Typing: Atom members

propka/atom.py

@@ -43,6 +43,43 @@ class Atom:
        :meth:`make_input_line` and :meth:`get_input_parameters` have been
        removed as reading/writing PROPKA input is no longer supported.
     """
+    group: Optional["Group"] = None
+    group_type: Optional[str] = None
+    cysteine_bridge: bool = False
+    residue: NoReturn = None  # type: ignore[assignment]
+    conformation_container: Optional["ConformationContainer"] = None
+    molecular_container: Optional["MolecularContainer"] = None
+    is_protonated: bool = False
+    steric_num_lone_pairs_set: bool = False
+    terminal: Optional[str] = None
+    charge: float = 0.0
+    charge_set: bool = False
+    steric_number: int = 0
+    number_of_lone_pairs: int = 0
+    number_of_protons_to_add: int = 0
+    num_pi_elec_2_3_bonds: int = 0
+    num_pi_elec_conj_2_3_bonds: int = 0
+    groups_extracted: bool = False
+
+    # PDB attributes
+    name: str = ''
+    numb: int = 0
+    x: float = 0.0
+    y: float = 0.0
+    z: float = 0.0
+    res_num: int = 0
+    res_name: str = ''
+    chain_id: str = 'A'
+    type: str = ''
+    occ: str = '1.0'
+    beta: str = '0.0'
+    element: str = ''
+    icode: str = ''
+
+    # ligand atom types
+    sybyl_type = ''
+    sybyl_assigned = False
+    marvin_pka = False
 
     def __init__(self, line: Optional[str] = None):
         """Initialize Atom object.
@@ -51,53 +88,17 @@ class Atom:
             line:  Line from a PDB file to set properties of atom.
         """
         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: Optional[ConformationContainer] = None
-        self.molecular_container: Optional[MolecularContainer] = None
-        self.is_protonated = False
-        self.steric_num_lone_pairs_set = False
-        self.terminal: Optional[str] = None
-        self.charge = 0.0
-        self.charge_set = False
-        self.steric_number = 0
-        self.number_of_lone_pairs = 0
-        self.number_of_protons_to_add = 0
-        self.num_pi_elec_2_3_bonds = 0
-        self.num_pi_elec_conj_2_3_bonds = 0
-        self.groups_extracted = 0
         self.set_properties(line)
         fmt = "{r.name:3s}{r.res_num:>4d}{r.chain_id:>2s}"
         self.residue_label = fmt.format(r=self)
 
-        # ligand atom types
-        self.sybyl_type = ''
-        self.sybyl_assigned = False
-        self.marvin_pka = False
-
     def set_properties(self, line: Optional[str]):
         """Line from PDB file to set properties of atom.
 
         Args:
             line:  PDB file line
         """
-        self.name = ''
-        self.numb = 0
-        self.x = 0.0
-        self.y = 0.0
-        self.z = 0.0
-        self.res_num = 0
-        self.res_name = ''
-        self.chain_id = 'A'
-        self.type = ''
-        self.occ = '1.0'
-        self.beta = '0.0'
-        self.element = ''
-        self.icode = ''
-
         if line:
             self.name = line[12:16].strip()
             self.numb = int(hybrid36.decode(line[6:11]))
@@ -184,9 +185,17 @@ class Atom:
                     return True
         return False
 
-    def set_property(self, numb=None, name=None, res_name=None, chain_id=None,
+    def set_property(self,
-                     res_num=None, x=None, y=None, z=None, occ=None,
+                     numb: Optional[int] = None,
-                     beta=None):
+                     name: Optional[str] = None,
+                     res_name: Optional[str] = None,
+                     chain_id: Optional[str] = None,
+                     res_num: Optional[int] = None,
+                     x: Optional[float] = None,
+                     y: Optional[float] = None,
+                     z: Optional[float] = None,
+                     occ: Optional[str] = None,
+                     beta: Optional[str] = None):
         """Set properties of the atom object.
 
         Args:
@@ -345,7 +354,7 @@ class Atom:
         """Return an undefined-format string version of this atom."""
         return STR_FMT.format(r=self)
 
-    def set_residue(self, residue):
+    def set_residue(self, residue: NoReturn):
         """ Makes a reference to the parent residue
 
         Args:

propka/group.py

@@ -1230,7 +1230,7 @@ def is_group(parameters: Parameters, atom: Atom) -> Optional[Group]:
     Returns:
         group for atom or None
     """
-    atom.groups_extracted = 1
+    atom.groups_extracted = True
     # check if this atom belongs to a protein group
     protein_group = is_protein_group(parameters, atom)
     if protein_group:
@@ -1386,6 +1386,7 @@ def is_ligand_group_by_marvin_pkas(parameters: Parameters, atom: Atom) -> Option
     # calculate Marvin ligand pkas for this conformation container
     # if not already done
     # TODO - double-check testing coverage of these functions.
+    assert atom.molecular_container is not None
     assert atom.conformation_container is not None
     if not atom.conformation_container.marvin_pkas_calculated:
         lpka = LigandPkaValues(parameters)

propka/ligand_pka_values.py

@@ -15,10 +15,14 @@ import shutil
 import subprocess
 import sys
 import warnings
+from typing import TYPE_CHECKING, NoReturn
+
 from propka.output import write_mol2_for_atoms
 from propka.lib import split_atoms_into_molecules
 from propka.parameters import Parameters
 
+if TYPE_CHECKING:
+    from propka.molecular_container import MolecularContainer
 
 _LOGGER = logging.getLogger(__name__)
 
@@ -58,7 +62,8 @@ class LigandPkaValues:
         return loc
 
     def get_marvin_pkas_for_pdb_file(
-            self, molecule, parameters, num_pkas=10, min_ph=-10.0, max_ph=20.0):
+            self, molecule: "MolecularContainer", parameters: NoReturn,
+            num_pkas=10, min_ph=-10.0, max_ph=20.0):
         """Use Marvin executables to get pKas for a PDB file.
 
         Args:
@@ -72,7 +77,7 @@ class LigandPkaValues:
         self.get_marvin_pkas_for_molecular_container(
             molecule, num_pkas=num_pkas, min_ph=min_ph, max_ph=max_ph)
 
-    def get_marvin_pkas_for_molecular_container(self, molecule, num_pkas=10,
+    def get_marvin_pkas_for_molecular_container(self, molecule: "MolecularContainer", num_pkas=10,
                                                 min_ph=-10.0, max_ph=20.0):
         """Use Marvin executables to calculate pKas for a molecular container.