refactor: fix wrong type Residue -> DefinitionResidue

pdb2pqr/main.py

@@ -7,8 +7,6 @@
 .. codeauthor:: Nathan Baker (et al.)
 """
 
-from __future__ import annotations
-
 import argparse
 import logging
 import sys

pdb2pqr/na.py

@@ -8,22 +8,24 @@
 
 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 +44,11 @@ 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 +72,7 @@ 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 +115,7 @@ 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 +146,7 @@ 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 +177,7 @@ 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 +208,7 @@ 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 +237,7 @@ 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

pdb2pqr/residue.py

@@ -4,8 +4,6 @@
 .. codeauthor:: Nathan Baker
 """
 
-from __future__ import annotations
-
 import logging
 
 from . import pdb, structures

pdb2pqr/structures.py

@@ -7,9 +7,10 @@
 .. codeauthor:: Nathan Baker
 """
 
-# from . import pdb
+from typing import Self
 
 from .config import BACKBONE
+from .pdb import ATOM, HETATM
 
 
 class Chain:
@@ -19,7 +20,7 @@ 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 +75,12 @@ 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 +142,11 @@ 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):

pyproject.toml

@@ -1,3 +1,90 @@
+[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 = "[email protected]" },
+]
+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",
+  "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
@@ -19,7 +106,7 @@ typeCheckingMode = "standard"
 useLibraryCodeForTypes = true
 autoImportCompletions = true
 
-pythonVersion = "3.8"
+pythonVersion = "3.11"
 # pythonPlatform = "Linux"
 
 reportDuplicateImport = true
@@ -94,6 +181,7 @@ ignore = [
   "UP017",   # datetime.timezone.utc -> datetime.UTC
   "SIM108",  # use ternary operator instead of if-else
   "TRY003",  # long message in except
+  "PLR2004", # magic value comparison
 ]
 
 [tool.ruff.lint.per-file-ignores]

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`
 ]