omic/propka
1
0
Fork 0
Code Issues Pull Requests Actions 1 Packages Projects Releases Wiki Activity

Merge pull request #172 from speleo3/mypy

Browse Source 
Add type annotations and mypy CI job
This commit is contained in:
Thomas Holder
2023-11-03 12:46:28 +01:00
committed by GitHub
parent ee89e36f58 57d7c6721b
commit a62e2a4dae
14 changed files with 233 additions and 149 deletions
Download Patch File Download Diff File Expand all files Collapse all files

10
.github/workflows/python-package.yml vendored
View File

@@ -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

2
.gitignore vendored
View File

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

47
propka/atom.py
View File

@@ -7,9 +7,15 @@ The :class:`Atom` class contains all atom information found in the PDB file.
"""
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 @@ class Atom:
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 @@ class Atom:
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 @@ class Atom:
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:

6
propka/bonds.py
View File

@@ -10,6 +10,10 @@ import math
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 @@ class BondMaker:
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:

15
propka/calculations.py
View File

@@ -6,13 +6,17 @@ Mathematical helper functions.
"""
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)

46
propka/conformation_container.py
View File

@@ -6,6 +6,12 @@ Container data structure for molecular conformations.
"""
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
@@ -13,7 +19,6 @@ 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 @@ class ConformationContainer:
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 @@ class ConformationContainer:
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 @@ class ConformationContainer:
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 @@ class ConformationContainer:
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 @@ class ConformationContainer:
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 @@ class ConformationContainer:
# 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
@@ -475,7 +485,7 @@ class ConformationContainer:
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:
@@ -483,9 +493,11 @@ class ConformationContainer:
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:
@@ -493,7 +505,7 @@ class ConformationContainer:
"""
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 @@ class ConformationContainer:
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 @@ class ConformationContainer:
"""
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 @@ class ConformationContainer:
"""
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 @@ class ConformationContainer:
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:

21
propka/energy.py
View File

@@ -7,6 +7,12 @@ Energy calculations.
"""
import math
import logging
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from propka.conformation_container import ConformationContainer
from propka.group import Group
from propka.calculations import squared_distance, get_smallest_distance
@@ -27,13 +33,14 @@ COMBINED_NUM_BURIED_MAX = 900
SEPARATE_NUM_BURIED_MAX = 400
def radial_volume_desolvation(parameters, group):
def radial_volume_desolvation(parameters, group: "Group") -> None:
"""Calculate desolvation terms for group.
Args:
parameters: parameters for desolvation calculation
group: group of atoms for calculation
"""
assert group.atom.conformation_container is not None
all_atoms = group.atom.conformation_container.get_non_hydrogen_atoms()
volume = 0.0
group.num_volume = 0
@@ -66,7 +73,7 @@ def radial_volume_desolvation(parameters, group):
* volume_after_allowance * scale_factor)
def calculate_scale_factor(parameters, weight):
def calculate_scale_factor(parameters, weight: float) -> float:
"""Calculate desolvation scaling factor.
Args:
@@ -82,7 +89,7 @@ def calculate_scale_factor(parameters, weight):
return scale_factor
def calculate_weight(parameters, num_volume):
def calculate_weight(parameters, num_volume: int) -> float:
"""Calculate the atom-based desolvation weight.
TODO - figure out why a similar function exists in version.py
@@ -102,7 +109,7 @@ def calculate_weight(parameters, num_volume):
return weight
def calculate_pair_weight(parameters, num_volume1, num_volume2):
def calculate_pair_weight(parameters, num_volume1: int, num_volume2: int) -> float:
"""Calculate the atom-pair based desolvation weight.
Args:
@@ -120,7 +127,7 @@ def calculate_pair_weight(parameters, num_volume1, num_volume2):
return weight
def hydrogen_bond_energy(dist, dpka_max, cutoffs, f_angle=1.0):
def hydrogen_bond_energy(dist, dpka_max: float, cutoffs, f_angle=1.0) -> float:
"""Calculate hydrogen-bond interaction pKa shift.
Args:
@@ -319,7 +326,7 @@ def check_coulomb_pair(parameters, group1, group2, dist):
return do_coulomb
def coulomb_energy(dist, weight, parameters):
def coulomb_energy(dist: float, weight: float, parameters) -> float:
"""Calculates the Coulomb interaction pKa shift based on Coulomb's law.
Args:
@@ -340,7 +347,7 @@ def coulomb_energy(dist, weight, parameters):
return abs(dpka)
def backbone_reorganization(_, conformation):
def backbone_reorganization(_, conformation: "ConformationContainer") -> None:
"""Perform calculations related to backbone reorganizations.
NOTE - this was described in the code as "adding test stuff"

67
propka/group.py
View File

@@ -11,8 +11,11 @@ Routines and classes for storing groups important to PROPKA calculations.
"""
import logging
import math
from typing import cast, Dict, Iterable, List, NoReturn, Optional
import propka.ligand
import propka.protonate
from propka.atom import Atom
from propka.ligand_pka_values import LigandPkaValues
from propka.determinant import Determinant
@@ -57,7 +60,7 @@ class Group:
longer supported.
"""
def __init__(self, atom):
def __init__(self, atom: Atom):
"""Initialize with an atom.
Args:
@@ -67,7 +70,11 @@ class Group:
self.type = ''
atom.group = self
# set up data structures
self.determinants = {'sidechain': [], 'backbone': [], 'coulomb': []}
self.determinants: Dict[str, List[Determinant]] = {
'sidechain': [],
'backbone': [],
'coulomb': [],
}
self.pka_value = 0.0
self.model_pka = 0.0
# Energy associated with volume interactions
@@ -84,16 +91,16 @@ class Group:
self.z = 0.0
self.charge = 0
self.parameters = None
self.exclude_cys_from_results = None
self.interaction_atoms_for_acids = []
self.interaction_atoms_for_bases = []
self.exclude_cys_from_results = False
self.interaction_atoms_for_acids: List[Atom] = []
self.interaction_atoms_for_bases: List[Atom] = []
self.model_pka_set = False
self.intrinsic_pka = None
self.titratable = None
self.titratable = False
# information on covalent and non-covalent coupling
self.non_covalently_coupled_groups = []
self.covalently_coupled_groups = []
self.coupled_titrating_group = None
self.non_covalently_coupled_groups: List["Group"] = []
self.covalently_coupled_groups: List["Group"] = []
self.coupled_titrating_group: Optional["Group"] = None
self.common_charge_centre = False
self.residue_type = self.atom.res_name
if self.atom.terminal:
@@ -112,9 +119,9 @@ class Group:
self.label = fmt.format(
type=self.residue_type, name=atom.name, chain=atom.chain_id)
# container for squared distances
self.squared_distances = {}
self.squared_distances: NoReturn = cast(NoReturn, {}) # FIXME unused?
def couple_covalently(self, other):
def couple_covalently(self, other: "Group") -> None:
"""Couple this group with another group.
Args:
@@ -126,7 +133,7 @@ class Group:
if self not in other.covalently_coupled_groups:
other.covalently_coupled_groups.append(self)
def couple_non_covalently(self, other):
def couple_non_covalently(self, other: "Group") -> None:
"""Non-covalenthly couple this group with another group.
Args:
@@ -154,7 +161,7 @@ class Group:
"""
return self.non_covalently_coupled_groups
def share_determinants(self, others):
def share_determinants(self, others: Iterable["Group"]) -> None:
"""Share determinants between this group and others.
Args:
@@ -172,7 +179,7 @@ class Group:
self.calculate_total_pka()
the_other.calculate_total_pka()
def share_determinant(self, new_determinant, type_):
def share_determinant(self, new_determinant: Determinant, type_: str) -> None:
"""Add determinant to this group's list of determinants.
Args:
@@ -230,7 +237,7 @@ class Group:
self.add_determinant(determinant, type_)
return self
def add_determinant(self, new_determinant, type_):
def add_determinant(self, new_determinant: Determinant, type_: str) -> None:
"""Add to current and creates non-present determinants.
Args:
@@ -247,7 +254,7 @@ class Group:
self.determinants[type_].append(Determinant(new_determinant.group,
new_determinant.value))
def set_determinant(self, new_determinant, type_):
def set_determinant(self, new_determinant: Determinant, type_: str) -> None:
"""Overwrite current and create non-present determinants.
Args:
@@ -345,8 +352,8 @@ class Group:
# set the main atom as interaction atom
self.set_interaction_atoms([self.atom], [self.atom])
def set_interaction_atoms(self, interaction_atoms_for_acids,
interaction_atoms_for_bases):
def set_interaction_atoms(self, interaction_atoms_for_acids: List[Atom],
interaction_atoms_for_bases: List[Atom]):
"""Set interacting atoms and group types.
Args:
@@ -359,10 +366,10 @@ class Group:
self.interaction_atoms_for_bases = interaction_atoms_for_bases
# check if all atoms have been identified
ok = True
for [expect, found, _] in [[EXPECTED_ATOMS_ACID_INTERACTIONS,
self.interaction_atoms_for_acids, 'acid'],
[EXPECTED_ATOMS_BASE_INTERACTIONS,
self.interaction_atoms_for_bases, 'base']]:
for (expect, found) in [
(EXPECTED_ATOMS_ACID_INTERACTIONS, self.interaction_atoms_for_acids),
(EXPECTED_ATOMS_BASE_INTERACTIONS, self.interaction_atoms_for_bases),
]:
if self.type in expect.keys():
for elem in expect[self.type].keys():
if (len([a for a in found if a.element == elem])
@@ -395,7 +402,7 @@ class Group:
' {0:s}'.format(
str(self.interaction_atoms_for_bases[i])))
def get_interaction_atoms(self, interacting_group):
def get_interaction_atoms(self, interacting_group) -> List[Atom]:
"""Get atoms involved in interaction with other group.
Args:
@@ -403,6 +410,7 @@ class Group:
Returns:
list of atoms
"""
assert self.parameters is not None
if interacting_group.residue_type in self.parameters.base_list:
return self.interaction_atoms_for_bases
else:
@@ -518,7 +526,7 @@ class Group:
self.model_pka + self.energy_volume + self.energy_local
+ back_bone + side_chain)
def get_summary_string(self, remove_penalised_group=False):
def get_summary_string(self, remove_penalised_group: bool = False) -> str:
"""Create summary string for this group.
Args:
@@ -1210,7 +1218,7 @@ class TitratableLigandGroup(Group):
self.model_pka_set = True
def is_group(parameters, atom):
def is_group(parameters, atom: Atom) -> Optional[Group]:
"""Identify whether the atom belongs to a group.
Args:
@@ -1244,7 +1252,7 @@ def is_group(parameters, atom):
return None
def is_protein_group(parameters, atom):
def is_protein_group(parameters, atom: Atom) -> Optional[Group]:
"""Identify whether the atom belongs to a protein group.
Args:
@@ -1278,7 +1286,7 @@ def is_protein_group(parameters, atom):
return None
def is_ligand_group_by_groups(_, atom):
def is_ligand_group_by_groups(_, atom: Atom) -> Optional[Group]:
"""Identify whether the atom belongs to a ligand group by checking groups.
Args:
@@ -1360,7 +1368,7 @@ def is_ligand_group_by_groups(_, atom):
return None
def is_ligand_group_by_marvin_pkas(parameters, atom):
def is_ligand_group_by_marvin_pkas(parameters, atom: Atom) -> Optional[Group]:
"""Identify whether the atom belongs to a ligand group by calculating
'Marvin pKas'.
@@ -1375,6 +1383,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom):
# calculate Marvin ligand pkas for this conformation container
# if not already done
# TODO - double-check testing coverage of these functions.
assert atom.conformation_container is not None
if not atom.conformation_container.marvin_pkas_calculated:
lpka = LigandPkaValues(parameters)
lpka.get_marvin_pkas_for_molecular_container(
@@ -1396,7 +1405,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom):
return None
def is_ion_group(parameters, atom):
def is_ion_group(parameters, atom: Atom) -> Optional[Group]:
"""Identify whether the atom belongs to an ion group.
Args:

47
propka/hydrogens.py
View File

@@ -7,15 +7,19 @@ Calculations related to hydrogen placement.
"""
import math
import logging
from typing import List, Optional, Tuple, TYPE_CHECKING
from propka.protonate import Protonate
from propka.bonds import BondMaker
from propka.atom import Atom
if TYPE_CHECKING:
from propka.molecular_container import MolecularContainer
_LOGGER = logging.getLogger(__name__)
def setup_bonding_and_protonation(molecular_container):
def setup_bonding_and_protonation(molecular_container: "MolecularContainer") -> None:
"""Set up bonding and protonation for a molecule.
Args:
@@ -34,7 +38,7 @@ def setup_bonding_and_protonation(molecular_container):
protonator.protonate(molecular_container)
def setup_bonding(molecular_container):
def setup_bonding(molecular_container: "MolecularContainer") -> BondMaker:
"""Set up bonding for a molecular container.
Args:
@@ -47,7 +51,7 @@ def setup_bonding(molecular_container):
return my_bond_maker
def setup_bonding_and_protonation_30_style(molecular_container):
def setup_bonding_and_protonation_30_style(molecular_container: "MolecularContainer") -> BondMaker:
"""Set up bonding for a molecular container.
Args:
@@ -63,7 +67,7 @@ def setup_bonding_and_protonation_30_style(molecular_container):
return bond_maker
def protonate_30_style(molecular_container):
def protonate_30_style(molecular_container: "MolecularContainer") -> None:
"""Protonate the molecule.
Args:
@@ -73,9 +77,9 @@ def protonate_30_style(molecular_container):
_LOGGER.info('Now protonating %s', name)
# split atom into residues
curres = -1000000
residue = []
o_atom = None
c_atom = None
residue: List[Atom] = []
o_atom: Optional[Atom] = None
c_atom: Optional[Atom] = None
for atom in molecular_container.conformations[name].atoms:
if atom.res_num != curres:
curres = atom.res_num
@@ -100,7 +104,7 @@ def protonate_30_style(molecular_container):
residue.append(atom)
def set_ligand_atom_names(molecular_container):
def set_ligand_atom_names(molecular_container: "MolecularContainer") -> None:
"""Set names for ligands in molecular container.
Args:
@@ -110,7 +114,7 @@ def set_ligand_atom_names(molecular_container):
molecular_container.conformations[name].set_ligand_atom_names()
def add_arg_hydrogen(residue):
def add_arg_hydrogen(residue: List[Atom]) -> List[Atom]:
"""Adds Arg hydrogen atoms to residues according to the 'old way'.
Args:
@@ -142,7 +146,7 @@ def add_arg_hydrogen(residue):
return [h1_atom, h2_atom, h3_atom, h4_atom, h5_atom]
def add_his_hydrogen(residue):
def add_his_hydrogen(residue: List[Atom]) -> None:
"""Adds His hydrogen atoms to residues according to the 'old way'.
Args:
@@ -165,7 +169,7 @@ def add_his_hydrogen(residue):
he_atom.name = "HNE"
def add_trp_hydrogen(residue):
def add_trp_hydrogen(residue: List[Atom]) -> None:
"""Adds Trp hydrogen atoms to residues according to the 'old way'.
Args:
@@ -188,7 +192,7 @@ def add_trp_hydrogen(residue):
he_atom.name = "HNE"
def add_amd_hydrogen(residue):
def add_amd_hydrogen(residue: List[Atom]) -> None:
"""Adds Gln & Asn hydrogen atoms to residues according to the 'old way'.
Args:
@@ -217,7 +221,9 @@ def add_amd_hydrogen(residue):
h2_atom.name = "HN2"
def add_backbone_hydrogen(residue, o_atom, c_atom):
def add_backbone_hydrogen(residue: List[Atom],
o_atom: Optional[Atom],
c_atom: Optional[Atom]) -> Tuple[Optional[Atom], Optional[Atom]]:
"""Adds hydrogen backbone atoms to residues according to the old way.
dR is wrong for the N-terminus (i.e. first residue) but it doesn't affect
@@ -240,18 +246,18 @@ def add_backbone_hydrogen(residue, o_atom, c_atom):
new_c_atom = atom
if atom.name == "O":
new_o_atom = atom
if None in [c_atom, o_atom, n_atom]:
return [new_o_atom, new_c_atom]
if c_atom is None or o_atom is None or n_atom is None:
return (new_o_atom, new_c_atom)
if n_atom.res_name == "PRO":
# PRO doesn't have an H-atom; do nothing
pass
else:
h_atom = protonate_direction(n_atom, o_atom, c_atom)
h_atom.name = "H"
return [new_o_atom, new_c_atom]
return (new_o_atom, new_c_atom)
def protonate_direction(x1_atom, x2_atom, x3_atom):
def protonate_direction(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) -> Atom:
"""Protonates an atom, x1_atom, given a direction.
New direction for x1_atom proton is (x2_atom -> x3_atom).
@@ -275,7 +281,7 @@ def protonate_direction(x1_atom, x2_atom, x3_atom):
return h_atom
def protonate_average_direction(x1_atom, x2_atom, x3_atom):
def protonate_average_direction(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) -> Atom:
"""Protonates an atom, x1_atom, given a direction.
New direction for x1_atom is (x1_atom/x2_atom -> x3_atom).
@@ -301,7 +307,7 @@ def protonate_average_direction(x1_atom, x2_atom, x3_atom):
return h_atom
def protonate_sp2(x1_atom, x2_atom, x3_atom):
def protonate_sp2(x1_atom: Atom, x2_atom: Atom, x3_atom: Atom) -> Atom:
"""Protonates a SP2 atom, given a list of atoms
Args:
@@ -323,7 +329,7 @@ def protonate_sp2(x1_atom, x2_atom, x3_atom):
return h_atom
def make_new_h(atom, x, y, z):
def make_new_h(atom: Atom, x: float, y: float, z: float) -> Atom:
"""Add a new hydrogen to an atom at the specified position.
Args:
@@ -347,5 +353,6 @@ def make_new_h(atom, x, y, z):
new_h.number_of_protons_to_add = 0
new_h.num_pi_elec_2_3_bonds = 0
atom.bonded_atoms.append(new_h)
assert atom.conformation_container is not None
atom.conformation_container.add_atom(new_h)
return new_h

21
propka/input.py
View File

@@ -10,12 +10,15 @@ Input routines.
:func:`get_atom_lines_from_input`) have been removed.
"""
import typing
from typing import Iterator, Tuple
import contextlib
from pathlib import Path
from pkg_resources import resource_filename
from propka.lib import protein_precheck
from propka.atom import Atom
from propka.conformation_container import ConformationContainer
from propka.molecular_container import MolecularContainer
from propka.parameters import Parameters
def open_file_for_reading(
@@ -27,18 +30,14 @@ def open_file_for_reading(
input_file: path to file or file-like object. If file-like object,
then will attempt seek(0).
"""
try:
if not isinstance(input_file, (str, Path)):
input_file.seek(0)
except AttributeError:
pass
else:
# TODO use contextlib.nullcontext when dropping Python 3.6 support
return contextlib.contextmanager(lambda: (yield input_file))()
return contextlib.nullcontext(input_file)
return contextlib.closing(open(input_file, 'rt'))
def read_molecule_file(filename: str, mol_container, stream=None):
def read_molecule_file(filename: str, mol_container: MolecularContainer, stream=None) -> MolecularContainer:
"""Read input file or stream (PDB or PROPKA) for a molecular container
Args:
@@ -123,7 +122,7 @@ def read_molecule_file(filename: str, mol_container, stream=None):
return mol_container
def read_parameter_file(input_file, parameters):
def read_parameter_file(input_file, parameters: Parameters) -> Parameters:
"""Read a parameter file.
Args:
@@ -144,7 +143,7 @@ def read_parameter_file(input_file, parameters):
return parameters
def conformation_sorter(conf):
def conformation_sorter(conf: str) -> int:
"""TODO - figure out what this function does."""
model = int(conf[:-1])
altloc = conf[-1:]
@@ -152,7 +151,7 @@ def conformation_sorter(conf):
def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False,
tags=['ATOM ', 'HETATM'], chains=None):
tags=['ATOM ', 'HETATM'], chains=None) -> Iterator[Tuple[str, Atom]]:
"""Get atom lines from PDB file.
Args:
@@ -237,7 +236,7 @@ def read_pdb(pdb_file, parameters, molecule):
keep_protons=molecule.options.keep_protons,
chains=molecule.options.chains)
for (name, atom) in lines:
if not name in conformations.keys():
if name not in conformations.keys():
conformations[name] = ConformationContainer(
name=name, parameters=parameters, molecular_container=molecule)
conformations[name].add_atom(atom)

31
propka/molecular_container.py
View File

@@ -6,6 +6,8 @@ Molecular container for storing all contents of PDB files.
"""
import logging
import os
from typing import Dict, List, Optional, Tuple
import propka.version
from propka.output import write_pka, print_header, print_result
from propka.conformation_container import ConformationContainer
@@ -28,7 +30,12 @@ class MolecularContainer:
PROPKA input files is no longer supported.
"""
def __init__(self, parameters, options=None):
conformation_names: List[str]
conformations: Dict[str, ConformationContainer]
name: Optional[str]
version: propka.version.Version
def __init__(self, parameters, options=None) -> None:
"""Initialize molecular container.
Args:
@@ -50,7 +57,7 @@ class MolecularContainer:
parameters.version)
raise Exception(errstr)
def top_up_conformations(self):
def top_up_conformations(self) -> None:
"""Makes sure that all atoms are present in all conformations."""
ref_atoms = {
atom.residue_label: atom
@@ -60,24 +67,24 @@ class MolecularContainer:
for conf in self.conformations.values():
conf.top_up_from_atoms(ref_atoms.values())
def find_covalently_coupled_groups(self):
def find_covalently_coupled_groups(self) -> None:
"""Find covalently coupled groups."""
for name in self.conformation_names:
self.conformations[name].find_covalently_coupled_groups()
def find_non_covalently_coupled_groups(self):
def find_non_covalently_coupled_groups(self) -> None:
"""Find non-covalently coupled groups."""
verbose = self.options.display_coupled_residues
for name in self.conformation_names:
self.conformations[name].find_non_covalently_coupled_groups(
verbose=verbose)
def extract_groups(self):
def extract_groups(self) -> None:
"""Identify the groups needed for pKa calculation."""
for name in self.conformation_names:
self.conformations[name].extract_groups()
def calculate_pka(self):
def calculate_pka(self) -> None:
"""Calculate pKa values."""
# calculate for each conformation
for name in self.conformation_names:
@@ -90,7 +97,7 @@ class MolecularContainer:
# print out the conformation-average results
print_result(self, 'AVR', self.version.parameters)
def average_of_conformations(self):
def average_of_conformations(self) -> None:
"""Generate an average of conformations."""
parameters = self.conformations[self.conformation_names[0]].parameters
# make a new configuration to hold the average values
@@ -124,7 +131,7 @@ class MolecularContainer:
self.conformations['AVR'] = avr_conformation
def write_pka(self, filename=None, reference="neutral",
direction="folding", options=None):
direction="folding", options=None) -> None:
"""Write pKa information to a file.
Args:
@@ -187,7 +194,7 @@ class MolecularContainer:
stability_range = [min(stable_values), max(stable_values)]
return profile, opt, range_80pct, stability_range
def get_charge_profile(self, conformation='AVR', grid=[0., 14., .1]):
def get_charge_profile(self, conformation: str = 'AVR', grid=[0., 14., .1]):
"""Get charge profile for conformation as function of pH.
Args:
@@ -196,7 +203,7 @@ class MolecularContainer:
Returns:
list of charge state values
"""
charge_profile = []
charge_profile: List[List[float]] = []
for ph in make_grid(*grid):
conf = self.conformations[conformation]
q_unfolded, q_folded = conf.calculate_charge(
@@ -204,8 +211,8 @@ class MolecularContainer:
charge_profile.append([ph, q_unfolded, q_folded])
return charge_profile
def get_pi(self, conformation='AVR', grid=[0., 14., 1], *,
precision: float = 1e-4):
def get_pi(self, conformation: str = 'AVR', grid=[0., 14., 1], *,
precision: float = 1e-4) -> Tuple[float, float]:
"""Get the isoelectric points for folded and unfolded states.
Args:

49
propka/vector_algebra.py
View File

@@ -6,16 +6,35 @@ Vector algebra for PROPKA.
"""
import logging
import math
from typing import Optional, Protocol, Union
from propka.lib import get_sorted_configurations
_LOGGER = logging.getLogger(__name__)
class _XYZ(Protocol):
"""
Protocol for types which have x/y/z attributes, like Vector or Atom.
"""
x: float
y: float
z: float
class Vector:
"""Vector"""
def __init__(self, xi=0.0, yi=0.0, zi=0.0, atom1=None, atom2=None):
x: float
y: float
z: float
def __init__(self,
xi: float = 0.0,
yi: float = 0.0,
zi: float = 0.0,
atom1: Optional[_XYZ] = None,
atom2: Optional[_XYZ] = None):
"""Initialize vector.
Args:
@@ -41,17 +60,17 @@ class Vector:
self.y = atom2.y - self.y
self.z = atom2.z - self.z
def __add__(self, other):
def __add__(self, other: _XYZ):
return Vector(self.x + other.x,
self.y + other.y,
self.z + other.z)
def __sub__(self, other):
def __sub__(self, other: _XYZ):
return Vector(self.x - other.x,
self.y - other.y,
self.z - other.z)
def __mul__(self, other):
def __mul__(self, other: Union["Vector", "Matrix4x4", float]):
"""Dot product, scalar and matrix multiplication."""
if isinstance(other, Vector):
return self.x * other.x + self.y * other.y + self.z * other.z
@@ -66,14 +85,12 @@ class Vector:
)
elif type(other) in [int, float]:
return Vector(self.x * other, self.y * other, self.z * other)
else:
_LOGGER.info('{0:s} not supported'.format(type(other)))
raise TypeError
raise TypeError(f'{type(other)} not supported')
def __rmul__(self, other):
return self.__mul__(other)
def __pow__(self, other):
def __pow__(self, other: _XYZ):
"""Cross product."""
return Vector(self.y * other.z - self.z * other.y,
self.z * other.x - self.x * other.z,
@@ -89,7 +106,7 @@ class Vector:
"""Return vector squared-length"""
return self.x * self.x + self.y * self.y + self.z * self.z
def length(self):
def length(self) -> float:
"""Return vector length."""
return math.sqrt(self.sq_length())
@@ -107,7 +124,7 @@ class Vector:
res = Vector(self.z, 0, -self.x)
return res
def rescale(self, new_length):
def rescale(self, new_length: float):
""" Rescale vector to new length while preserving direction """
frac = new_length/(self.length())
res = Vector(xi=self.x*frac, yi=self.y*frac, zi=self.z*frac)
@@ -145,7 +162,7 @@ class Matrix4x4:
self.a44 = a44i
def angle(avec, bvec):
def angle(avec: Vector, bvec: Vector) -> float:
"""Get the angle between two vectors.
Args:
@@ -158,7 +175,7 @@ def angle(avec, bvec):
return math.acos(dot / (avec.length() * bvec.length()))
def angle_degrees(avec, bvec):
def angle_degrees(avec: Vector, bvec: Vector) -> float:
"""Get the angle between two vectors in degrees.
Args:
@@ -170,7 +187,7 @@ def angle_degrees(avec, bvec):
return math.degrees(angle(avec, bvec))
def signed_angle_around_axis(avec, bvec, axis):
def signed_angle_around_axis(avec: Vector, bvec: Vector, axis: Vector) -> float:
"""Get signed angle of two vectors around axis in radians.
Args:
@@ -189,7 +206,7 @@ def signed_angle_around_axis(avec, bvec, axis):
return ang
def rotate_vector_around_an_axis(theta, axis, vec):
def rotate_vector_around_an_axis(theta: float, axis: Vector, vec: Vector) -> Vector:
"""Rotate vector around an axis.
Args:
@@ -225,7 +242,7 @@ def rotate_vector_around_an_axis(theta, axis, vec):
return vec
def rotate_atoms_around_z_axis(theta):
def rotate_atoms_around_z_axis(theta: float) -> Matrix4x4:
"""Get rotation matrix for z-axis.
Args:
@@ -253,7 +270,7 @@ def rotate_atoms_around_z_axis(theta):
)
def rotate_atoms_around_y_axis(theta):
def rotate_atoms_around_y_axis(theta: float) -> Matrix4x4:
"""Get rotation matrix for y-axis.
Args:

12
setup.cfg
View File

@@ -19,3 +19,15 @@ omit =
exclude_lines =
pragma: no cover
[yapf]
column_limit = 88
based_on_style = pep8
allow_split_before_dict_value = False
[mypy]
files = propka,tests
exclude = (?x)(
/_version\.py$
)
explicit_package_bases = True
ignore_missing_imports = True

8
tests/test_basic_regression.py
View File

@@ -10,6 +10,7 @@ from propka.parameters import Parameters
from propka.molecular_container import MolecularContainer
from propka.input import read_parameter_file, read_molecule_file
from propka.lib import loadOptions
from typing import List
_LOGGER = logging.getLogger(__name__)
@@ -32,8 +33,6 @@ RESULTS_DIR = Path("tests/results")
if not RESULTS_DIR.is_dir():
_LOGGER.warning("Switching to sub-directory")
RESULTS_DIR = Path("results")
# Arguments to add to all tests
DEFAULT_ARGS = []
def get_test_dirs():
@@ -87,8 +86,8 @@ def run_propka(options, pdb_path, tmp_path):
def parse_pka(pka_path: Path) -> dict:
"""Parse testable data from a .pka file into a dictionary.
"""
pka_list = []
data = {"pKa": pka_list}
pka_list: List[float] = []
data: dict = {"pKa": pka_list}
with open(pka_path, "rt") as pka_file:
at_pka = False
@@ -98,6 +97,7 @@ def parse_pka(pka_path: Path) -> dict:
at_pka = False
else:
m = re.search(r'\d+\.\d+', line[13:])
assert m is not None
pka_list.append(float(m.group()))
elif "model-pKa" in line:
at_pka = True