb2pqr/_version.py

@@ -1,4 +1,5 @@
 """PDB2PQR Version number.
+
 Store the version here so:
 
 * we don't load dependencies by storing it in :file:`__init__.py`

pdb2pqr/aa.py

@@ -138,7 +138,6 @@ def set_state(self):
                 self.ffname = f"NEUTRAL-C{self.ffname}"
             else:
                 self.ffname = f"C{self.ffname}"
-        return
 
     def rebuild_tetrahedral(self, atomname):
         """Rebuild a tetrahedral hydrogen group.
@@ -167,7 +166,7 @@ def rebuild_tetrahedral(self, atomname):
         for bond in self.reference.map[bondname].bonds:
             if bond.startswith("H"):
                 hcount += 1
-            elif bond != "C-1" and bond != "N+1":
+            elif bond not in ("C-1", "N+1"):
                 nextatomname = bond
         # Check if this is a tetrahedral group
         if hcount != 3 or nextatomname is None:
@@ -275,7 +274,7 @@ def __init__(self, atoms, ref):
         Amino.__init__(self, atoms, ref)
         self.reference = ref
 
-    def letter_code(self):
+    def letter_code(self) -> str:
         """Return letter code for amino acid.
 
         :return:  amino acid 1-letter code
@@ -407,9 +406,7 @@ def set_state(self):
         If SS-bonded, use CYX.  If negatively charged, use CYM.  If HG is not
         present, use CYX.
         """
-        if "CYX" in self.patches or self.name == "CYX":
-            self.ffname = "CYX"
-        elif self.ss_bonded:
+        if "CYX" in self.patches or self.name == "CYX" or self.ss_bonded:
             self.ffname = "CYX"
         elif "CYM" in self.patches or self.name == "CYM":
             self.ffname = "CYM"
@@ -548,10 +545,7 @@ def set_state(self):
             elif (
                 self.get_atom("NE2").hdonor
                 and not self.get_atom("NE2").hacceptor
-            ):
-                if self.has_atom("HD1"):
-                    self.remove_atom("HD1")
-            elif (
+            ) or (
                 self.get_atom("ND1").hacceptor
                 and not self.get_atom("ND1").hdonor
             ):
@@ -568,7 +562,7 @@ def set_state(self):
             self.ffname = "HIE"
         else:
             errstr = (
-                f"Invalid type for {str(self)}! Missing both HD1 and HE2 "
+                f"Invalid type for {self!s}! Missing both HD1 and HE2 "
                 "atoms. If you receive this error while using the "
                 "--assign-only option you can only resolve it by adding HD1, "
                 "HE2 or both to this residue."

pdb2pqr/biomolecule.py

@@ -55,23 +55,27 @@ def __init__(self, pdblist, definition):
                 num_chains += 1
         for record in pdblist:
             if isinstance(record, (pdb.ATOM, pdb.HETATM)):
-                if record.chain_id == "":
-                    if num_chains > 1 and record.res_name not in [
+                if (
+                    record.chain_id == ""
+                    and num_chains > 1
+                    and record.res_name
+                    not in [
                         "WAT",
                         "HOH",
-                    ]:
-                        # Assign a chain ID
-                        try:
-                            record.chain_id = (
-                                string.ascii_uppercase
-                                + string.ascii_lowercase
-                                + string.digits
-                            )[count]
-                        except IndexError:
-                            raise Exception(
-                                "Too many chains exist in biomolecule. "
-                                "Consider preparing subsets."
-                            )
+                    ]
+                ):
+                    # Assign a chain ID
+                    try:
+                        record.chain_id = (
+                            string.ascii_uppercase
+                            + string.ascii_lowercase
+                            + string.digits
+                        )[count]
+                    except IndexError:
+                        raise Exception(
+                            "Too many chains exist in biomolecule. "
+                            "Consider preparing subsets."
+                        )
 
                 chain_id = record.chain_id
                 res_seq = record.res_seq
@@ -221,7 +225,7 @@ def set_hip(self):
             if isinstance(residue, aa.HIS):
                 self.apply_patch("HIP", residue)
 
-    def set_termini(self, neutraln=False, neutralc=False):
+    def set_termini(self, *, neutraln=False, neutralc=False):
         """Set the termini for a protein.
 
         First set all known termini by looking at the ends of the chain. Then
@@ -237,7 +241,7 @@ def set_termini(self, neutraln=False, neutralc=False):
         # First assign the known termini
         chain = None
         for chain in self.chains:
-            self.assign_termini(chain, neutraln, neutralc)
+            self.assign_termini(chain, neutraln=neutraln, neutralc=neutralc)
         # Now determine if there are any hidden chains
         letters = string.ascii_uppercase + string.ascii_lowercase
         ch_num = 0
@@ -255,11 +259,12 @@ def set_termini(self, neutraln=False, neutralc=False):
                 if isinstance(residue, aa.Amino):
                     if residue.has_atom("OXT") and not residue.is_c_term:
                         fixflag = 1
-                elif isinstance(residue, na.Nucleic):
-                    if (
-                        residue.has_atom("H3T") or residue.name.endswith("3")
-                    ) and not residue.is3term:
-                        fixflag = 1
+                elif (
+                    isinstance(residue, na.Nucleic)
+                    and (residue.has_atom("H3T") or residue.name.endswith("3"))
+                    and not residue.is3term
+                ):
+                    fixflag = 1
                 if fixflag:
                     # Get an available chain ID
                     chainid = letters[0]
@@ -284,8 +289,12 @@ def set_termini(self, neutraln=False, neutralc=False):
                         newchain.add_residue(res)
                         chain.residues.remove(res)
                         res.set_chain_id(chainid[0])
-                    self.assign_termini(chain, neutraln, neutralc)
-                    self.assign_termini(newchain, neutraln, neutralc)
+                    self.assign_termini(
+                        chain, neutraln=neutraln, neutralc=neutralc
+                    )
+                    self.assign_termini(
+                        newchain, neutraln=neutraln, neutralc=neutralc
+                    )
                     reslist = []
                     ch_num += 1
             ch_num += 1
@@ -459,9 +468,7 @@ def set_reference_distance(self):
                     atom.refdistance = -1
                 elif residue.is_c_term and atom.name == "HO":
                     atom.refdistance = 3
-                elif residue.is_n_term and (
-                    atom.name == "H3" or atom.name == "H2"
-                ):
+                elif residue.is_n_term and (atom.name in ("H3", "H2")):
                     atom.refdistance = 2
                 else:
                     path = util.shortest_path(map_, atom, caatom)
@@ -482,7 +489,7 @@ def remove_hydrogens(self):
                 if atom.is_hydrogen:
                     residue.remove_atom(atom.name)
 
-    def assign_termini(self, chain, neutraln=False, neutralc=False):
+    def assign_termini(self, chain, *, neutraln=False, neutralc=False):
         """Assign the termini for the given chain.
 
         Assignment made by looking at the start and end residues.
@@ -612,7 +619,7 @@ def update_bonds(self):
                     res2.peptide_c = None
                     res1.peptide_n = None
 
-    def apply_patch(self, patchname, residue):
+    def apply_patch(self, patchname: str, residue: residue_.Residue):
         """Apply a patch to the given residue.
 
         This is one of the key functions in PDB2PQR.  A similar function

pdb2pqr/debump.py

@@ -132,7 +132,7 @@ def get_bump_score_atom(self, atom):
             cutoff = atom_size + other_size
             if dist < cutoff:
                 bumpscore += 1000.0
-        _LOGGER.debug(f"BUMPSCORE {str(bumpscore)}")
+        _LOGGER.debug(f"BUMPSCORE {bumpscore!s}")
         return bumpscore
 
     def debump_biomolecule(self):
@@ -159,7 +159,9 @@ def debump_biomolecule(self):
             if not isinstance(residue, aa.Amino):
                 continue
             # Initialize variables
-            conflict_names = self.find_residue_conflicts(residue, True)
+            conflict_names = self.find_residue_conflicts(
+                residue, write_conflict_info=True
+            )
             if not conflict_names:
                 continue
             # Otherwise debump the residue
@@ -177,7 +179,7 @@ def debump_biomolecule(self):
                 _LOGGER.warning(text)
         _LOGGER.debug("Done checking if we must debump any residues.")
 
-    def find_residue_conflicts(self, residue, write_conflict_info=False):
+    def find_residue_conflicts(self, residue, *, write_conflict_info=False):
         """Find conflicts between residues.
 
         :param residue:  residue to check
@@ -269,7 +271,7 @@ def debump_residue(self, residue, conflict_names):
                 if score == 0:
                     if not self.find_residue_conflicts(residue):
                         _LOGGER.debug(
-                            f"No conflicts found at angle {repr(newangle)}"
+                            f"No conflicts found at angle {newangle!r}"
                         )
                         return True
                     else:

pdb2pqr/definitions.py

@@ -227,7 +227,7 @@ def __str__(self):
         text += f"Apply to: {self.applyto}\n"
         text += "Atoms to add: \n"
         for atom in self.map:
-            text += f"\t{str(self.map[atom])}\n"
+            text += f"\t{self.map[atom]!s}\n"
         text += "Atoms to remove: \n"
         for remove in self.remove:
             text += f"\t{remove}\n"
@@ -249,7 +249,7 @@ def __str__(self):
         text = f"{self.name}\n"
         text += "Atoms: \n"
         for atom in self.map:
-            text += f"\t{str(self.map[atom])}\n"
+            text += f"\t{self.map[atom]!s}\n"
         text += "Dihedrals: \n"
         for dihedral in self.dihedrals:
             text += f"\t{dihedral}\n"

pdb2pqr/forcefield.py

@@ -38,8 +38,7 @@ def __init__(self, map_, reference):
 
     @classmethod
     def update_map(cls, toname, fromname, map_):
-        """Update the given map by adding a pointer from a new name to an
-        object.
+        """Update the given map by adding a pointer from a new name to an object.
 
         .. todo:: Should this be a staticmethod instead of classmethod?
 
@@ -195,7 +194,7 @@ def __init__(self, ff_name, definition, userff, usernames=None):
         self.name = str(ff_name)
         defpath = ""
         defpath = io.test_dat_file(ff_name) if userff is None else userff
-        with open(defpath, "rt", encoding="utf-8") as ff_file:
+        with open(defpath, encoding="utf-8") as ff_file:
             lines = ff_file.readlines()
             for line in lines:
                 if not line.startswith("#"):
@@ -243,7 +242,7 @@ def __init__(self, ff_name, definition, userff, usernames=None):
             raise ValueError("Unable to identify .names file.")
         handler = ForcefieldHandler(self.map, definition.map)
         sax.make_parser()
-        with open(names_path, "rt", encoding="utf-8") as namesfile:
+        with open(names_path, encoding="utf-8") as namesfile:
             sax.parseString(namesfile.read(), handler)
 
     def has_residue(self, resname):
@@ -1048,11 +1047,11 @@ def get(self, name):
         """
         try:
             return getattr(self, name)
-        except AttributeError:
+        except AttributeError as e:
             message = (
                 f'Unable to access object "{name}" in class ForcefieldAtom'
             )
-            raise KeyError(message)
+            raise KeyError(message) from e
 
     def __str__(self):
         txt = f"{self.name}:\n"