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Typing: Atom members

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This commit is contained in:
Thomas Holder
2023-12-13 19:53:16 +01:00
parent 0aafca7f73
commit 1d50cf4b0b
3 changed files with 58 additions and 43 deletions
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89
propka/atom.py
View File

@@ -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,
res_num=None, x=None, y=None, z=None, occ=None,
beta=None):
def set_property(self,
numb: Optional[int] = 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:

3
propka/group.py
View File

@@ -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)

9
propka/ligand_pka_values.py
View File

@@ -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.