Merge 57d7c67 into ee89e36

.github/workflows/python-package.yml

@@ -56,3 +56,13 @@ jobs:
       with:
         name: coverage-html
         path: htmlcov/*
+
+  static_type_check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v2
+    - uses: actions/setup-python@v2
+      with:
+        python-version: "3.12"
+    - run: python -m pip install mypy types-setuptools
+    - run: mypy

.gitignore

@@ -13,3 +13,5 @@
 docs/build
 docs/source/api/*.rst
 build/
+dist/
+.coverage

propka/atom.py

@@ -7,9 +7,15 @@
 """
 
 import string
+from typing import cast, List, NoReturn, Optional, TYPE_CHECKING
+
 from propka.lib import make_tidy_atom_label
 from . import hybrid36
 
+if TYPE_CHECKING:
+    from propka.group import Group
+    from propka.molecular_container import MolecularContainer
+    from propka.conformation_container import ConformationContainer
 
 # Format strings that get used in multiple places (or are very complex)
 PDB_LINE_FMT1 = (
@@ -37,37 +43,24 @@ class Atom:
        removed as reading/writing PROPKA input is no longer supported.
     """
 
-    def __init__(self, line=None):
+    def __init__(self, line: Optional[str] = None):
         """Initialize Atom object.
 
         Args:
             line:  Line from a PDB file to set properties of atom.
         """
-        self.occ = None
-        self.numb = None
-        self.res_name = None
-        self.type = None
-        self.chain_id = None
-        self.beta = None
-        self.icode = None
-        self.res_num = None
-        self.name = None
-        self.element = None
-        self.x = None
-        self.y = None
-        self.z = None
-        self.group = None
-        self.group_type = None
-        self.number_of_bonded_elements = {}
-        self.cysteine_bridge = False
-        self.bonded_atoms = []
+        self.number_of_bonded_elements: NoReturn = cast(NoReturn, {})  # FIXME unused?
+        self.group: Optional[Group] = None
+        self.group_type: Optional[str] = None
+        self.cysteine_bridge: bool = False
+        self.bonded_atoms: List[Atom] = []
         self.residue = None
-        self.conformation_container = None
-        self.molecular_container = None
+        self.conformation_container: Optional[ConformationContainer] = None
+        self.molecular_container: Optional[MolecularContainer] = None
         self.is_protonated = False
         self.steric_num_lone_pairs_set = False
-        self.terminal = None
-        self.charge = 0
+        self.terminal: Optional[str] = None
+        self.charge = 0.0
         self.charge_set = False
         self.steric_number = 0
         self.number_of_lone_pairs = 0
@@ -84,7 +77,7 @@ def __init__(self, line=None):
         self.sybyl_assigned = False
         self.marvin_pka = False
 
-    def set_properties(self, line):
+    def set_properties(self, line: Optional[str]):
         """Line from PDB file to set properties of atom.
 
         Args:
@@ -112,10 +105,8 @@ def set_properties(self, line):
             self.z = float(line[46:54].strip())
             self.res_num = int(line[22:26].strip())
             self.res_name = "{0:<3s}".format(line[17:20].strip())
-            self.chain_id = line[21]
             # Set chain id to "_" if it is just white space.
-            if not self.chain_id.strip():
-                self.chain_id = '_'
+            self.chain_id = line[21].strip() or '_'
             self.type = line[:6].strip().lower()
 
             # TODO - define nucleic acid residue names elsewhere
@@ -134,7 +125,7 @@ def set_properties(self, line):
                 self.element = '{0:1s}{1:1s}'.format(
                     self.element[0], self.element[1].lower())
 
-    def set_group_type(self, type_):
+    def set_group_type(self, type_: str):
         """Set group type of atom.
 
         Args:

propka/bonds.py

@@ -10,6 +10,10 @@
 import json
 import pkg_resources
 import propka.calculations
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from propka.molecular_container import MolecularContainer
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -329,7 +333,7 @@ def check_distance(self, atom1, atom2):
                 return True
         return False
 
-    def find_bonds_for_molecules_using_boxes(self, molecules):
+    def find_bonds_for_molecules_using_boxes(self, molecules: "MolecularContainer"):
         """ Finds all bonds for a molecular container.
 
         Args:

propka/calculations.py

@@ -6,13 +6,17 @@
 """
 
 import math
+from typing import Iterable, Optional, Tuple, TypeVar
+from .vector_algebra import _XYZ
 
+_BoundXYZ_1 = TypeVar("_BoundXYZ_1", bound=_XYZ)
+_BoundXYZ_2 = TypeVar("_BoundXYZ_2", bound=_XYZ)
 
 #: Maximum distance used to bound calculations of smallest distance
 MAX_DISTANCE = 1e6
 
 
-def squared_distance(atom1, atom2):
+def squared_distance(atom1: _XYZ, atom2: _XYZ) -> float:
     """Calculate the squared distance between two atoms.
 
     Args:
@@ -28,7 +32,7 @@ def squared_distance(atom1, atom2):
     return res
 
 
-def distance(atom1, atom2):
+def distance(atom1: _XYZ, atom2: _XYZ) -> float:
     """Calculate the distance between two atoms.
 
     Args:
@@ -40,7 +44,10 @@ def distance(atom1, atom2):
     return math.sqrt(squared_distance(atom1, atom2))
 
 
-def get_smallest_distance(atoms1, atoms2):
+def get_smallest_distance(
+    atoms1: Iterable[_BoundXYZ_1],
+    atoms2: Iterable[_BoundXYZ_2],
+) -> Tuple[Optional[_BoundXYZ_1], float, Optional[_BoundXYZ_2]]:
     """Calculate the smallest distance between two groups of atoms.
 
     Args:
@@ -59,4 +66,4 @@ def get_smallest_distance(atoms1, atoms2):
                 res_dist = dist
                 res_atom1 = atom1
                 res_atom2 = atom2
-    return [res_atom1, math.sqrt(res_dist), res_atom2]
+    return (res_atom1, math.sqrt(res_dist), res_atom2)

propka/conformation_container.py

@@ -6,14 +6,19 @@
 """
 import logging
 import functools
+from typing import Iterable, List, NoReturn, Optional, TYPE_CHECKING, Set
+
+if TYPE_CHECKING:
+    from propka.atom import Atom
+    from propka.molecular_container import MolecularContainer
+
 import propka.ligand
 from propka.output import make_interaction_map
 from propka.determinant import Determinant
 from propka.coupled_groups import NCCG
 from propka.determinants import set_backbone_determinants, set_ion_determinants
 from propka.determinants import set_determinants
 from propka.group import Group, is_group
-from typing import Iterable
 
 
 _LOGGER = logging.getLogger(__name__)
@@ -38,7 +43,10 @@ class ConformationContainer:
        PROPKA inputs is no longer supported.
     """
 
-    def __init__(self, name='', parameters=None, molecular_container=None):
+    def __init__(self,
+                 name: str = '',
+                 parameters=None,
+                 molecular_container: Optional["MolecularContainer"] = None):
         """Initialize conformation container.
 
         Args:
@@ -49,9 +57,9 @@ def __init__(self, name='', parameters=None, molecular_container=None):
         self.molecular_container = molecular_container
         self.name = name
         self.parameters = parameters
-        self.atoms = []
-        self.groups = []
-        self.chains = []
+        self.atoms: List["Atom"] = []
+        self.groups: List[Group] = []
+        self.chains: List[str] = []
         self.current_iter_item = 0
         self.marvin_pkas_calculated = False
         self.non_covalently_coupled_groups = False
@@ -126,7 +134,8 @@ def find_non_covalently_coupled_groups(self, verbose=False):
                            self.get_titratable_groups()))) > 0:
             self.non_covalently_coupled_groups = True
 
-    def find_bonded_titratable_groups(self, atom, num_bonds, original_atom):
+    def find_bonded_titratable_groups(self, atom: "Atom", num_bonds: int,
+                                      original_atom: "Atom"):
         """Find bonded titrable groups.
 
         Args:
@@ -136,7 +145,7 @@ def find_bonded_titratable_groups(self, atom, num_bonds, original_atom):
         Returns:
             a set of bonded atom groups
         """
-        res = set()
+        res: Set[Group] = set()
         for bond_atom in atom.bonded_atoms:
             # skip the original atom
             if bond_atom == original_atom:
@@ -152,7 +161,7 @@ def find_bonded_titratable_groups(self, atom, num_bonds, original_atom):
                     bond_atom, num_bonds+1, original_atom)
         return res
 
-    def setup_and_add_group(self, group):
+    def setup_and_add_group(self, group: Optional[Group]):
         """Check if we want to include this group in the calculations.
 
         Args:
@@ -166,7 +175,7 @@ def setup_and_add_group(self, group):
         self.init_group(group)
         self.groups.append(group)
 
-    def init_group(self, group):
+    def init_group(self, group: Group):
         """Initialize the given Group object.
 
         Args:
@@ -178,10 +187,11 @@ def init_group(self, group):
 
         # If --titrate_only option is set, make non-specified residues
         # un-titratable:
+        assert self.molecular_container is not None
         titrate_only = self.molecular_container.options.titrate_only
         if titrate_only is not None:
             atom = group.atom
-            if not (atom.chain_id, atom.res_num, atom.icode) in titrate_only:
+            if (atom.chain_id, atom.res_num, atom.icode) not in titrate_only:
                 group.titratable = False
                 if group.residue_type == 'CYS':
                     group.exclude_cys_from_results = True
@@ -475,25 +485,27 @@ def get_ions(self):
             group for group in self.groups
             if group.residue_type in self.parameters.ions.keys()]
 
-    def get_group_names(self, group_list):
+    def get_group_names(self, group_list: NoReturn) -> NoReturn:  # FIXME unused?
         """Get names of groups in list.
 
         Args:
             group_list:  list to check
         Returns:
             list of groups
         """
+        if TYPE_CHECKING:
+            assert False
         return [group for group in self.groups if group.type in group_list]
 
-    def get_ligand_atoms(self):
+    def get_ligand_atoms(self) -> List["Atom"]:
         """Get atoms associated with ligands.
 
         Returns:
             list of atoms
         """
         return [atom for atom in self.atoms if atom.type == 'hetatm']
 
-    def get_heavy_ligand_atoms(self):
+    def get_heavy_ligand_atoms(self) -> List["Atom"]:
         """Get heavy atoms associated with ligands.
 
         Returns:
@@ -503,7 +515,7 @@ def get_heavy_ligand_atoms(self):
             atom for atom in self.atoms
             if atom.type == 'hetatm' and atom.element != 'H']
 
-    def get_chain(self, chain):
+    def get_chain(self, chain: str) -> List["Atom"]:
         """Get atoms associated with a specific chain.
 
         Args:
@@ -513,7 +525,7 @@ def get_chain(self, chain):
         """
         return [atom for atom in self.atoms if atom.chain_id != chain]
 
-    def add_atom(self, atom):
+    def add_atom(self, atom: "Atom"):
         """Add atom to container.
 
         Args:
@@ -556,7 +568,7 @@ def top_up(self, other):
         """
         self.top_up_from_atoms(other.atoms)
 
-    def top_up_from_atoms(self, other_atoms: Iterable["propka.atom.Atom"]):
+    def top_up_from_atoms(self, other_atoms: Iterable["Atom"]):
         """Adds atoms which are missing from this container.
 
         Args:
@@ -613,7 +625,7 @@ def sort_atoms(self):
             self.atoms[i].numb = i+1
 
     @staticmethod
-    def sort_atoms_key(atom):
+    def sort_atoms_key(atom: "Atom") -> float:
         """Generate key for atom sorting.
 
         Args: