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Merge pull request #177 from speleo3/mypy-2

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More static typing
This commit is contained in:
Thomas Holder
2023-12-19 10:51:58 +01:00
committed by GitHub
parent 9d4b59c825 abd3d05910
commit 5a00d059b2
27 changed files with 763 additions and 330 deletions
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3
MANIFEST.in
View File

@@ -4,3 +4,6 @@ include propka.cfg
include versioneer.py
include propka/_version.py
# Python type annotation declarations, see PEP-561
include propka/py.typed

92
propka/atom.py
View File

@@ -8,6 +8,7 @@ The :class:`Atom` class contains all atom information found in the PDB file.
import string
from typing import cast, List, NoReturn, Optional, TYPE_CHECKING
import warnings
from propka.lib import make_tidy_atom_label
from . import hybrid36
@@ -42,6 +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.
@@ -50,53 +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]))
@@ -183,9 +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:
@@ -303,6 +313,7 @@ class Atom:
Returns:
String with PDB line.
"""
warnings.warn("only used by unused function")
if numb is None:
numb = self.numb
if name is None:
@@ -343,11 +354,12 @@ 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:
residue: the parent residue
"""
raise NotImplementedError("unused")
if self.residue is None:
self.residue = residue

2
propka/bonds.py
View File

@@ -93,6 +93,7 @@ class BondMaker:
Args:
protein: the protein to search for bonds
"""
raise NotImplementedError("unused")
_LOGGER.info('++++ Side chains ++++')
# side chains
for chain in protein.chains:
@@ -132,6 +133,7 @@ class BondMaker:
cys1: one of the cysteines to check
cys1: one of the cysteines to check
"""
raise NotImplementedError("unused")
for atom1 in cys1.atoms:
if atom1.name == 'SG':
for atom2 in cys2.atoms:

40
propka/conformation_container.py
View File

@@ -6,7 +6,10 @@ Container data structure for molecular conformations.
"""
import logging
import functools
from typing import Iterable, List, NoReturn, Optional, TYPE_CHECKING, Set
from typing import Callable, Dict, Iterable, Iterator, List, NoReturn, Optional, TYPE_CHECKING, Set
from propka.lib import Options
from propka.version import Version
if TYPE_CHECKING:
from propka.atom import Atom
@@ -19,10 +22,13 @@ 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 propka.parameters import Parameters
_LOGGER = logging.getLogger(__name__)
CallableGroupToGroups = Callable[[Group], List[Group]]
#: A large number that gets multipled with the integer obtained from applying
#: :func:`ord` to the atom chain ID. Used in calculating atom keys for
@@ -44,9 +50,9 @@ class ConformationContainer:
"""
def __init__(self,
name: str = '',
parameters=None,
molecular_container: Optional["MolecularContainer"] = None):
name: str,
parameters: Parameters,
molecular_container: "MolecularContainer"):
"""Initialize conformation container.
Args:
@@ -145,6 +151,7 @@ class ConformationContainer:
Returns:
a set of bonded atom groups
"""
assert self.parameters is not None
res: Set[Group] = set()
for bond_atom in atom.bonded_atoms:
# skip the original atom
@@ -187,7 +194,7 @@ class ConformationContainer:
# If --titrate_only option is set, make non-specified residues
# un-titratable:
assert self.molecular_container is not None
assert self.molecular_container.options is not None
titrate_only = self.molecular_container.options.titrate_only
if titrate_only is not None:
atom = group.atom
@@ -196,7 +203,7 @@ class ConformationContainer:
if group.residue_type == 'CYS':
group.exclude_cys_from_results = True
def calculate_pka(self, version, options):
def calculate_pka(self, version: Version, options: Options):
"""Calculate pKas for conformation container.
Args:
@@ -272,7 +279,7 @@ class ConformationContainer:
return penalised_labels
@staticmethod
def share_determinants(groups):
def share_determinants(groups: Iterable[Group]):
"""Share sidechain, backbone, and Coloumb determinants between groups.
Args:
@@ -282,7 +289,7 @@ class ConformationContainer:
types = ['sidechain', 'backbone', 'coulomb']
for type_ in types:
# find maximum value for each determinant
max_dets = {}
max_dets: Dict[Group, float] = {}
for group in groups:
for det in group.determinants[type_]:
# update max dets
@@ -298,7 +305,11 @@ class ConformationContainer:
for group in groups:
group.set_determinant(new_determinant, type_)
def get_coupled_systems(self, groups, get_coupled_groups):
def get_coupled_systems(
self,
groups: Iterable[Group],
get_coupled_groups: CallableGroupToGroups,
) -> Iterator[Set[Group]]:
"""A generator that yields covalently coupled systems.
Args:
@@ -310,15 +321,16 @@ class ConformationContainer:
groups = set(groups)
while len(groups) > 0:
# extract a system of coupled groups ...
system = set()
system: Set[Group] = set()
self.get_a_coupled_system_of_groups(
groups.pop(), system, get_coupled_groups)
# ... and remove them from the list
groups -= system
yield system
def get_a_coupled_system_of_groups(self, new_group, coupled_groups,
get_coupled_groups):
def get_a_coupled_system_of_groups(self, new_group: Group,
coupled_groups: Set[Group],
get_coupled_groups: CallableGroupToGroups):
"""Set up coupled systems of groups.
Args:
@@ -349,7 +361,7 @@ class ConformationContainer:
reference=reference)
return ddg
def calculate_charge(self, parameters, ph=None):
def calculate_charge(self, parameters: Parameters, ph: float):
"""Calculate charge for folded and unfolded states.
Args:
@@ -367,7 +379,7 @@ class ConformationContainer:
state='folded')
return unfolded, folded
def get_backbone_groups(self):
def get_backbone_groups(self) -> List[Group]:
"""Get backbone groups needed for the pKa calculations.
Returns:

13
propka/coupled_groups.py
View File

@@ -6,9 +6,11 @@ Describe and analyze energetic coupling between groups.
"""
import logging
import itertools
from typing import Optional
import propka.lib
from propka.group import Group
from propka.output import make_interaction_map
from propka.parameters import Parameters
_LOGGER = logging.getLogger(__name__)
@@ -16,9 +18,8 @@ _LOGGER = logging.getLogger(__name__)
class NonCovalentlyCoupledGroups:
"""Groups that are coupled without covalent bonding."""
def __init__(self):
self.parameters = None
self.do_prot_stat = True
parameters: Optional[Parameters] = None
do_prot_stat = True
def is_coupled_protonation_state_probability(self, group1, group2,
energy_method,
@@ -33,6 +34,7 @@ class NonCovalentlyCoupledGroups:
Returns:
dictionary describing coupling
"""
assert self.parameters is not None
# check if the interaction energy is high enough
interaction_energy = max(self.get_interaction(group1, group2),
self.get_interaction(group2, group1))
@@ -105,6 +107,7 @@ class NonCovalentlyCoupledGroups:
Returns:
float value of scaling factor
"""
assert self.parameters is not None
intrinsic_pka_diff = abs(pka1-pka2)
res = 0.0
if intrinsic_pka_diff <= self.parameters.max_intrinsic_pka_diff:
@@ -122,6 +125,7 @@ class NonCovalentlyCoupledGroups:
Returns:
float value of scaling factor
"""
assert self.parameters is not None
free_energy_diff = abs(energy1-energy2)
res = 0.0
if free_energy_diff <= self.parameters.max_free_energy_diff:
@@ -136,6 +140,7 @@ class NonCovalentlyCoupledGroups:
Returns:
float value of scaling factor
"""
assert self.parameters is not None
res = 0.0
interaction_energy = abs(interaction_energy)
if interaction_energy >= self.parameters.min_interaction_energy:
@@ -260,7 +265,7 @@ class NonCovalentlyCoupledGroups:
_LOGGER.info(swap_info)
@staticmethod
def get_interaction(group1, group2, include_side_chain_hbs=True):
def get_interaction(group1: Group, group2: Group, include_side_chain_hbs=True):
"""Get interaction energy between two groups.
Args:

9
propka/determinant.py
View File

@@ -15,6 +15,11 @@ Provides the :class:`Determinant` class.
"""
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from propka.group import Group
class Determinant:
"""Determinant class.
@@ -25,7 +30,7 @@ class Determinant:
TODO - figure out what this class does.
"""
def __init__(self, group, value):
def __init__(self, group: "Group", value: float):
"""Initialize the object.
Args:
@@ -36,7 +41,7 @@ class Determinant:
self.label = group.label
self.value = value
def add(self, value):
def add(self, value: float):
"""Increment determinant value.
Args:

14
propka/determinants.py
View File

@@ -14,12 +14,18 @@ Functions to manipulate :class:`propka.determinant.Determinant` objects.
"""
import math
from typing import List
import propka.calculations
import propka.iterative
import propka.lib
import propka.vector_algebra
from propka.calculations import squared_distance, get_smallest_distance
from propka.energy import angle_distance_factors, hydrogen_bond_energy
from propka.determinant import Determinant
from propka.group import Group
from propka.iterative import Interaction
from propka.version import Version
# Cutoff for angle factor
@@ -28,7 +34,7 @@ from propka.determinant import Determinant
FANGLE_MIN = 0.001
def set_determinants(propka_groups, version=None, options=None):
def set_determinants(propka_groups: List[Group], version: Version, options=None):
"""Add side-chain and coulomb determinants/perturbations to all residues.
NOTE - backbone determinants are set separately
@@ -38,7 +44,7 @@ def set_determinants(propka_groups, version=None, options=None):
version: version object
options: options object
"""
iterative_interactions = []
iterative_interactions: List[Interaction] = []
# --- NonIterative section ---#
for group1 in propka_groups:
for group2 in propka_groups:
@@ -77,7 +83,7 @@ def add_determinants(group1, group2, distance, version):
add_coulomb_determinants(group1, group2, distance, version)
def add_sidechain_determinants(group1, group2, version=None):
def add_sidechain_determinants(group1: Group, group2: Group, version: Version):
"""Add side-chain determinants and perturbations.
NOTE - res_num1 > res_num2
@@ -236,6 +242,8 @@ def set_backbone_determinants(titratable_groups, backbone_groups, version):
get_smallest_distance(
backbone_interaction_atoms,
titratable_group_interaction_atoms))
assert backbone_atom is not None
assert titratable_atom is not None
# get the parameters
parameters = (
version.get_backbone_hydrogen_bond_parameters(

23
propka/energy.py
View File

@@ -7,11 +7,15 @@ Energy calculations.
"""
import math
import logging
from typing import TYPE_CHECKING
from typing import TYPE_CHECKING, Optional, Sequence
from propka.atom import Atom
from propka.parameters import Parameters
if TYPE_CHECKING:
from propka.conformation_container import ConformationContainer
from propka.group import Group
from propka.version import Version
from propka.calculations import squared_distance, get_smallest_distance
@@ -89,7 +93,7 @@ def calculate_scale_factor(parameters, weight: float) -> float:
return scale_factor
def calculate_weight(parameters, num_volume: int) -> float:
def calculate_weight(parameters: Parameters, num_volume: float) -> float:
"""Calculate the atom-based desolvation weight.
TODO - figure out why a similar function exists in version.py
@@ -109,7 +113,7 @@ def calculate_weight(parameters, num_volume: int) -> float:
return weight
def calculate_pair_weight(parameters, num_volume1: int, num_volume2: int) -> float:
def calculate_pair_weight(parameters: Parameters, num_volume1: int, num_volume2: int) -> float:
"""Calculate the atom-pair based desolvation weight.
Args:
@@ -148,7 +152,11 @@ def hydrogen_bond_energy(dist, dpka_max: float, cutoffs, f_angle=1.0) -> float:
return abs(dpka)
def angle_distance_factors(atom1=None, atom2=None, atom3=None, center=None):
def angle_distance_factors(
atom1: Optional[Atom] = None,
atom2: Atom = None, # type: ignore[assignment]
atom3: Atom = None, # type: ignore[assignment]
center: Optional[Sequence[float]] = None):
"""Calculate distance and angle factors for three atoms for backbone
interactions.
@@ -182,6 +190,7 @@ def angle_distance_factors(atom1=None, atom2=None, atom3=None, center=None):
dy_32 = dy_32/dist_23
dz_32 = dz_32/dist_23
if atom1 is None:
assert center is not None
dx_21 = center[0] - atom2.x
dy_21 = center[1] - atom2.y
dz_21 = center[2] - atom2.z
@@ -197,7 +206,7 @@ def angle_distance_factors(atom1=None, atom2=None, atom3=None, center=None):
return dist_12, f_angle, dist_23
def hydrogen_bond_interaction(group1, group2, version):
def hydrogen_bond_interaction(group1: "Group", group2: "Group", version: "Version"):
"""Calculate energy for hydrogen bond interactions between two groups.
Args:
@@ -213,7 +222,7 @@ def hydrogen_bond_interaction(group1, group2, version):
[closest_atom1, dist, closest_atom2] = get_smallest_distance(
atoms1, atoms2
)
if None in [closest_atom1, closest_atom2]:
if closest_atom1 is None or closest_atom2 is None:
_LOGGER.warning(
'Side chain interaction failed for {0:s} and {1:s}'.format(
group1.label, group2.label))
@@ -297,7 +306,7 @@ def electrostatic_interaction(group1, group2, dist, version):
return value
def check_coulomb_pair(parameters, group1, group2, dist):
def check_coulomb_pair(parameters: Parameters, group1: "Group", group2: "Group", dist: float) -> bool:
"""Checks if this Coulomb interaction should be done.
NOTE - this is a propka2.0 hack

21
propka/group.py
View File

@@ -14,6 +14,7 @@ import math
from typing import cast, Dict, Iterable, List, NoReturn, Optional
import propka.ligand
from propka.parameters import Parameters
import propka.protonate
from propka.atom import Atom
from propka.ligand_pka_values import LigandPkaValues
@@ -90,7 +91,7 @@ class Group:
self.y = 0.0
self.z = 0.0
self.charge = 0
self.parameters = None
self.parameters: Optional[Parameters] = None
self.exclude_cys_from_results = False
self.interaction_atoms_for_acids: List[Atom] = []
self.interaction_atoms_for_bases: List[Atom] = []
@@ -167,6 +168,7 @@ class Group:
Args:
others: list of other groups
"""
raise NotImplementedError("unused")
# for each determinant type
for other in others:
if other == self:
@@ -319,6 +321,7 @@ class Group:
def setup(self):
"""Set up a group."""
assert self.parameters is not None
# set the charges
if self.type in self.parameters.charge.keys():
self.charge = self.parameters.charge[self.type]
@@ -402,7 +405,7 @@ class Group:
' {0:s}'.format(
str(self.interaction_atoms_for_bases[i])))
def get_interaction_atoms(self, interacting_group) -> List[Atom]:
def get_interaction_atoms(self, interacting_group: "Group") -> List[Atom]:
"""Get atoms involved in interaction with other group.
Args:
@@ -591,7 +594,7 @@ class Group:
ddg = ddg_neutral + ddg_low
return ddg
def calculate_charge(self, _, ph=7.0, state='folded'):
def calculate_charge(self, _, ph: float = 7.0, state: str = 'folded') -> float:
"""Calculate the charge of the specified state at the specified pH.
Args:
@@ -609,7 +612,7 @@ class Group:
charge = self.charge*(conc_ratio/(1.0+conc_ratio))
return charge
def use_in_calculations(self):
def use_in_calculations(self) -> bool:
"""Indicate whether group should be included in results report.
If --titrate_only option is specified, only residues that are
@@ -1218,7 +1221,7 @@ class TitratableLigandGroup(Group):
self.model_pka_set = True
def is_group(parameters, atom: Atom) -> Optional[Group]:
def is_group(parameters: Parameters, atom: Atom) -> Optional[Group]:
"""Identify whether the atom belongs to a group.
Args:
@@ -1227,7 +1230,7 @@ def is_group(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:
@@ -1245,7 +1248,7 @@ def is_group(parameters, atom: Atom) -> Optional[Group]:
ligand_group = is_ligand_group_by_groups(parameters, atom)
else:
raise Exception(
'Unknown ligand typing method \'{0.s}\''.format(
'Unknown ligand typing method \'{0:s}\''.format(
parameters.ligand_typing))
if ligand_group:
return ligand_group
@@ -1368,7 +1371,7 @@ def is_ligand_group_by_groups(_, atom: Atom) -> Optional[Group]:
return None
def is_ligand_group_by_marvin_pkas(parameters, atom: Atom) -> Optional[Group]:
def is_ligand_group_by_marvin_pkas(parameters: Parameters, atom: Atom) -> Optional[Group]:
"""Identify whether the atom belongs to a ligand group by calculating
'Marvin pKas'.
@@ -1383,6 +1386,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom: Atom) -> Optional[Group]:
# 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)
@@ -1400,6 +1404,7 @@ def is_ligand_group_by_marvin_pkas(parameters, atom: Atom) -> Optional[Group]:
if not o == atom][0]
atom.marvin_pka = other_oxygen.marvin_pka
return TitratableLigandGroup(atom)
raise NotImplementedError("hydrogen_bonds")
if atom.element in parameters.hydrogen_bonds.elements:
return NonTitratableLigandGroup(atom)
return None

23
propka/hydrogens.py
View File

@@ -122,6 +122,12 @@ def add_arg_hydrogen(residue: List[Atom]) -> List[Atom]:
Returns:
list of hydrogen atoms
"""
cd_atom: Optional[Atom] = None
cz_atom: Optional[Atom] = None
ne_atom: Optional[Atom] = None
nh1_atom: Optional[Atom] = None
nh2_atom: Optional[Atom] = None
for atom in residue:
if atom.name == "CD":
cd_atom = atom
@@ -133,6 +139,11 @@ def add_arg_hydrogen(residue: List[Atom]) -> List[Atom]:
nh1_atom = atom
elif atom.name == "NH2":
nh2_atom = atom
if (cd_atom is None or cz_atom is None or ne_atom is None or nh1_atom is None
or nh2_atom is None):
raise ValueError("Unable to find all atoms")
h1_atom = protonate_sp2(cd_atom, ne_atom, cz_atom)
h1_atom.name = "HE"
h2_atom = protonate_direction(nh1_atom, ne_atom, cz_atom)
@@ -152,6 +163,12 @@ def add_his_hydrogen(residue: List[Atom]) -> None:
Args:
residue: histidine residue to protonate
"""
cg_atom: Optional[Atom] = None
nd_atom: Optional[Atom] = None
cd_atom: Optional[Atom] = None
ce_atom: Optional[Atom] = None
ne_atom: Optional[Atom] = None
for atom in residue:
if atom.name == "CG":
cg_atom = atom
@@ -163,6 +180,11 @@ def add_his_hydrogen(residue: List[Atom]) -> None:
ce_atom = atom
elif atom.name == "NE2":
ne_atom = atom
if (cg_atom is None or nd_atom is None or cd_atom is None or ce_atom is None
or ne_atom is None):
raise ValueError("Unable to find all atoms")
hd_atom = protonate_sp2(cg_atom, nd_atom, ce_atom)
hd_atom.name = "HND"
he_atom = protonate_sp2(cd_atom, ne_atom, ce_atom)
@@ -177,6 +199,7 @@ def add_trp_hydrogen(residue: List[Atom]) -> None:
"""
cd_atom = None
ne_atom = None
ce_atom = None
for atom in residue:
if atom.name == "CD1":
cd_atom = atom

40
propka/input.py
View File

@@ -9,8 +9,7 @@ Input routines.
Methods to read PROPKA input files (:func:`read_propka` and
:func:`get_atom_lines_from_input`) have been removed.
"""
import typing
from typing import Iterator, Tuple, Union
from typing import IO, ContextManager, Dict, Iterable, Iterator, Optional, Tuple
import contextlib
import io
import zipfile
@@ -19,19 +18,18 @@ 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.output import _PathArg, _PathLikeTypes, _TextIOSource
from propka.parameters import Parameters
def open_file_for_reading(
input_file: typing.Union[str, Path, typing.TextIO]
) -> typing.ContextManager[typing.TextIO]:
def open_file_for_reading(input_file: _TextIOSource) -> ContextManager[IO[str]]:
"""Open file or file-like stream for reading.
Args:
input_file: path to file or file-like object. If file-like object,
then will attempt seek(0).
"""
if not isinstance(input_file, (str, Path)):
if not isinstance(input_file, _PathLikeTypes):
input_file.seek(0)
return contextlib.nullcontext(input_file)
@@ -48,7 +46,11 @@ def open_file_for_reading(
return contextlib.closing(open(input_file, 'rt'))
def read_molecule_file(filename: str, mol_container: MolecularContainer, stream=None) -> MolecularContainer:
def read_molecule_file(
filename: _PathArg,
mol_container: MolecularContainer,
stream: Optional[IO[str]] = None,
) -> MolecularContainer:
"""Read input file or stream (PDB or PROPKA) for a molecular container
Args:
@@ -96,11 +98,7 @@ def read_molecule_file(filename: str, mol_container: MolecularContainer, stream=
input_path = Path(filename)
mol_container.name = input_path.stem
input_file_extension = input_path.suffix
if stream is not None:
input_file = stream
else:
input_file = filename
input_file = filename if stream is None else stream
if input_file_extension.lower() == '.pdb':
# input is a pdb file. read in atoms and top up containers to make
@@ -133,7 +131,7 @@ def read_molecule_file(filename: str, mol_container: MolecularContainer, stream=
return mol_container
def read_parameter_file(input_file: Union[Path, str], parameters: Parameters) -> Parameters:
def read_parameter_file(input_file: _PathArg, parameters: Parameters) -> Parameters:
"""Read a parameter file.
Args:
@@ -161,8 +159,13 @@ def conformation_sorter(conf: str) -> int:
return model*100+ord(altloc)
def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False,
tags=['ATOM ', 'HETATM'], chains=None) -> Iterator[Tuple[str, Atom]]:
def get_atom_lines_from_pdb(
pdb_file: _TextIOSource,
ignore_residues: Iterable[str] = (),
keep_protons: bool = False,
tags: Iterable[str] = ('ATOM ', 'HETATM'),
chains: Optional[Iterable[str]] = None,
) -> Iterator[Tuple[str, Atom]]:
"""Get atom lines from PDB file.
Args:
@@ -228,7 +231,8 @@ def get_atom_lines_from_pdb(pdb_file, ignore_residues=[], keep_protons=False,
terminal = None
def read_pdb(pdb_file, parameters, molecule):
def read_pdb(pdb_file: _TextIOSource, parameters: Parameters,
molecule: MolecularContainer):
"""Parse a PDB file.
Args:
@@ -240,7 +244,7 @@ def read_pdb(pdb_file, parameters, molecule):
1. list of conformations
2. list of names
"""
conformations = {}
conformations: Dict[str, ConformationContainer] = {}
# read in all atoms in the file
lines = get_atom_lines_from_pdb(
pdb_file, ignore_residues=parameters.ignore_residues,
@@ -253,4 +257,4 @@ def read_pdb(pdb_file, parameters, molecule):
conformations[name].add_atom(atom)
# make a sorted list of conformation names
names = sorted(conformations.keys(), key=conformation_sorter)
return [conformations, names]
return conformations, names

51
propka/iterative.py
View File

@@ -7,7 +7,10 @@ involve :class:`propka.determinant.Determinant` instances.
"""
import logging
from typing import Dict, Iterable, List, Optional, Sequence, Tuple
from propka.determinant import Determinant
from propka.group import Group
from propka.version import Version
_LOGGER = logging.getLogger(__name__)
@@ -16,9 +19,11 @@ _LOGGER = logging.getLogger(__name__)
# TODO - these are undocumented constants
UNK_MIN_VALUE = 0.005
Interaction = list
def add_to_determinant_list(group1, group2, distance, iterative_interactions,
version):
def add_to_determinant_list(group1: Group, group2: Group, distance: float,
iterative_interactions: List[Interaction], version: Version):
"""Add iterative determinantes to the list.
[[R1, R2], [side-chain, coulomb], [A1, A2]], ...
@@ -48,7 +53,8 @@ def add_to_determinant_list(group1, group2, distance, iterative_interactions,
iterative_interactions.append(interaction)
def add_iterative_acid_pair(object1, object2, interaction):
def add_iterative_acid_pair(object1: "Iterative", object2: "Iterative",
interaction: Interaction):
"""Add the Coulomb 'iterative' interaction (an acid pair).
The higher pKa is raised with QQ+HB
@@ -90,7 +96,8 @@ def add_iterative_acid_pair(object1, object2, interaction):
annihilation[1] = -diff
def add_iterative_base_pair(object1, object2, interaction):
def add_iterative_base_pair(object1: "Iterative", object2: "Iterative",
interaction: Interaction):
"""Add the Coulomb 'iterative' interaction (a base pair).
The lower pKa is lowered
@@ -132,7 +139,8 @@ def add_iterative_base_pair(object1, object2, interaction):
annihilation[1] = -diff
def add_iterative_ion_pair(object1, object2, interaction, version):
def add_iterative_ion_pair(object1: "Iterative", object2: "Iterative",
interaction: Interaction, version: Version):
"""Add the Coulomb 'iterative' interaction (an acid-base pair)
the pKa of the acid is lowered & the pKa of the base is raised
@@ -194,7 +202,7 @@ def add_iterative_ion_pair(object1, object2, interaction, version):
object2.determinants['sidechain'].append(interaction)
def add_determinants(iterative_interactions, version, _=None):
def add_determinants(iterative_interactions: List[Interaction], version: Version, _=None):
"""Add determinants iteratively.
The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'
@@ -205,7 +213,7 @@ def add_determinants(iterative_interactions, version, _=None):
_: options object
"""
# --- setup ---
iteratives = []
iteratives: List[Iterative] = []
done_group = []
# create iterative objects with references to their real group counterparts
for interaction in iterative_interactions:
@@ -270,6 +278,7 @@ def add_determinants(iterative_interactions, version, _=None):
# reset pka_old & storing pka_new in pka_iter
for itres in iteratives:
assert itres.pka_new is not None
itres.pka_old = itres.pka_new
itres.pka_iter.append(itres.pka_new)
@@ -295,14 +304,17 @@ def add_determinants(iterative_interactions, version, _=None):
for itres in iteratives:
for type_ in ['sidechain', 'backbone', 'coulomb']:
for interaction in itres.determinants[type_]:
value = interaction[1]
value: float = interaction[1]
if value > UNK_MIN_VALUE or value < -UNK_MIN_VALUE:
group = interaction[0]
new_det = Determinant(group, value)
itres.group.determinants[type_].append(new_det)
def find_iterative(pair, iteratives):
def find_iterative(
pair: Sequence[Group],
iteratives: Iterable["Iterative"],
) -> Tuple["Iterative", "Iterative"]:
"""Find the 'iteratives' that correspond to the groups in 'pair'.
Args:
@@ -312,11 +324,15 @@ def find_iterative(pair, iteratives):
1. first matched iterative
2. second matched iterative
"""
iterative0: Optional[Iterative] = None
iterative1: Optional[Iterative] = None
for iterative in iteratives:
if iterative.group == pair[0]:
iterative0 = iterative
elif iterative.group == pair[1]:
iterative1 = iterative
if iterative0 is None or iterative1 is None:
raise LookupError("iteratives not found")
return iterative0, iterative1
@@ -327,7 +343,7 @@ class Iterative:
after the iterations are finished.
"""
def __init__(self, group):
def __init__(self, group: Group):
"""Initialize object with group.
Args:
@@ -337,11 +353,15 @@ class Iterative:
self.atom = group.atom
self.res_name = group.residue_type
self.q = group.charge
self.pka_old = None
self.pka_new = None
self.pka_iter = []
self.pka_old: Optional[float] = None
self.pka_new: Optional[float] = None
self.pka_iter: List[float] = []
self.pka_noniterative = 0.00
self.determinants = {'sidechain': [], 'backbone': [], 'coulomb': []}
self.determinants: Dict[str, list] = {
'sidechain': [],
'backbone': [],
'coulomb': []
}
self.group = group
self.converged = True
# Calculate the Non-Iterative part of pKa from the group object
@@ -368,8 +388,9 @@ class Iterative:
self.pka_noniterative += coulomb
self.pka_old = self.pka_noniterative
def __eq__(self, other):
def __eq__(self, other) -> bool:
"""Needed to use objects in sets."""
assert isinstance(other, (Iterative, Group)), type(other)
if self.atom.type == 'atom':
# In case of protein atoms we trust the labels
return self.label == other.label

84
propka/lib.py
View File

@@ -5,11 +5,19 @@ Set-up of a PROPKA calculation
Implements many of the main functions used to call PROPKA.
"""
import sys
import logging
import argparse
from pathlib import Path
from typing import Iterable, Iterator, List, TYPE_CHECKING, NoReturn, Optional, Tuple, TypeVar
if TYPE_CHECKING:
from propka.atom import Atom
T = TypeVar("T")
Number = TypeVar("Number", int, float)
_T_RESIDUE_TUPLE = Tuple[str, int, str]
_LOGGER = logging.getLogger(__name__)
@@ -20,6 +28,29 @@ EXPECTED_ATOM_NUMBERS = {'ALA': 5, 'ARG': 11, 'ASN': 8, 'ASP': 8, 'CYS': 6,
'SER': 6, 'THR': 7, 'TRP': 14, 'TYR': 12, 'VAL': 7}
class Options:
# Note: All the "NoReturn" members appear to be unused
alignment: NoReturn # Optional[List[str]]
chains: Optional[List[str]]
display_coupled_residues: bool = False
filenames: List[str] # List[Path]?
grid: Tuple[float, float, float] = (0.0, 14.0, 0.1)
input_pdb: str # Path?
keep_protons: bool = False
log_level: str = 'INFO'
mutations: NoReturn # Optional[List[str]]
mutator: NoReturn # Optional[str] # alignment/scwrl/jackal
mutator_options: NoReturn # Optional[List[str]]
pH: NoReturn # float = 7.0
parameters: Path
protonate_all: bool = False
reference: NoReturn # str = 'neutral'
reuse_ligand_mol2_file: bool = False # only used by unused function
thermophiles: NoReturn # Optional[List[str]]
titrate_only: Optional[List[_T_RESIDUE_TUPLE]]
window: Tuple[float, float, float] = (0.0, 14.0, 1.0)
def protein_precheck(conformations, names):
"""Check protein for correct number of atoms, etc.
@@ -73,7 +104,7 @@ def resid_from_atom(atom):
atom.res_num, atom.chain_id, atom.icode)
def split_atoms_into_molecules(atoms):
def split_atoms_into_molecules(atoms: List["Atom"]):
"""Maps atoms into molecules.
Args:
@@ -81,14 +112,14 @@ def split_atoms_into_molecules(atoms):
Returns:
list of molecules
"""
molecules = []
molecules: List[List["Atom"]] = []
while len(atoms) > 0:
initial_atom = atoms.pop()
molecules.append(make_molecule(initial_atom, atoms))
return molecules
def make_molecule(atom, atoms):
def make_molecule(atom: "Atom", atoms: List["Atom"]):
"""Make a molecule from atoms.
Args:
@@ -106,11 +137,11 @@ def make_molecule(atom, atoms):
return res_atoms
def make_grid(min_, max_, step):
def make_grid(min_: Number, max_: Number, step: Number) -> Iterator[Number]:
"""Make a grid across the specified tange.
TODO - figure out if this duplicates existing generators like `range` or
numpy function.
Like range() for integers or numpy.arange() for floats, except that `max_`
is not excluded from the range.
Args:
min_: minimum value of grid
@@ -123,7 +154,7 @@ def make_grid(min_, max_, step):
x += step
def generate_combinations(interactions):
def generate_combinations(interactions: Iterable[T]) -> List[List[T]]:
"""Generate combinations of interactions.
Args:
@@ -131,14 +162,14 @@ def generate_combinations(interactions):
Returns:
list of combinations
"""
res = [[]]
res: List[List[T]] = [[]]
for interaction in interactions:
res = make_combination(res, interaction)
res.remove([])
return res
def make_combination(combis, interaction):
def make_combination(combis: List[List[T]], interaction: T) -> List[List[T]]:
"""Make a specific set of combinations.
Args:
@@ -154,7 +185,7 @@ def make_combination(combis, interaction):
return res
def parse_res_string(res_str):
def parse_res_string(res_str: str) -> _T_RESIDUE_TUPLE:
"""Parse a residue string.
Args:
@@ -183,6 +214,16 @@ def parse_res_string(res_str):
return chain, resnum, inscode
def parse_res_list(titrate_only: str):
res_list: List[_T_RESIDUE_TUPLE] = []
for res_str in titrate_only.split(','):
try:
res_list.append(parse_res_string(res_str))
except ValueError as ex:
raise argparse.ArgumentTypeError(f'{ex}: "{res_str:s}"')
return res_list
def build_parser(parser=None):
"""Build an argument parser for PROPKA.
@@ -227,6 +268,7 @@ def build_parser(parser=None):
'" " for chains without ID [all]'))
group.add_argument(
"-i", "--titrate_only", dest="titrate_only",
type=parse_res_list,
help=('Treat only the specified residues as titratable. Value should '
'be a comma-separated list of "chain:resnum" values; for '
'example: -i "A:10,A:11"'))
@@ -246,8 +288,8 @@ def build_parser(parser=None):
"--version", action="version", version=f"%(prog)s {propka.__version__}")
group.add_argument(
"-p", "--parameters", dest="parameters",
default=str(Path(__file__).parent / "propka.cfg"),
help="set the parameter file [{default:s}]")
type=Path, default=Path(__file__).parent / "propka.cfg",
help="set the parameter file")
try:
group.add_argument(
"--log-level",
@@ -302,7 +344,7 @@ def build_parser(parser=None):
return parser
def loadOptions(args=None):
def loadOptions(args=None) -> Options:
"""
Load the arguments parser with options. Note that verbosity is set as soon
as this function is invoked.
@@ -315,22 +357,10 @@ def loadOptions(args=None):
# loading the parser
parser = build_parser()
# parsing and returning options and arguments
options = parser.parse_args(args)
options = parser.parse_args(args, namespace=Options())
# adding specified filenames to arguments
options.filenames.append(options.input_pdb)
# Convert titrate_only string to a list of (chain, resnum) items:
if options.titrate_only is not None:
res_list = []
for res_str in options.titrate_only.split(','):
try:
chain, resnum, inscode = parse_res_string(res_str)
except ValueError:
_LOGGER.critical(
'Invalid residue string: "{0:s}"'.format(res_str))
sys.exit(1)
res_list.append((chain, resnum, inscode))
options.titrate_only = res_list
# Set the no-print variable
level = getattr(logging, options.log_level)
_LOGGER.setLevel(level)

4
propka/ligand.py
View File

@@ -319,11 +319,11 @@ def are_atoms_planar(atoms):
return False
vec1 = Vector(atom1=atoms[0], atom2=atoms[1])
vec2 = Vector(atom1=atoms[0], atom2=atoms[2])
norm = (vec1**vec2).rescale(1.0)
norm = vec1.cross(vec2).rescale(1.0)
margin = PLANARITY_MARGIN
for atom in atoms[3:]:
vec = Vector(atom1=atoms[0], atom2=atom).rescale(1.0)
if abs(vec*norm) > margin:
if abs(vec.dot(norm)) > margin:
return False
return True

37
propka/ligand_pka_values.py
View File

@@ -11,11 +11,18 @@ programs are required).
"""
import logging
import os
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__)
@@ -23,7 +30,7 @@ _LOGGER = logging.getLogger(__name__)
class LigandPkaValues:
"""Ligand pKa value class."""
def __init__(self, parameters):
def __init__(self, parameters: Parameters):
"""Initialize object with parameters.
Args:
@@ -46,20 +53,17 @@ class LigandPkaValues:
Returns:
location of program
"""
path = os.environ.get('PATH').split(os.pathsep)
locs = [
i for i in filter(lambda loc: os.access(loc, os.F_OK),
map(lambda dir: os.path.join(dir, program),
path))]
if len(locs) == 0:
loc = shutil.which(program)
if loc is None:
str_ = "'Error: Could not find {0:s}.".format(program)
str_ += ' Please make sure that it is found in the path.'
_LOGGER.info(str_)
sys.exit(-1)
return locs[0]
return loc
def get_marvin_pkas_for_pdb_file(
self, molecule, parameters, num_pkas=10, min_ph=-10, max_ph=20):
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:
@@ -69,11 +73,12 @@ class LigandPkaValues:
min_ph: minimum pH value
max_ph: maximum pH value
"""
warnings.warn("unused and untested by propka")
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,
min_ph=-10, max_ph=20):
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.
Args:
@@ -91,8 +96,8 @@ class LigandPkaValues:
def get_marvin_pkas_for_conformation_container(self, conformation,
name='temp', reuse=False,
num_pkas=10, min_ph=-10,
max_ph=20):
num_pkas=10, min_ph=-10.0,
max_ph=20.0):
"""Use Marvin executables to calculate pKas for a conformation container.
Args:
@@ -109,7 +114,7 @@ class LigandPkaValues:
num_pkas=num_pkas, min_ph=min_ph, max_ph=max_ph)
def get_marvin_pkas_for_atoms(self, atoms, name='temp', reuse=False,
num_pkas=10, min_ph=-10, max_ph=20):
num_pkas=10, min_ph=-10.0, max_ph=20.0):
"""Use Marvin executables to calculate pKas for a list of atoms.
Args:
@@ -129,8 +134,8 @@ class LigandPkaValues:
min_ph=min_ph, max_ph=max_ph)
def get_marvin_pkas_for_molecule(self, atoms, filename='__tmp_ligand.mol2',
reuse=False, num_pkas=10, min_ph=-10,
max_ph=20):
reuse=False, num_pkas=10, min_ph=-10.0,
max_ph=20.0):
"""Use Marvin executables to calculate pKas for a molecule.
Args:

21
propka/molecular_container.py
View File

@@ -7,11 +7,12 @@ Molecular container for storing all contents of PDB files.
import logging
import os
from typing import Dict, List, Optional, Tuple
from propka.parameters import Parameters
import propka.version
from propka.output import write_pka, print_header, print_result
from propka.conformation_container import ConformationContainer
from propka.lib import make_grid
from propka.lib import make_grid, Options
_LOGGER = logging.getLogger(__name__)
@@ -35,7 +36,7 @@ class MolecularContainer:
name: Optional[str]
version: propka.version.Version
def __init__(self, parameters, options=None) -> None:
def __init__(self, parameters: Parameters, options: Options) -> None:
"""Initialize molecular container.
Args:
@@ -156,7 +157,7 @@ class MolecularContainer:
conformation='AVR', reference=reference)
def get_folding_profile(self, conformation='AVR', reference="neutral",
grid=[0., 14., 0.1]):
grid: Tuple[float, float, float] = (0., 14., 0.1)):
"""Get a folding profile.
Args:
@@ -173,25 +174,25 @@ class MolecularContainer:
4. stability_range
"""
# calculate stability profile
profile = []
profile: List[Tuple[float, float]] = []
for ph in make_grid(*grid):
conf = self.conformations[conformation]
ddg = conf.calculate_folding_energy(ph=ph, reference=reference)
profile.append([ph, ddg])
profile.append((ph, ddg))
# find optimum
opt = [None, 1e6]
opt: Tuple[Optional[float], float] = (None, 1e6)
for point in profile:
opt = min(opt, point, key=lambda v: v[1])
# find values within 80 % of optimum
range_80pct = [None, None]
range_80pct: Tuple[Optional[float], Optional[float]] = (None, None)
values_within_80pct = [p[0] for p in profile if p[1] < 0.8*opt[1]]
if len(values_within_80pct) > 0:
range_80pct = [min(values_within_80pct), max(values_within_80pct)]
range_80pct = (min(values_within_80pct), max(values_within_80pct))
# find stability range
stability_range = [None, None]
stability_range: Tuple[Optional[float], Optional[float]] = (None, None)
stable_values = [p[0] for p in profile if p[1] < 0.0]
if len(stable_values) > 0:
stability_range = [min(stable_values), max(stable_values)]
stability_range = (min(stable_values), max(stable_values))
return profile, opt, range_80pct, stability_range
def get_charge_profile(self, conformation: str = 'AVR', grid=[0., 14., .1]):

73
propka/output.py
View File

@@ -12,13 +12,29 @@ Output routines.
import logging
from datetime import date
from decimal import Decimal
from os import PathLike
from pathlib import Path
from typing import IO, AnyStr, List, NoReturn, Optional, Union, TYPE_CHECKING
import warnings
from .parameters import Parameters
from . import __version__
if TYPE_CHECKING:
from .atom import Atom
from .conformation_container import ConformationContainer
from .molecular_container import MolecularContainer
# https://docs.python.org/3/glossary.html#term-path-like-object
_PathLikeTypes = (PathLike, str)
_PathArg = Union[PathLike, str]
_IOSource = Union[IO[AnyStr], PathLike, str]
_TextIOSource = _IOSource[str]
_LOGGER = logging.getLogger(__name__)
def open_file_for_writing(input_file):
def open_file_for_writing(input_file: _TextIOSource) -> IO[str]:
"""Open file or file-like stream for writing.
TODO - convert this to a context manager.
@@ -27,17 +43,13 @@ def open_file_for_writing(input_file):
input_file: path to file or file-like object. If file-like object,
then will attempt to get file mode.
"""
try:
if not input_file.writable():
raise IOError("File/stream not open for writing")
return input_file
except AttributeError:
pass
try:
file_ = open(input_file, 'wt')
except FileNotFoundError:
raise Exception('Could not open {0:s}'.format(input_file))
return file_
if isinstance(input_file, _PathLikeTypes):
return open(input_file, 'wt')
if not input_file.writable():
raise IOError("File/stream not open for writing")
return input_file
def write_file(filename, lines):
@@ -47,6 +59,7 @@ def write_file(filename, lines):
filename: name of file
lines: lines to write to file
"""
warnings.warn("unused and untested by propka")
file_ = open_file_for_writing(filename)
for line in lines:
file_.write("{0:s}\n".format(line))
@@ -72,6 +85,7 @@ def write_pdb_for_protein(
include_hydrogens: Boolean indicating whether to include hydrogens
options: options object
"""
raise NotImplementedError("unused")
if pdbfile is None:
# opening file if not given
if filename is None:
@@ -100,17 +114,22 @@ def write_pdb_for_protein(
pdbfile.close()
def write_pdb_for_conformation(conformation, filename):
def write_pdb_for_conformation(conformation: "ConformationContainer",
filename: _PathArg):
"""Write PDB conformation to a file.
Args:
conformation: conformation container
filename: filename for output
"""
warnings.warn("unused and untested by propka")
write_pdb_for_atoms(conformation.atoms, filename)
def write_pka(protein, parameters, filename=None, conformation='1A',
def write_pka(protein: "MolecularContainer",
parameters: Parameters,
filename: Optional[_PathArg] = None,
conformation='1A',
reference="neutral", _="folding", verbose=False,
__=None):
"""Write the pKa-file based on the given protein.
@@ -128,8 +147,6 @@ def write_pka(protein, parameters, filename=None, conformation='1A',
verbose = True
if filename is None:
filename = "{0:s}.pka".format(protein.name)
# TODO - this would be much better with a context manager
file_ = open(filename, 'w')
if verbose:
_LOGGER.info("Writing {0:s}".format(filename))
# writing propka header
@@ -148,11 +165,10 @@ def write_pka(protein, parameters, filename=None, conformation='1A',
# printing Protein Charge Profile
str_ += get_charge_profile_section(protein, conformation=conformation)
# now, writing the pka text to file
file_.write(str_)
file_.close()
Path(filename).write_text(str_, encoding="utf-8")
def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.],
def print_tm_profile(protein: NoReturn, reference="neutral", window=[0., 14., 1.],
__=[0., 0.], tms=None, ref=None, _=False,
options=None):
"""Print Tm profile.
@@ -169,6 +185,7 @@ def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.],
_: Boolean for verbosity
options: options object
"""
raise NotImplementedError("unused")
profile = protein.getTmProfile(
reference=reference, grid=[0., 14., 0.1], tms=tms, ref=ref,
options=options)
@@ -184,7 +201,7 @@ def print_tm_profile(protein, reference="neutral", window=[0., 14., 1.],
_LOGGER.info(str_)
def print_result(protein, conformation, parameters):
def print_result(protein: "MolecularContainer", conformation: str, parameters: Parameters):
"""Prints all resulting output from determinants and down.
Args:
@@ -195,7 +212,7 @@ def print_result(protein, conformation, parameters):
print_pka_section(protein, conformation, parameters)
def print_pka_section(protein, conformation, parameters):
def print_pka_section(protein: "MolecularContainer", conformation: str, parameters: Parameters):
"""Prints out pKa section of results.
Args:
@@ -210,7 +227,7 @@ def print_pka_section(protein, conformation, parameters):
_LOGGER.info("pKa summary:\n%s", str_)
def get_determinant_section(protein, conformation, parameters):
def get_determinant_section(protein: "MolecularContainer", conformation: str, parameters: Parameters):
"""Returns string with determinant section of results.
Args:
@@ -242,7 +259,8 @@ def get_determinant_section(protein, conformation, parameters):
return str_
def get_summary_section(protein, conformation, parameters):
def get_summary_section(protein: "MolecularContainer", conformation: str,
parameters: Parameters):
"""Returns string with summary section of the results.
Args:
@@ -264,7 +282,8 @@ def get_summary_section(protein, conformation, parameters):
def get_folding_profile_section(
protein, conformation='AVR', direction="folding", reference="neutral",
protein: "MolecularContainer",
conformation='AVR', direction="folding", reference="neutral",
window=[0., 14., 1.0], _=False, __=None):
"""Returns string with the folding profile section of the results.
@@ -358,11 +377,12 @@ def write_jackal_scap_file(mutation_data=None, filename="1xxx_scap.list",
TODO - figure out what this is
"""
raise NotImplementedError("unused")
with open(filename, 'w') as file_:
for chain_id, _, res_num, code2 in mutation_data:
str_ = "{chain:s}, {num:d}, {code:s}\n".format(
chain=chain_id, num=res_num, code=code2)
file_.write(str_)
file_.write(str_)
def write_scwrl_sequence_file(sequence, filename="x-ray.seq", _=None):
@@ -370,6 +390,7 @@ def write_scwrl_sequence_file(sequence, filename="x-ray.seq", _=None):
TODO - figure out what this is
"""
warnings.warn("unused and untested by propka")
with open(filename, 'w') as file_:
start = 0
while len(sequence[start:]) > 60:
@@ -533,7 +554,7 @@ def make_interaction_map(name, list_, interaction):
return res
def write_pdb_for_atoms(atoms, filename, make_conect_section=False):
def write_pdb_for_atoms(atoms: List["Atom"], filename: _PathArg, make_conect_section=False):
"""Write out PDB file for atoms.
Args:

220
propka/parameters.py
View File

@@ -11,67 +11,128 @@ in configuration file.
"""
import logging
from dataclasses import dataclass, field
from typing import Dict, List
try:
# New in version 3.10, deprecated since version 3.12
from typing import TypeAlias
except ImportError:
TypeAlias = "TypeAlias" # type: ignore
_LOGGER = logging.getLogger(__name__)
#: matrices
MATRICES = ['interaction_matrix']
#: pari-wise matrices
PAIR_WISE_MATRICES = ['sidechain_cutoffs']
#: :class:`dict` containing numbers
NUMBER_DICTIONARIES = [
'VanDerWaalsVolume', 'charge', 'model_pkas', 'ions', 'valence_electrons',
'custom_model_pkas']
#: :class:`dict` containing lists
LIST_DICTIONARIES = ['backbone_NH_hydrogen_bond', 'backbone_CO_hydrogen_bond']
#: :class:`dict` containing strings
STRING_DICTIONARIES = ['protein_group_mapping']
#: :class:`list` containing strings
STRING_LISTS = [
'ignore_residues', 'angular_dependent_sidechain_interactions',
'acid_list', 'base_list', 'exclude_sidechain_interactions',
'backbone_reorganisation_list', 'write_out_order']
#: distances (:class:`float`)
DISTANCES = ['desolv_cutoff', 'buried_cutoff', 'coulomb_cutoff1',
'coulomb_cutoff2']
#: other parameters
PARAMETERS = [
'Nmin', 'Nmax', 'desolvationSurfaceScalingFactor', 'desolvationPrefactor',
'desolvationAllowance', 'coulomb_diel', 'COO_HIS_exception',
'OCO_HIS_exception', 'CYS_HIS_exception', 'CYS_CYS_exception',
'min_ligand_model_pka', 'max_ligand_model_pka',
'include_H_in_interactions', 'coupling_max_number_of_bonds',
'min_bond_distance_for_hydrogen_bonds', 'coupling_penalty',
'shared_determinants', 'common_charge_centre', 'hide_penalised_group',
'remove_penalised_group', 'max_intrinsic_pka_diff',
'min_interaction_energy', 'max_free_energy_diff', 'min_swap_pka_shift',
'min_pka', 'max_pka', 'sidechain_interaction']
# :class:`str` parameters
STRINGS = ['version', 'output_file_tag', 'ligand_typing', 'pH', 'reference']
class squared_property:
def __set_name__(self, owner, name: str):
assert name.endswith("_squared")
self._name_not_squared = name[:-len("_squared")] # removesuffix()
def __get__(self, instance, owner=None) -> float:
if instance is None:
return self # type: ignore[return-value]
return getattr(instance, self._name_not_squared)**2
def __set__(self, instance, value: float):
setattr(instance, self._name_not_squared, value**0.5)
_T_MATRIX: TypeAlias = "InteractionMatrix"
_T_PAIR_WISE_MATRIX: TypeAlias = "PairwiseMatrix"
_T_NUMBER_DICTIONARY = Dict[str, float]
_T_LIST_DICTIONARY = Dict[str, list]
_T_STRING_DICTIONARY = Dict[str, str]
_T_STRING_LIST = List[str]
_T_STRING = str
_T_BOOL = bool
@dataclass
class Parameters:
"""PROPKA parameter class."""
def __init__(self):
"""Initialize parameter class.
# MATRICES
interaction_matrix: _T_MATRIX = field(
default_factory=lambda: InteractionMatrix("interaction_matrix"))
Args:
parameter_file: file with parameters
"""
# TODO - need to define all members explicitly
self.model_pkas = {}
self.interaction_matrix = InteractionMatrix("interaction_matrix")
self.sidechain_cutoffs = None
# TODO - it would be nice to rename these; they're defined everywhere
self.COO_HIS_exception = None
self.OCO_HIS_exception = None
self.CYS_HIS_exception = None
self.CYS_CYS_exception = None
# These functions set up remaining data structures implicitly
self.set_up_data_structures()
# PAIR_WISE_MATRICES
sidechain_cutoffs: _T_PAIR_WISE_MATRIX = field(
default_factory=lambda: PairwiseMatrix("sidechain_cutoffs"))
# NUMBER_DICTIONARIES
VanDerWaalsVolume: _T_NUMBER_DICTIONARY = field(default_factory=dict)
charge: _T_NUMBER_DICTIONARY = field(default_factory=dict)
model_pkas: _T_NUMBER_DICTIONARY = field(default_factory=dict)
ions: _T_NUMBER_DICTIONARY = field(default_factory=dict)
valence_electrons: _T_NUMBER_DICTIONARY = field(default_factory=dict)
custom_model_pkas: _T_NUMBER_DICTIONARY = field(default_factory=dict)
# LIST_DICTIONARIES
backbone_NH_hydrogen_bond: _T_LIST_DICTIONARY = field(default_factory=dict)
backbone_CO_hydrogen_bond: _T_LIST_DICTIONARY = field(default_factory=dict)
# STRING_DICTIONARIES
protein_group_mapping: _T_STRING_DICTIONARY = field(default_factory=dict)
# STRING_LISTS
ignore_residues: _T_STRING_LIST = field(default_factory=list)
angular_dependent_sidechain_interactions: _T_STRING_LIST = field(default_factory=list)
acid_list: _T_STRING_LIST = field(default_factory=list)
base_list: _T_STRING_LIST = field(default_factory=list)
exclude_sidechain_interactions: _T_STRING_LIST = field(default_factory=list)
backbone_reorganisation_list: _T_STRING_LIST = field(default_factory=list)
write_out_order: _T_STRING_LIST = field(default_factory=list)
# DISTANCES
desolv_cutoff: float = 20.0
buried_cutoff: float = 15.0
coulomb_cutoff1: float = 4.0
coulomb_cutoff2: float = 10.0
# DISTANCES SQUARED
desolv_cutoff_squared = squared_property()
buried_cutoff_squared = squared_property()
coulomb_cutoff1_squared = squared_property()
coulomb_cutoff2_squared = squared_property()
# STRINGS
version: _T_STRING = "VersionA"
output_file_tag: _T_STRING = ""
ligand_typing: _T_STRING = "groups"
pH: _T_STRING = "variable"
reference: _T_STRING = "neutral"
# PARAMETERS
Nmin: int = 280
Nmax: int = 560
desolvationSurfaceScalingFactor: float = 0.25
desolvationPrefactor: float = -13.0
desolvationAllowance: float = 0.0
coulomb_diel: float = 80.0
# TODO - it would be nice to rename these; they're defined everywhere
COO_HIS_exception: float = 1.60
OCO_HIS_exception: float = 1.60
CYS_HIS_exception: float = 1.60
CYS_CYS_exception: float = 3.60
min_ligand_model_pka: float = -10.0
max_ligand_model_pka: float = 20.0
# include_H_in_interactions: NoReturn = None
coupling_max_number_of_bonds: int = 3
min_bond_distance_for_hydrogen_bonds: int = 4
# coupling_penalty: NoReturn = None
shared_determinants: _T_BOOL = False
common_charge_centre: _T_BOOL = False
# hide_penalised_group: NoReturn = None
remove_penalised_group: _T_BOOL = True
max_intrinsic_pka_diff: float = 2.0
min_interaction_energy: float = 0.5
max_free_energy_diff: float = 1.0
min_swap_pka_shift: float = 1.0
min_pka: float = 0.0
max_pka: float = 10.0
sidechain_interaction: float = 0.85
def parse_line(self, line):
"""Parse parameter file line."""
@@ -84,22 +145,21 @@ class Parameters:
if len(words) == 0:
return
# parse the words
if len(words) == 3 and words[0] in NUMBER_DICTIONARIES:
typeannotation = self.__annotations__.get(words[0])
if typeannotation is _T_NUMBER_DICTIONARY:
self.parse_to_number_dictionary(words)
elif len(words) == 2 and words[0] in STRING_LISTS:
elif typeannotation is _T_STRING_LIST:
self.parse_to_string_list(words)
elif len(words) == 2 and words[0] in DISTANCES:
self.parse_distance(words)
elif len(words) == 2 and words[0] in PARAMETERS:
self.parse_parameter(words)
elif len(words) == 2 and words[0] in STRINGS:
elif typeannotation is _T_STRING:
self.parse_string(words)
elif len(words) > 2 and words[0] in LIST_DICTIONARIES:
elif typeannotation is _T_LIST_DICTIONARY:
self.parse_to_list_dictionary(words)
elif words[0] in MATRICES+PAIR_WISE_MATRICES:
elif typeannotation is _T_MATRIX or typeannotation is _T_PAIR_WISE_MATRIX:
self.parse_to_matrix(words)
elif len(words) == 3 and words[0] in STRING_DICTIONARIES:
elif typeannotation is _T_STRING_DICTIONARY:
self.parse_to_string_dictionary(words)
else:
self.parse_parameter(words)
def parse_to_number_dictionary(self, words):
"""Parse field to number dictionary.
@@ -107,6 +167,7 @@ class Parameters:
Args:
words: strings to parse.
"""
assert len(words) == 3, words
dict_ = getattr(self, words[0])
key = words[1]
value = words[2]
@@ -118,17 +179,19 @@ class Parameters:
Args:
words: strings to parse
"""
assert len(words) == 3, words
dict_ = getattr(self, words[0])
key = words[1]
value = words[2]
dict_[key] = value
def parse_to_list_dictionary(self, words):
def parse_to_list_dictionary(self, words: List[str]):
"""Parse field to list dictionary.
Args:
words: strings to parse.
"""
assert len(words) > 2, words
dict_ = getattr(self, words[0])
key = words[1]
if key not in dict_:
@@ -144,6 +207,7 @@ class Parameters:
Args:
words: strings to parse
"""
assert len(words) == 2, words
list_ = getattr(self, words[0])
value = words[1]
list_.append(value)
@@ -158,24 +222,13 @@ class Parameters:
value = tuple(words[1:])
matrix.add(value)
def parse_distance(self, words):
"""Parse field to distance.
Args:
words: strings to parse
"""
value = float(words[1])
setattr(self, words[0], value)
value_sq = value*value
attr = "{0:s}_squared".format(words[0])
setattr(self, attr, value_sq)
def parse_parameter(self, words):
"""Parse field to parameters.
Args:
words: strings to parse
"""
assert len(words) == 2, words
value = float(words[1])
setattr(self, words[0], value)
@@ -185,28 +238,9 @@ class Parameters:
Args:
words: strings to parse
"""
assert len(words) == 2, words
setattr(self, words[0], words[1])
def set_up_data_structures(self):
"""Set up internal data structures.
TODO - it would be better to make these assignments explicit in
__init__.
"""
for key_word in (NUMBER_DICTIONARIES + LIST_DICTIONARIES
+ STRING_DICTIONARIES):
setattr(self, key_word, {})
for key_word in STRING_LISTS:
setattr(self, key_word, [])
for key_word in STRINGS:
setattr(self, key_word, "")
for key_word in MATRICES:
matrix = InteractionMatrix(key_word)
setattr(self, key_word, matrix)
for key_word in PAIR_WISE_MATRICES:
matrix = PairwiseMatrix(key_word)
setattr(self, key_word, matrix)
def print_interaction_parameters(self):
"""Print interaction parameters."""
_LOGGER.info('--------------- Model pKa values ----------------------')

2
propka/propka.cfg
View File

@@ -107,7 +107,7 @@ interaction_matrix SH I N N N N N N N N N N I I I I I I N N N N N N N N N N N I
sidechain_cutoffs default 3.0 4.0
# COO
sidechain_cutoffs COO COO 2.5 3.5
Sidechain_cutoffs COO SER 2.65 3.65
sidechain_cutoffs COO SER 2.65 3.65
sidechain_cutoffs COO ARG 1.85 2.85
sidechain_cutoffs COO LYS 2.85 3.85
sidechain_cutoffs COO HIS 2.0 3.0

41
propka/protonate.py
View File

@@ -9,10 +9,16 @@ protons.
"""
import logging
import math
from typing import Iterable, TYPE_CHECKING
import propka.bonds
import propka.atom
from propka.atom import Atom
from propka.vector_algebra import rotate_vector_around_an_axis, Vector
if TYPE_CHECKING:
from propka.molecular_container import MolecularContainer
_LOGGER = logging.getLogger(__name__)
@@ -58,7 +64,7 @@ class Protonate:
'Br': 1.41, 'I': 1.61, 'S': 1.35}
self.protonation_methods = {4: self.tetrahedral, 3: self.trigonal}
def protonate(self, molecules):
def protonate(self, molecules: "MolecularContainer"):
"""Protonate all atoms in the molecular container.
Args:
@@ -75,7 +81,7 @@ class Protonate:
self.protonate_atom(atom)
@staticmethod
def remove_all_hydrogen_atoms(molecular_container):
def remove_all_hydrogen_atoms(molecular_container: "MolecularContainer"):
"""Remove all hydrogen atoms from molecule.
Args:
@@ -86,7 +92,7 @@ class Protonate:
molecular_container.conformations[name]
.get_non_hydrogen_atoms())
def set_charge(self, atom):
def set_charge(self, atom: Atom):
"""Set charge for atom.
Args:
@@ -109,7 +115,7 @@ class Protonate:
atom.sybyl_type = atom.sybyl_type.replace('-', '')
atom.charge_set = True
def protonate_atom(self, atom):
def protonate_atom(self, atom: Atom):
"""Protonate an atom.
Args:
@@ -126,7 +132,7 @@ class Protonate:
atom.is_protonated = True
@staticmethod
def set_proton_names(heavy_atoms):
def set_proton_names(heavy_atoms: Iterable[Atom]):
"""Set names for protons.
Args:
@@ -139,7 +145,7 @@ class Protonate:
bonded.name += str(i)
i += 1
def set_number_of_protons_to_add(self, atom):
def set_number_of_protons_to_add(self, atom: Atom):
"""Set the number of protons to add to this atom.
Args:
@@ -169,7 +175,7 @@ class Protonate:
_LOGGER.debug('-'*10)
_LOGGER.debug(atom.number_of_protons_to_add)
def set_steric_number_and_lone_pairs(self, atom):
def set_steric_number_and_lone_pairs(self, atom: Atom):
"""Set steric number and lone pairs for atom.
Args:
@@ -207,8 +213,7 @@ class Protonate:
atom.steric_number += 0
_LOGGER.debug('{0:>65s}: {1:>4.1f}'.format(
'Charge(-)', atom.charge))
atom.steric_number -= atom.charge
atom.steric_number = math.floor(atom.steric_number/2.0)
atom.steric_number = math.floor((atom.steric_number - atom.charge) / 2)
atom.number_of_lone_pairs = (
atom.steric_number - len(atom.bonded_atoms)
- atom.number_of_protons_to_add
@@ -220,7 +225,7 @@ class Protonate:
'Number of lone pairs', atom.number_of_lone_pairs))
atom.steric_num_lone_pairs_set = True
def add_protons(self, atom):
def add_protons(self, atom: Atom):
"""Add protons to atom.
Args:
@@ -236,7 +241,7 @@ class Protonate:
'(steric number: {0:d})'.format(atom.steric_number)
)
def trigonal(self, atom):
def trigonal(self, atom: Atom):
"""Add hydrogens in trigonal geometry.
Args:
@@ -269,15 +274,15 @@ class Protonate:
vec2 = Vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0]
.bonded_atoms[other_atom_indices[0]])
axis = vec1**vec2
axis = vec1.cross(vec2)
# this is a trick to make sure that the order of atoms doesn't
# influence the final postions of added protons
if len(other_atom_indices) > 1:
vec3 = Vector(atom1=atom.bonded_atoms[0],
atom2=atom.bonded_atoms[0]
.bonded_atoms[other_atom_indices[1]])
axis2 = vec1**vec3
if axis*axis2 > 0:
axis2 = vec1.cross(vec3)
if axis.dot(axis2) > 0:
axis = axis+axis2
else:
axis = axis-axis2
@@ -296,7 +301,7 @@ class Protonate:
new_a = self.set_bond_distance(new_a, atom.element)
self.add_proton(atom, cvec+new_a)
def tetrahedral(self, atom):
def tetrahedral(self, atom: Atom):
"""Protonate atom in tetrahedral geometry.
Args:
@@ -338,13 +343,14 @@ class Protonate:
self.add_proton(atom, cvec+new_a)
@staticmethod
def add_proton(atom, position):
def add_proton(atom: Atom, position: Vector):
"""Add a proton to an atom at a specific position.
Args:
atom: atom to protonate
position: position for proton
"""
assert atom.conformation_container is not None
# Create the new proton
new_h = propka.atom.Atom()
new_h.set_property(
@@ -368,7 +374,6 @@ class Protonate:
new_h.number_of_lone_pairs = 0
new_h.number_of_protons_to_add = 0
new_h.num_pi_elec_2_3_bonds = 0
new_h.is_protonates = True
atom.bonded_atoms.append(new_h)
atom.number_of_protons_to_add -= 1
atom.conformation_container.add_atom(new_h)
@@ -386,7 +391,7 @@ class Protonate:
i += 1
_LOGGER.debug('added %s %s %s', new_h, 'to', atom)
def set_bond_distance(self, bvec, element):
def set_bond_distance(self, bvec: Vector, element: str) -> Vector:
"""Set bond distance between atom and element.
Args:

0
propka/py.typed Normal file
View File

7
propka/run.py
View File

@@ -12,10 +12,12 @@ function. If similar functionality is desired from a Python script
"""
import logging
import sys
from typing import IO, Iterable, Optional
from propka.lib import loadOptions
from propka.input import read_parameter_file, read_molecule_file
from propka.parameters import Parameters
from propka.molecular_container import MolecularContainer
from propka.output import _PathArg
_LOGGER = logging.getLogger(__name__)
@@ -44,7 +46,9 @@ def main(optargs=None):
my_molecule.write_pka()
def single(filename: str, optargs: tuple = (), stream=None,
def single(filename: _PathArg,
optargs: Iterable[str] = (),
stream: Optional[IO[str]] = None,
write_pka: bool = True):
"""Run a single PROPKA calculation using ``filename`` as input.
@@ -105,6 +109,7 @@ def single(filename: str, optargs: tuple = (), stream=None,
.. versionchanged:: 3.4.0
Removed ability to write out PROPKA input files.
"""
filename = str(filename)
# Deal with input optarg options
optargs = tuple(optargs)
optargs += (filename,)

75
propka/vector_algebra.py
View File

@@ -6,7 +6,8 @@ Vector algebra for PROPKA.
"""
import logging
import math
from typing import Optional, Protocol, Union
from typing import Optional, Protocol, overload
import warnings
_LOGGER = logging.getLogger(__name__)
@@ -69,20 +70,31 @@ class Vector:
self.y - other.y,
self.z - other.z)
def __mul__(self, other: Union["Vector", "Matrix4x4", float]):
def dot(self, other: _XYZ) -> float:
return self.x * other.x + self.y * other.y + self.z * other.z
@overload
def __mul__(self, other: "Vector") -> float:
...
@overload
def __mul__(self, other: "Matrix4x4") -> "Vector":
...
@overload
def __mul__(self, other: float) -> "Vector":
...
def __mul__(self, other):
"""Dot product, scalar and matrix multiplication."""
if isinstance(other, Vector):
return self.x * other.x + self.y * other.y + self.z * other.z
elif isinstance(other, Matrix4x4):
return Vector(
xi=other.a11*self.x + other.a12*self.y + other.a13*self.z
+ other.a14*1.0,
yi=other.a21*self.x + other.a22*self.y + other.a23*self.z
+ other.a24*1.0,
zi=other.a31*self.x + other.a32*self.y + other.a33*self.z
+ other.a34*1.0
)
elif type(other) in [int, float]:
warnings.warn("Use Vector.dot() instead of operator.mul()", DeprecationWarning, stacklevel=2)
return self.dot(other)
if isinstance(other, Matrix4x4):
warnings.warn("Use M @ v (operator.matmul()) instead of M * v (operator.mul())",
DeprecationWarning, stacklevel=2)
return other @ self
if isinstance(other, (int, float)):
return Vector(self.x * other, self.y * other, self.z * other)
raise TypeError(f'{type(other)} not supported')
@@ -90,6 +102,10 @@ class Vector:
return self.__mul__(other)
def __pow__(self, other: _XYZ):
warnings.warn("Use Vector.cross() instead of operator.pow()", DeprecationWarning, stacklevel=2)
return self.cross(other)
def cross(self, other: _XYZ):
"""Cross product."""
return Vector(self.y * other.z - self.z * other.y,
self.z * other.x - self.x * other.z,
@@ -160,6 +176,17 @@ class Matrix4x4:
self.a43 = a43i
self.a44 = a44i
def __matmul__(self, v: _XYZ) -> Vector:
"""Matrix vector multiplication with homogeneous coordinates.
Assumes that the last row is (0, 0, 0, 1).
"""
return Vector(
self.a11 * v.x + self.a12 * v.y + self.a13 * v.z + self.a14,
self.a21 * v.x + self.a22 * v.y + self.a23 * v.z + self.a24,
self.a31 * v.x + self.a32 * v.y + self.a33 * v.z + self.a34,
)
def angle(avec: Vector, bvec: Vector) -> float:
"""Get the angle between two vectors.
@@ -170,7 +197,7 @@ def angle(avec: Vector, bvec: Vector) -> float:
Returns:
angle in radians
"""
dot = avec * bvec
dot = avec.dot(bvec)
return math.acos(dot / (avec.length() * bvec.length()))
@@ -196,10 +223,10 @@ def signed_angle_around_axis(avec: Vector, bvec: Vector, axis: Vector) -> float:
Returns:
angle in radians
"""
norma = avec**axis
normb = bvec**axis
norma = avec.cross(axis)
normb = bvec.cross(axis)
ang = angle(norma, normb)
dot_ = bvec*(avec**axis)
dot_ = bvec.dot(avec.cross(axis))
if dot_ < 0:
ang = -ang
return ang
@@ -223,21 +250,21 @@ def rotate_vector_around_an_axis(theta: float, axis: Vector, vec: Vector) -> Vec
else:
gamma = math.pi/2.0
rot_z = rotate_atoms_around_z_axis(gamma)
vec = rot_z * vec
axis = rot_z * axis
vec = rot_z @ vec
axis = rot_z @ axis
beta = 0.0
if axis.x != 0:
beta = -axis.x/abs(axis.x)*math.acos(
axis.z/math.sqrt(axis.x*axis.x + axis.z*axis.z))
rot_y = rotate_atoms_around_y_axis(beta)
vec = rot_y * vec
axis = rot_y * axis
vec = rot_y @ vec
axis = rot_y @ axis
rot_z = rotate_atoms_around_z_axis(theta)
vec = rot_z * vec
vec = rot_z @ vec
rot_y = rotate_atoms_around_y_axis(-beta)
vec = rot_y * vec
vec = rot_y @ vec
rot_z = rotate_atoms_around_z_axis(-gamma)
vec = rot_z * vec
vec = rot_z @ vec
return vec

5
propka/version.py
View File

@@ -7,6 +7,7 @@ Contains version-specific methods and parameters.
TODO - this module unnecessarily confuses the code. Can we eliminate it?
"""
import logging
from propka.atom import Atom
from propka.hydrogens import setup_bonding_and_protonation, setup_bonding
from propka.hydrogens import setup_bonding_and_protonation_30_style
from propka.energy import radial_volume_desolvation, calculate_pair_weight
@@ -98,6 +99,10 @@ class Version:
"""Setup bonding using assigned model."""
return self.prepare_bonds(self.parameters, molecular_container)
def get_hydrogen_bond_parameters(self, atom1: Atom, atom2: Atom) -> tuple:
"""Get hydrogen bond parameters for two atoms."""
raise NotImplementedError("abstract method")
class VersionA(Version):
"""TODO - figure out what this is."""

3
tests/test_basic_regression.py
View File

@@ -68,11 +68,11 @@ def run_propka(options, pdb_path, tmp_path):
"""
options += [str(pdb_path)]
args = loadOptions(options)
cwd = Path.cwd()
try:
_LOGGER.warning(
"Working in tmpdir {0:s} because of PROPKA file output; "
"need to fix this.".format(str(tmp_path)))
cwd = Path.cwd()
os.chdir(tmp_path)
parameters = read_parameter_file(args.parameters, Parameters())
molecule = MolecularContainer(parameters, args)
@@ -148,6 +148,7 @@ def compare_output(pdb, tmp_path, ref_path):
def test_regression(pdb, options, tmp_path):
"""Basic regression test of PROPKA functionality."""
path_dict = get_test_dirs()
ref_path = None
for ext in ["json", "dat"]:
ref_path = path_dict["results"] / f"{pdb}.{ext}"

27
tests/test_lib.py Normal file
View File

@@ -0,0 +1,27 @@
import propka.lib as m
import argparse
import pytest
def test_parse_res_string():
assert m.parse_res_string("C:123") == ("C", 123, " ")
assert m.parse_res_string("C:123B") == ("C", 123, "B")
assert m.parse_res_string("ABC:123x") == ("ABC", 123, "x")
with pytest.raises(ValueError):
m.parse_res_string("C:B123")
with pytest.raises(ValueError):
m.parse_res_string("123B")
with pytest.raises(ValueError):
m.parse_res_string("C:123:B")
def test_parse_res_list():
assert m.parse_res_list("C:123") == [("C", 123, " ")]
assert m.parse_res_list("ABC:123,D:4,F:56X") == [
("ABC", 123, " "),
("D", 4, " "),
("F", 56, "X"),
]
with pytest.raises(argparse.ArgumentTypeError):
m.parse_res_list("C:B123")

163
tests/test_vector_algebra.py Normal file
View File

@@ -0,0 +1,163 @@
import propka.vector_algebra as m
import math
import pytest
from pytest import approx
RADIANS_90 = math.pi / 2
def assert_vector_equal(v1: m.Vector, v2: m.Vector):
assert isinstance(v1, m.Vector)
assert isinstance(v2, m.Vector)
assert v1.x == approx(v2.x)
assert v1.y == approx(v2.y)
assert v1.z == approx(v2.z)
def _matrix4x4_tolist(self: m.Matrix4x4) -> list:
return [
self.a11, self.a12, self.a13, self.a14, self.a21, self.a22, self.a23, self.a24,
self.a31, self.a32, self.a33, self.a34, self.a41, self.a42, self.a43, self.a44
]
def assert_matrix4x4_equal(m1: m.Matrix4x4, m2: m.Matrix4x4):
assert isinstance(m1, m.Matrix4x4)
assert isinstance(m2, m.Matrix4x4)
assert _matrix4x4_tolist(m1) == approx(_matrix4x4_tolist(m2))
def test_Vector__init():
v = m.Vector()
assert v.x == 0.0
assert v.y == 0.0
assert v.z == 0.0
v = m.Vector(12, 34, 56)
assert v.x == 12
assert v.y == 34
assert v.z == 56
v1 = m.Vector(atom1=v)
assert v1.x == 12
assert v1.y == 34
assert v1.z == 56
v2 = m.Vector(5, 4, 3)
v3 = m.Vector(atom1=v2, atom2=v1)
assert v3.x == 7
assert v3.y == 30
assert v3.z == 53
def test_Vector__plusminus():
v1 = m.Vector(1, 2, 3)
v2 = m.Vector(4, 5, 6)
v3 = v1 + v2
assert v3.x == 5
assert v3.y == 7
assert v3.z == 9
v3 = v1 - v2
assert v3.x == -3
assert v3.y == -3
assert v3.z == -3
v4 = -v1
assert v4.x == -1
assert v4.y == -2
assert v4.z == -3
def test_Vector__mul__number():
v1 = m.Vector(1, 2, 3)
assert_vector_equal(v1 * 2, m.Vector(2, 4, 6))
def test_Vector__mul__Vector():
v1 = m.Vector(1, 2, 3)
v2 = m.Vector(4, 5, 6)
with pytest.deprecated_call():
assert v1 * v2 == 32
assert v1.dot(v2) == 32
with pytest.raises(TypeError):
v1 @ v2 # type: ignore
def test_Vector__mul__Matrix4x4():
v1 = m.Vector(1, 2, 3)
assert_vector_equal(m.Matrix4x4() @ v1, m.Vector())
m2 = m.Matrix4x4(0, 1, 0, 0, 20, 0, 0, 0, 0, 0, 300, 0, 0, 0, 0, 1)
with pytest.deprecated_call():
assert_vector_equal(v1 * m2, m.Vector(2, 20, 900))
with pytest.deprecated_call():
assert_vector_equal(m2 * v1, m.Vector(2, 20, 900))
assert_vector_equal(m2 @ v1, m.Vector(2, 20, 900))
with pytest.raises(TypeError):
v1 @ m2 # type: ignore
def test_Vector__cross():
v1 = m.Vector(1, 2, 3)
v2 = m.Vector(4, 5, 6)
with pytest.deprecated_call():
assert_vector_equal(v1**v2, m.Vector(-3, 6, -3))
assert_vector_equal(v1.cross(v2), m.Vector(-3, 6, -3))
assert_vector_equal(v2.cross(v1), m.Vector(3, -6, 3))
def test_Vector__length():
v1 = m.Vector(1, 2, 3)
assert v1.length() == 14**0.5
assert v1.sq_length() == 14
def test_Vector__orthogonal():
v1 = m.Vector(1, 2, 3)
assert v1.dot(v1.orthogonal()) == 0
def test_Vector__rescale():
v1 = m.Vector(1, 2, 3)
v2 = v1.rescale(4)
assert v2.length() == 4
assert v2.x / v1.x == approx(4 / 14**0.5)
assert v2.y / v1.y == approx(4 / 14**0.5)
assert v2.z / v1.z == approx(4 / 14**0.5)
def test_angle():
v1 = m.Vector(0, 0, 1)
v2 = m.Vector(0, 2, 0)
assert m.angle(v1, v2) == RADIANS_90
def test_angle_degrees():
v1 = m.Vector(0, 0, 3)
v2 = m.Vector(5, 0, 0)
assert m.angle_degrees(v1, v2) == 90
def test_signed_angle_around_axis():
v1 = m.Vector(0, 0, 3)
v2 = m.Vector(5, 0, 0)
v3 = m.Vector(0, 1, 0)
assert m.signed_angle_around_axis(v1, v2, v3) == -RADIANS_90
v1 = m.Vector(0, 2, 3)
v2 = m.Vector(5, 4, 0)
assert m.signed_angle_around_axis(v1, v2, v3) == -RADIANS_90
def test_rotate_vector_around_an_axis():
v1 = m.Vector(0, 0, 3)
v2 = m.Vector(3, 0, 0)
v3 = m.Vector(0, -1, 0)
v4 = m.rotate_vector_around_an_axis(RADIANS_90, v3, v2)
assert_vector_equal(v4, v1)
def test_rotate_atoms_around_z_axis():
m_rot = m.rotate_atoms_around_z_axis(-RADIANS_90)
assert_matrix4x4_equal(m_rot,
m.Matrix4x4(0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1))
def test_rotate_atoms_around_y_axis():
m_rot = m.rotate_atoms_around_y_axis(RADIANS_90)
assert_matrix4x4_equal(m_rot,
m.Matrix4x4(0, 0, 1, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 0, 1))