From 0b02c33e2f23158f1c04a184e8da6251da77c5b2 Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Mon, 16 Dec 2024 10:26:37 +0900
Subject: [PATCH 1/8] refactor: fix Residue -> DefinitionResidue

---
 pdb2pqr/aa.py         | 106 +++++++++++++++++++++++-------------------
 pdb2pqr/structures.py |  20 ++++++--
 setup.py              |   7 +--
 3 files changed, 76 insertions(+), 57 deletions(-)

diff --git a/pdb2pqr/aa.py b/pdb2pqr/aa.py
index 82df94d9..810f3f80 100644
--- a/pdb2pqr/aa.py
+++ b/pdb2pqr/aa.py
@@ -6,12 +6,16 @@
 .. codeauthor:: Nathan Baker
 """
 
+from __future__ import annotations
+
 import logging
 
 from . import quatfit as quat
 from . import residue
 from . import structures as struct
 from . import utilities as util
+from .definitions import DefinitionResidue
+from .pdb import ATOM, HETATM
 
 _LOGGER = logging.getLogger(__name__)
 
@@ -22,7 +26,7 @@ class Amino(residue.Residue):
     This class provides standard features of the amino acids.
     """
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms: list[ATOM | HETATM], ref: DefinitionResidue):
         """Initialize object.
 
         .. todo:: need to see whether :func:`super().__init__()` should be
@@ -34,16 +38,16 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         sample_atom = atoms[-1]
-        self.atoms = []
+        self.atoms: list[struct.Atom] = []
         self.name = sample_atom.res_name
         self.chain_id = sample_atom.chain_id
         self.res_seq = sample_atom.res_seq
         self.ins_code = sample_atom.ins_code
         self.ffname = self.name
-        self.map = {}
+        self.map: dict[str, struct.Atom] = {}
         self.dihedrals = []
         self.patches = []
         self.peptide_c = None
@@ -66,7 +70,11 @@ def __init__(self, atoms, ref):
             else:
                 _LOGGER.debug(f"Ignoring atom {atom_.name}")
 
-    def create_atom(self, atomname, newcoords):
+    def create_atom(
+        self,
+        atomname: str,
+        newcoords: list[float] | tuple[float, float, float],
+    ):
         """Create an atom.
 
         .. todo:: Determine why this is different than superclass method.
@@ -90,7 +98,7 @@ def create_atom(self, atomname, newcoords):
         newatom.added = 1
         self.add_atom(newatom)
 
-    def add_atom(self, atom):
+    def add_atom(self, atom: struct.Atom):
         """Add atom to residue.
 
         Override the existing add_atom; include the link to the reference
@@ -260,7 +268,7 @@ def rebuild_tetrahedral(self, atomname):
 class ALA(Amino):
     """Alanine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -269,7 +277,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -286,7 +294,7 @@ def letter_code(self) -> str:
 class ARG(Amino):
     """Arginine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -295,7 +303,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -318,7 +326,7 @@ def set_state(self):
 class ASN(Amino):
     """Asparagine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -327,7 +335,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -344,7 +352,7 @@ def letter_code(self):
 class ASP(Amino):
     """Aspartic acid class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -353,7 +361,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -376,7 +384,7 @@ def set_state(self):
 class CYS(Amino):
     """Cysteine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -385,7 +393,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -418,7 +426,7 @@ def set_state(self):
 class GLN(Amino):
     """Glutamine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -427,7 +435,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -444,7 +452,7 @@ def letter_code(self):
 class GLU(Amino):
     """Glutamic acid class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -453,7 +461,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -476,7 +484,7 @@ def set_state(self):
 class GLY(Amino):
     """Glycine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -485,7 +493,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -502,7 +510,7 @@ def letter_code(self):
 class HIS(Amino):
     """Histidine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -511,7 +519,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -574,7 +582,7 @@ def set_state(self):
 class ILE(Amino):
     """Isoleucine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -583,7 +591,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -600,7 +608,7 @@ def letter_code(self):
 class LEU(Amino):
     """Leucine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -609,7 +617,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -626,7 +634,7 @@ def letter_code(self):
 class LYS(Amino):
     """Lysine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -635,7 +643,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -658,7 +666,7 @@ def set_state(self):
 class MET(Amino):
     """Methionine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -667,7 +675,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -684,7 +692,7 @@ def letter_code(self):
 class PHE(Amino):
     """Phenylalanine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -693,7 +701,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -710,7 +718,7 @@ def letter_code(self):
 class PRO(Amino):
     """Proline class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -719,7 +727,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -749,7 +757,7 @@ def set_state(self):
 class SER(Amino):
     """Serine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -758,7 +766,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -775,7 +783,7 @@ def letter_code(self):
 class THR(Amino):
     """Threonine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -784,7 +792,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -801,7 +809,7 @@ def letter_code(self):
 class TRP(Amino):
     """Tryptophan class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -810,7 +818,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -827,7 +835,7 @@ def letter_code(self):
 class TYR(Amino):
     """Tyrosine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -836,7 +844,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -859,7 +867,7 @@ def set_state(self):
 class VAL(Amino):
     """Valine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -868,7 +876,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the amino acid.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         Amino.__init__(self, atoms, ref)
         self.reference = ref
@@ -891,7 +899,7 @@ class WAT(residue.Residue):
 
     water_residue_names = ["HOH", "WAT"]
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize object.
 
         :param atoms:  A list of :class:`Atom` objects to be stored in this
@@ -900,7 +908,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the residue.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         sample_atom = atoms[-1]
         self.atoms = []
@@ -988,7 +996,7 @@ def __init__(self, atoms, ref):
         :param ref:  The reference object for the residue.
             Used to convert from the alternate naming scheme to the main naming
             scheme.
-        :type ref:  Residue
+        :type ref:  DefinitionResidue
         """
         sample_atom = atoms[-1]
         self.atoms = []
diff --git a/pdb2pqr/structures.py b/pdb2pqr/structures.py
index a7bf94e4..c2d61024 100644
--- a/pdb2pqr/structures.py
+++ b/pdb2pqr/structures.py
@@ -8,8 +8,12 @@
 """
 
 # from . import pdb
+from __future__ import annotations
+
+from typing_extensions import Self
 
 from .config import BACKBONE
+from .pdb import ATOM, HETATM
 
 
 class Chain:
@@ -19,7 +23,7 @@ class Chain:
     :class:`Biomolecule` object.
     """
 
-    def __init__(self, chain_id):
+    def __init__(self, chain_id: str):
         """Initialize the class.
 
         :param chain_id:  ID for this chain as denoted in the PDB
@@ -74,7 +78,12 @@ class Atom:
     :class:`HETATM` objects into a single class.
     """
 
-    def __init__(self, atom=None, type_="ATOM", residue=None):
+    def __init__(
+        self,
+        atom: ATOM | HETATM | Self | None = None,
+        type_="ATOM",
+        residue=None,
+    ):
         """Initialize the new Atom object by using the old object.
 
         :param atom:  the original ATOM object (could be None)
@@ -136,10 +145,11 @@ def __init__(self, atom=None, type_="ATOM", residue=None):
             self.element = atom.element
             self.charge = atom.charge
             self.residue = residue
-            try:
-                self.mol2charge = atom.mol2charge
-            except AttributeError:
+            if isinstance(atom, ATOM):
+                # ATOM class doesn't have mol2charge
                 self.mol2charge = None
+            else:
+                self.mol2charge = atom.mol2charge
 
     @classmethod
     def from_pqr_line(cls, line):
diff --git a/setup.py b/setup.py
index 3fd2a693..a34da00b 100644
--- a/setup.py
+++ b/setup.py
@@ -25,8 +25,6 @@
 to the biomedical community.
 """
 
-from sys import version_info
-
 from setuptools import find_packages, setup
 
 # NOTE: The following reads the version number and makes
@@ -36,7 +34,7 @@
 with open("pdb2pqr/_version.py") as fobj:
     exec(fobj.read())
 
-with open("README.md", "r") as fobj:
+with open("README.md") as fobj:
     LONG_DESCRIPTION = fobj.read()
 
 setup(
@@ -57,6 +55,7 @@
         "propka >= 3.5",
         "requests",
         "docutils < 0.18",
+        "typing-extensions",
     ],
     url="http://www.poissonboltzmann.org",
     packages=find_packages(
@@ -94,6 +93,8 @@
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",
+        "Programming Language :: Python :: 3.12",
+        "Programming Language :: Python :: 3.13",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
         "Topic :: Scientific/Engineering :: Chemistry",
     ],

From 162d4b6378f34e66c9f2b4afca9d5f9588bcf76b Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Mon, 16 Dec 2024 10:34:25 +0900
Subject: [PATCH 2/8] build: ruff ignore magic-value-comparison

---
 pyproject.toml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyproject.toml b/pyproject.toml
index ff710239..a67012c4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -94,6 +94,7 @@ ignore = [
   "UP017",   # datetime.timezone.utc -> datetime.UTC
   "SIM108",  # use ternary operator instead of if-else
   "TRY003",  # long message in except
+  "PLW2004", # magic value comparison
 ]
 
 [tool.ruff.lint.per-file-ignores]

From e5a91c08da445de637b96bf9f670ffaac3391ea5 Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Mon, 16 Dec 2024 10:39:59 +0900
Subject: [PATCH 3/8] build: ruff fix wrong setting

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a67012c4..10eb4b27 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -94,7 +94,7 @@ ignore = [
   "UP017",   # datetime.timezone.utc -> datetime.UTC
   "SIM108",  # use ternary operator instead of if-else
   "TRY003",  # long message in except
-  "PLW2004", # magic value comparison
+  "PLR2004", # magic value comparison
 ]
 
 [tool.ruff.lint.per-file-ignores]

From 27eb2a773df9f9904acf85f6e48bbe10bac44cf7 Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Mon, 16 Dec 2024 11:43:39 +0900
Subject: [PATCH 4/8] refactor: Residue -> DefinitionResidue in na.py

---
 pdb2pqr/na.py | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/pdb2pqr/na.py b/pdb2pqr/na.py
index b01d7625..c3e95a82 100644
--- a/pdb2pqr/na.py
+++ b/pdb2pqr/na.py
@@ -6,24 +6,28 @@
 .. codeauthor::  Nathan Baker
 """
 
+from __future__ import annotations
+
 from . import residue
 from . import structures as struct
+from .definitions import DefinitionResidue
+from .pdb import ATOM, HETATM
 
 
 class Nucleic(residue.Residue):
     """This class provides standard features of the nucleic acids listed below."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms: list[ATOM | HETATM], ref: DefinitionResidue):
         sample_atom = atoms[-1]
 
-        self.atoms = []
+        self.atoms: list[struct.Atom] = []
         self.name = sample_atom.res_name
         self.chain_id = sample_atom.chain_id
         self.res_seq = sample_atom.res_seq
         self.ins_code = sample_atom.ins_code
 
         self.ffname = self.name
-        self.map = {}
+        self.map: dict[str, struct.Atom] = {}
         self.dihedrals = []
         self.patches = []
         self.is3term = 0
@@ -42,7 +46,11 @@ def __init__(self, atoms, ref):
                 atom_ = struct.Atom(atom, "ATOM", self)
                 self.add_atom(atom_)
 
-    def create_atom(self, atomname, newcoords):
+    def create_atom(
+        self,
+        atomname: str,
+        newcoords: list[float] | tuple[float, float, float],
+    ):
         """Create an atom.
 
         Overrides the generic residue's create_atom().
@@ -66,7 +74,7 @@ def create_atom(self, atomname, newcoords):
         newatom.added = 1
         self.add_atom(newatom)
 
-    def add_atom(self, atom):
+    def add_atom(self, atom: struct.Atom):
         """Add existing atom to system.
 
         Override the existing add_atom - include the link to the reference
@@ -109,7 +117,7 @@ def set_state(self):
 class ADE(Nucleic):
     """Adenosine class."""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize residue.
 
         :param atoms:  add atoms to residue
@@ -140,7 +148,7 @@ def set_state(self):
 class CYT(Nucleic):
     """Cytidine class"""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize residue.
 
         :param atoms:  add atoms to residue
@@ -171,7 +179,7 @@ def set_state(self):
 class GUA(Nucleic):
     """Guanosine class"""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize residue.
 
         :param atoms:  add atoms to residue
@@ -202,7 +210,7 @@ def set_state(self):
 class THY(Nucleic):
     """Thymine class"""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize residue.
 
         :param atoms:  add atoms to residue
@@ -231,7 +239,7 @@ def set_state(self):
 class URA(Nucleic):
     """Uridine class"""
 
-    def __init__(self, atoms, ref):
+    def __init__(self, atoms, ref: DefinitionResidue):
         """Initialize residue.
 
         :param atoms:  add atoms to residue

From e2dc211b2b4dc27ea02ff27fe4f7b154cb562ddf Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Fri, 27 Dec 2024 08:48:06 +0900
Subject: [PATCH 5/8] chore: remove __future__ annotations

---
 pdb2pqr/aa.py         | 2 --
 pdb2pqr/main.py       | 2 --
 pdb2pqr/na.py         | 2 --
 pdb2pqr/residue.py    | 2 --
 pdb2pqr/structures.py | 3 ---
 5 files changed, 11 deletions(-)

diff --git a/pdb2pqr/aa.py b/pdb2pqr/aa.py
index 810f3f80..569e8a92 100644
--- a/pdb2pqr/aa.py
+++ b/pdb2pqr/aa.py
@@ -6,8 +6,6 @@
 .. codeauthor:: Nathan Baker
 """
 
-from __future__ import annotations
-
 import logging
 
 from . import quatfit as quat
diff --git a/pdb2pqr/main.py b/pdb2pqr/main.py
index bc82bdc8..f2fc72ea 100644
--- a/pdb2pqr/main.py
+++ b/pdb2pqr/main.py
@@ -7,8 +7,6 @@
 .. codeauthor:: Nathan Baker (et al.)
 """
 
-from __future__ import annotations
-
 import argparse
 import logging
 import sys
diff --git a/pdb2pqr/na.py b/pdb2pqr/na.py
index c3e95a82..c2ad4782 100644
--- a/pdb2pqr/na.py
+++ b/pdb2pqr/na.py
@@ -6,8 +6,6 @@
 .. codeauthor::  Nathan Baker
 """
 
-from __future__ import annotations
-
 from . import residue
 from . import structures as struct
 from .definitions import DefinitionResidue
diff --git a/pdb2pqr/residue.py b/pdb2pqr/residue.py
index 54f7731f..743f7fd8 100644
--- a/pdb2pqr/residue.py
+++ b/pdb2pqr/residue.py
@@ -4,8 +4,6 @@
 .. codeauthor:: Nathan Baker
 """
 
-from __future__ import annotations
-
 import logging
 
 from . import pdb, structures
diff --git a/pdb2pqr/structures.py b/pdb2pqr/structures.py
index c2d61024..69615608 100644
--- a/pdb2pqr/structures.py
+++ b/pdb2pqr/structures.py
@@ -7,9 +7,6 @@
 .. codeauthor:: Nathan Baker
 """
 
-# from . import pdb
-from __future__ import annotations
-
 from typing_extensions import Self
 
 from .config import BACKBONE

From 94974337e889169a8dd759215e5e7aa211ab1e21 Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Fri, 27 Dec 2024 12:20:07 +0900
Subject: [PATCH 6/8] build: pyproject.toml

---
 pyproject.toml |  86 +++++++++++++++++++++++++++++++++++++
 setup.cfg      |   2 -
 setup.py       | 114 -------------------------------------------------
 3 files changed, 86 insertions(+), 116 deletions(-)
 delete mode 100644 setup.cfg
 delete mode 100644 setup.py

diff --git a/pyproject.toml b/pyproject.toml
index 10eb4b27..a687bf35 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,3 +1,89 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.version]
+source = "code"
+path = "pdb2pqr/_version.py"
+# expression = "__version__"  # default
+
+[tool.hatch.build.targets.sdist]
+include = [
+  "pdb2pqr",
+  "docs",
+  "examples",
+  "tests",
+]
+
+[tool.hatch.build.targets.wheel]
+packages = ["pdb2pqr"]
+
+[project]
+name = "pdb2pqr"
+dynamic = ["version"]
+description = """
+Automates many of the common tasks of preparing structures for \
+continuum solvation calculations as well as many other types of \
+biomolecular structure modeling, analysis, and simulation."""
+authors = [
+  { name = "Jens Erik Nielsen" },
+  { name = "Nathan Baker", email = "nathanandrewbaker@gmail.com" },
+]
+readme = "README.md"
+license = { file = "LICENSE.md" }
+requires-python = ">=3.11,<4"
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Environment :: Console",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved :: BSD License",
+  "Natural Language :: English",
+  "Operating System :: MacOS",
+  "Operating System :: Microsoft :: Windows",
+  "Operating System :: POSIX",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Topic :: Scientific/Engineering :: Bio-Informatics",
+  "Topic :: Scientific/Engineering :: Chemistry",
+]
+keywords = ["science", "chemistry", "molecular biology"]
+
+dependencies = [
+  "mmcif_pdbx>=1.1.2",
+  "numpy",
+  "propka >= 3.5",
+  "requests",
+  "docutils < 0.18",
+]
+
+[project.optional-dependencies]
+dev = ["check-manifest"]
+test = [
+  "ruff",
+  "coverage",
+  "pandas >= 1.0",
+  "pytest",
+  "testfixtures",
+]
+
+[project.urls]
+"Homepage" = "https://www.poissonboltzmann.org"
+"Documentation"= "https://pdb2pqr.readthedocs.io/"
+"Get help"= "https://github.com/Electrostatics/pdb2pqr/issues"
+"Publications"= "https://pubmed.ncbi.nlm.nih.gov/?term=R01+GM069702"
+"Funding"= "https://bit.ly/apbs-funding"
+"Source"= "https://github.com/Electrostatics/pdb2pqr"
+
+[project.scripts]
+pdb2pqr = "pdb2pqr.main:main"
+pdb2pqr30 = "pdb2pqr.main:main"
+dx2cube = "pdb2pqr.main:dx_to_cube"
+inputgen = "pdb2pqr.inputgen:main"
+
+
 [tool.pytest.ini_options]
 testpaths = ["tests"]
 log_cli = true
diff --git a/setup.cfg b/setup.cfg
deleted file mode 100644
index 3c6e79cf..00000000
--- a/setup.cfg
+++ /dev/null
@@ -1,2 +0,0 @@
-[bdist_wheel]
-universal=1
diff --git a/setup.py b/setup.py
deleted file mode 100644
index 637628bc..00000000
--- a/setup.py
+++ /dev/null
@@ -1,114 +0,0 @@
-#!/usr/bin/python3
-
-"""
-The use of continuum solvation methods such as APBS requires accurate and
-complete structural data as well as force field parameters such as atomic
-charges and radii. Unfortunately, the limiting step in continuum electrostatics
-calculations is often the addition of missing atomic coordinates to molecular
-structures from the Protein Data Bank and the assignment of parameters to these
-structures. To adds this problem, we have developed PDB2PQR. This software
-automates many of the common tasks of preparing structures for continuum
-solvation calculations as well as many other types of biomolecular structure
-modeling, analysis, and simulation. These tasks include:
-
-* Adding a limited number of missing heavy (non-hydrogen) atoms to biomolecular
-  structures.
-* Estimating titration states and protonating biomolecules in a manner
-  consistent with favorable hydrogen bonding.
-* Assigning charge and radius parameters from a variety of force fields.
-* Generating "PQR" output compatible with several popular computational
-  modeling and analysis packages.
-
-This service is intended to facilitate the setup and execution of
-electrostatics calculations for both experts and non-experts and thereby
-broaden the accessibility of biomolecular solvation and electrostatics analyses
-to the biomedical community.
-"""
-
-from setuptools import find_packages, setup
-
-# NOTE: The following reads the version number and makes
-#       if available to the packaging tools before installation.
-#       REF: https://stackoverflow.com/questions/458550/standard-way-to-embed-version-into-python-package  # noqa: E501
-#       This makes __version__ valid below
-with open("pdb2pqr/_version.py") as fobj:
-    exec(fobj.read())
-
-with open("README.md") as fobj:
-    LONG_DESCRIPTION = fobj.read()
-
-setup(
-    name="pdb2pqr",
-    version=__version__,  # noqa: F821
-    author="Jens Erik Nielsen, Nathan Baker, and many others.",
-    author_email="nathanandrewbaker@gmail.com",
-    description=(
-        "Automates many of the common tasks of preparing structures for "
-        "continuum solvation calculations as well as many other types of "
-        "biomolecular structure modeling, analysis, and simulation."
-    ),
-    long_description=LONG_DESCRIPTION,
-    long_description_content_type="text/markdown",
-    install_requires=[
-        "mmcif_pdbx>=1.1.2",
-        "numpy",
-        "propka >= 3.5",
-        "requests",
-        "docutils < 0.18",
-        "typing-extensions",
-    ],
-    url="http://www.poissonboltzmann.org",
-    packages=find_packages(
-        exclude=["pdb2pka", "*.pdb2pka", "pdb2pka.*", "*.pdb2pka.*"]
-    ),
-    package_data={"pdb2pqr": ["dat/*.xml", "dat/*.DAT", "dat/*.names"]},
-    python_requires=">=3.8",
-    extras_require={
-        "dev": ["check-manifest"],
-        "test": [
-            "ruff",
-            "coverage[toml]",
-            "pandas >= 1.0",
-            "pytest",
-            "testfixtures",
-        ],
-    },
-    tests_require=[
-        "pandas >= 1.0",
-        "pytest",
-        "testfixtures",
-    ],
-    test_suite="tests",
-    license="BSD",
-    classifiers=[
-        "Development Status :: 4 - Beta",
-        "Environment :: Console",
-        "Intended Audience :: Science/Research",
-        "License :: OSI Approved :: BSD License",
-        "Natural Language :: English",
-        "Operating System :: MacOS",
-        "Operating System :: Microsoft :: Windows",
-        "Operating System :: POSIX",
-        "Programming Language :: Python :: 3.11",
-        "Programming Language :: Python :: 3.12",
-        "Programming Language :: Python :: 3.13",
-        "Topic :: Scientific/Engineering :: Bio-Informatics",
-        "Topic :: Scientific/Engineering :: Chemistry",
-    ],
-    project_urls={
-        "Documentation": "https://pdb2pqr.readthedocs.io/",
-        "Get help": "https://github.com/Electrostatics/pdb2pqr/issues",
-        "Publications": "https://pubmed.ncbi.nlm.nih.gov/?term=R01+GM069702",
-        "Funding": "https://bit.ly/apbs-funding",
-        "Source": "https://github.com/Electrostatics/pdb2pqr",
-    },
-    keywords="science chemistry molecular biology",
-    entry_points={
-        "console_scripts": [
-            "pdb2pqr=pdb2pqr.main:main",
-            "pdb2pqr30=pdb2pqr.main:main",
-            "dx2cube=pdb2pqr.main:dx_to_cube",
-            "inputgen=pdb2pqr.inputgen:main",
-        ]
-    },
-)

From 2023a72829e1475d3e17671999263a3b3d96f923 Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Fri, 27 Dec 2024 12:20:31 +0900
Subject: [PATCH 7/8] chore: remove unnecessary lint (not active anyway)

---
 ruff_essential.toml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/ruff_essential.toml b/ruff_essential.toml
index 8ffc4af1..e76e4ee5 100644
--- a/ruff_essential.toml
+++ b/ruff_essential.toml
@@ -7,5 +7,4 @@ select = [
   "F63",
   "F7",
   "F82",
-  "FA102",  # Python 3.10-style union typing is used so we need to import `from __future__ import annotations`
 ]

From e2708a54715c336672403f8f6d15ef1a7651236a Mon Sep 17 00:00:00 2001
From: Kiyoon Kim <kiyoon@users.noreply.github.com>
Date: Fri, 27 Dec 2024 12:28:06 +0900
Subject: [PATCH 8/8] fix: python version in pyright

---
 pdb2pqr/structures.py | 2 +-
 pyproject.toml        | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/pdb2pqr/structures.py b/pdb2pqr/structures.py
index 69615608..4d21e749 100644
--- a/pdb2pqr/structures.py
+++ b/pdb2pqr/structures.py
@@ -7,7 +7,7 @@
 .. codeauthor:: Nathan Baker
 """
 
-from typing_extensions import Self
+from typing import Self
 
 from .config import BACKBONE
 from .pdb import ATOM, HETATM
diff --git a/pyproject.toml b/pyproject.toml
index a687bf35..d3f4f16a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -31,6 +31,7 @@ authors = [
 ]
 readme = "README.md"
 license = { file = "LICENSE.md" }
+# NOTE: make sure you change [tool.pyright] pythonVersion to match this
 requires-python = ">=3.11,<4"
 classifiers = [
   "Development Status :: 4 - Beta",
@@ -105,7 +106,7 @@ typeCheckingMode = "standard"
 useLibraryCodeForTypes = true
 autoImportCompletions = true
 
-pythonVersion = "3.8"
+pythonVersion = "3.11"
 # pythonPlatform = "Linux"
 
 reportDuplicateImport = true