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haddock3 / data /tests /test_gear_preprocessing.py
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introvoyz042
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"""Test preprocessing operations."""
import os
from itertools import zip_longest
from pathlib import Path
import pytest
from haddock.gear import preprocessing as pp
from . import broken_pdb, corrected_pdb, residues_top
def test_open_or_give():
in1 = open(broken_pdb)
input_ = [
broken_pdb, # path inside list
str(broken_pdb), # path inside list
in1,
broken_pdb.read_text().split(os.linesep), # list
tuple(broken_pdb.read_text().split(os.linesep)), # tuple
]
result = pp._open_or_give(input_)
assert len(result) == 5
for r in result:
assert len(r) == 192
in1.close()
@pytest.mark.parametrize(
"value",
[1, 1.1, {1: None}, None],
)
def test_open_or_give_wrong(value):
with pytest.raises(TypeError):
pp._open_or_give(value)
def test_read_additional_residues():
result = pp.read_additional_residues(residues_top)
assert isinstance(result, tuple)
assert result == ("DA2", "DE3", "DI", "DO", "DU1")
def test_read_additional_residues_lines():
lines = Path(residues_top).read_text().split(os.linesep)
result = pp.read_additional_residues.original(lines)
assert isinstance(result, tuple)
assert result == ("DA2", "DE3", "DI", "DO", "DU1")
def test_wrep_pdb_tidy():
pp.wrep_pdb_tidy(pp._open_or_give([broken_pdb])[0], strict=False)
def test_wrep_pdb_tidy_strict():
pp.wrep_pdb_tidy(pp._open_or_give([broken_pdb])[0], strict=True)
models_okay = """MODEL 1
ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
MODEL 2
ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
MODEL 3
ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
"""
models_wrong_2 = """MODEL 1
ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
MODEL 2
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
MODEL 3
ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
"""
models_wrong_3 = """MODEL 1
ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
MODEL 2
ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
MODEL 3
ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C
ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C
TER
ENDMDL
"""
def test_check_models():
pp.models_should_have_the_same_labels(models_okay.split(os.linesep))
def test_check_models_wrong_2():
_lines = models_wrong_2.split(os.linesep)
with pytest.raises(pp.ModelsDifferError) as error:
pp.models_should_have_the_same_labels(_lines)
assert str(error.value) == "Labels in MODEL 2 differ from MODEL 1."
def test_check_models_wrong_3():
_lines = models_wrong_3.split(os.linesep)
with pytest.raises(pp.ModelsDifferError) as error:
pp.models_should_have_the_same_labels(_lines)
assert str(error.value) == "Labels in MODEL 3 differ from MODEL 1."
rep_chains_1 = [
[
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C ',
'ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C ',
],
[
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C ',
'ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C ',
],
]
expected_rep_chains_1 = [
[
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C ',
'ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C ',
],
[
'ATOM 3 CA ARG A 4 37.080 43.455 -3.421 1.00 0.00 A C ',
'ATOM 3 CA GLU A 6 33.861 45.127 -2.233 1.00 0.00 A C ',
'ATOM 3 CA ALA A 7 35.081 45.036 1.305 1.00 0.00 A C ',
],
]
rep_chains_no_rep = [
[
'ATOM 3 CA ARG A 4 37.080 43.455 -3.421 1.00 0.00 C ',
'ATOM 3 CA GLU A 6 33.861 45.127 -2.233 1.00 0.00 C ',
'ATOM 3 CA ALA A 7 35.081 45.036 1.305 1.00 0.00 C ',
],
[
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 C ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C ',
'ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 C ',
],
]
@pytest.mark.parametrize(
'in_, expected',
[
(rep_chains_1, expected_rep_chains_1),
(rep_chains_no_rep, rep_chains_no_rep),
],
)
def test_correct_equal_chain_segids(in_, expected):
result = pp.correct_equal_chain_segids(in_)
# made for loop to facilitate visualization of errors
for r, e in zip(result, expected):
assert r == e
multiple_chainIDs_1 = [
'ATOM 3 CA ARG A 4 37.080 43.455 -3.421 1.00 0.00 C ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C ',
'TER',
'ATOM 3 CA ALA C 7 35.081 45.036 1.305 1.00 0.00 C ',
]
multiple_chainIDs_2 = [
'ATOM 3 CA ARG C 4 37.080 43.455 -3.421 1.00 0.00 C ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 C ',
'ATOM 3 CA ALA A 7 35.081 45.036 1.305 1.00 0.00 C ',
]
# mind the added segID
expected_multiple_chainIDs_1 = [
'ATOM 3 CA ARG A 4 37.080 43.455 -3.421 1.00 0.00 A C ',
'ATOM 3 CA GLU A 6 33.861 45.127 -2.233 1.00 0.00 A C ',
'TER A ', # why this extra space?
'ATOM 3 CA ALA A 7 35.081 45.036 1.305 1.00 0.00 A C ',
]
expected_multiple_chainIDs_2 = [
'ATOM 3 CA ARG C 4 37.080 43.455 -3.421 1.00 0.00 C C ',
'ATOM 3 CA GLU C 6 33.861 45.127 -2.233 1.00 0.00 C C ',
'ATOM 3 CA ALA C 7 35.081 45.036 1.305 1.00 0.00 C C ',
]
@pytest.mark.parametrize(
"in_,expected",
[
(multiple_chainIDs_1, expected_multiple_chainIDs_1),
(multiple_chainIDs_2, expected_multiple_chainIDs_2),
# returns the same thing
(expected_multiple_chainIDs_2, expected_multiple_chainIDs_2),
]
)
def test_homogenize_chainIDs(in_, expected):
"""Test homogenize chain IDs."""
result = pp.homogenize_chains(in_)
# assert line by line to facilitate finding errors
for r_line, e_line in zip(result, expected):
assert len(r_line) == len(e_line)
for r_line, e_line in zip(result, expected):
assert r_line == e_line
nochain_chainIDs_1 = [
'ATOM 3 CA ARG 4 37.080 43.455 -3.421 1.00 0.00 ',
'ATOM 3 CA GLU 6 33.861 45.127 -2.233 1.00 0.00 ',
'ATOM 3 CA ALA 7 35.081 45.036 1.305 1.00 0.00 ',
]
nochain_chainIDs_2 = [
'ATOM 3 CA ARG A 4 37.080 43.455 -3.421 1.00 0.00 ',
'ATOM 3 CA GLU A 6 33.861 45.127 -2.233 1.00 0.00 ',
'ATOM 3 CA ALA A 7 35.081 45.036 1.305 1.00 0.00 ',
]
nochain_chainIDs_3 = [
'ATOM 3 CA ARG 4 37.080 43.455 -3.421 1.00 0.00 A ',
'ATOM 3 CA GLU 6 33.861 45.127 -2.233 1.00 0.00 A ',
'ATOM 3 CA ALA 7 35.081 45.036 1.305 1.00 0.00 A ',
]
nochain_chainIDs_4 = [
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 A ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 A ',
'ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 A ',
]
expected_nochain_chainIDs_1 = [
'ATOM 3 CA ARG A 4 37.080 43.455 -3.421 1.00 0.00 A ',
'ATOM 3 CA GLU A 6 33.861 45.127 -2.233 1.00 0.00 A ',
'ATOM 3 CA ALA A 7 35.081 45.036 1.305 1.00 0.00 A ',
]
expected_nochain_chainIDs_4 = [
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 B ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 B ',
'ATOM 3 CA ALA B 7 35.081 45.036 1.305 1.00 0.00 B ',
]
chain_and_seg_IDs = [
'ATOM 3 CA ARG A 4 37.080 43.455 -3.421 1.00 0.00 A ',
'ATOM 3 CA GLU A 6 33.861 45.127 -2.233 1.00 0.00 A ',
'ATOM 3 CA ALA A 7 35.081 45.036 1.305 1.00 0.00 A ',
]
@pytest.mark.parametrize(
'in_,expected',
[
(nochain_chainIDs_1, expected_nochain_chainIDs_1),
(nochain_chainIDs_2, expected_nochain_chainIDs_1),
(nochain_chainIDs_3, expected_nochain_chainIDs_1),
(nochain_chainIDs_4, expected_nochain_chainIDs_4),
(chain_and_seg_IDs, chain_and_seg_IDs),
]
)
def test_solve_nochainID(in_, expected):
"""Test solve nochainID function."""
result = pp.solve_no_chainID_no_segID(in_)
for r, e in zip(result, expected):
assert r == e
# test cases to test adding the ion charges
# even indexes are the input, odd indexes are the expected results
ion_cases = [
# 0
'HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN ',
'HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN+2',
# 1
'HETATM 3833 ZN ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN ',
'HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN+2',
# 2
'HETATM 3833 ZN+2 ZN A 42 21.391 -8.794 33.944 1.00 24.37 ZN ',
'HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN+2',
# 3
'HETATM 3833 ZN ZN A 42 21.391 -8.794 33.944 1.00 24.37 ZN ',
'HETATM 3833 ZN ZN A 42 21.391 -8.794 33.944 1.00 24.37 ZN ',
# 4
'HETATM 3833 ZN ZN A 42 21.391 -8.794 33.944 1.00 24.37 ZN+2',
'HETATM 3833 ZN+2 ZN2 A 42 21.391 -8.794 33.944 1.00 24.37 ZN+2',
# 5
'HETATM 3834 K K1 A 42 21.391 -8.794 33.944 1.00 24.37 ',
'HETATM 3834 K+1 K1 A 42 21.391 -8.794 33.944 1.00 24.37 K+1',
# 6
'HETATM 3835 NI NI A 42 21.391 -8.794 33.944 1.00 24.37 ',
'HETATM 3835 NI NI A 42 21.391 -8.794 33.944 1.00 24.37 NI ',
# 7
'HETATM 3834 F-1 F A 42 21.391 -8.794 33.944 1.00 24.37 ',
'HETATM 3834 F-1 F1 A 42 21.391 -8.794 33.944 1.00 24.37 F-1',
# 8
'HETATM 3 CA CA B 4 37.080 43.455 -3.421 1.00 0.00 B CA+2',
'HETATM 3 CA+2 CA2 B 4 37.080 43.455 -3.421 1.00 0.00 B CA+2',
# 9 lines not concerning ions - note element is not defined
# carbon alpha conflicting with calcium
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 B ',
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 B ',
# 10 other lines not concerning ions - atom not CA (carbon alpha)
'ATOM 1 N ALA A 1 0.000 0.000 0.000 0.00 0.00 N ',
'ATOM 1 N ALA A 1 0.000 0.000 0.000 0.00 0.00 N ',
# 11 lines not concerning ions - here the element is defined
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 B C ',
'ATOM 3 CA ARG B 4 37.080 43.455 -3.421 1.00 0.00 B C ',
# 12 exception
'HETATM 3834 F FA A 42 21.391 -8.794 33.944 1.00 24.37 ',
'HETATM 3834 F F A 42 21.391 -8.794 33.944 1.00 24.37 F ',
]
# made this way to make each line a separate tests
@pytest.fixture(params=list(zip(ion_cases[::2], ion_cases[1::2])))
def ion_cases_fixture(request):
"""Give ion test cases."""
return request.param[0], request.param[1]
def test_correct_ion_charges(ion_cases_fixture):
input_, expected = ion_cases_fixture
# 1. puts input_ inside a list because the function only accepts lists
# 2. the function is wrapped around list() because it is a generator
result = list(pp.add_charges_to_ions([input_]))
assert len(result) == 1
# compares two strings
assert result[0] == expected
def test_process_ion_case_atom():
"""Test processing an exception case."""
inp = 'HETATM 3834 F FA A 42 21.391 -8.794 33.944 1.00 24.37 ' # noqa: E501
exp = 'HETATM 3834 F F A 42 21.391 -8.794 33.944 1.00 24.37 F ' # noqa: E501
result = pp._process_ion_case_atom(inp)
assert result == exp
@pytest.mark.parametrize(
"lines, expected",
[
(
'ATOM 3 CA GLU A 6 33.861 45.127 -2.233 1.00 0.00 A ',
'ATOM 3 CA GLU B 6 33.861 45.127 -2.233 1.00 0.00 A ',
),
]
)
def test_wrep_chain(lines, expected):
"""Test if dry report works."""
result = pp.wrep_pdb_chain([lines], "B", report=True)
assert result[0] == expected
def test_process_pdbs():
"""."""
result = pp.process_pdbs(broken_pdb)
assert len(result) == 1
expected = corrected_pdb.read_text().rstrip(os.linesep).split(os.linesep)
for i, (rline, eline) in enumerate(zip_longest(result[0], expected)):
assert rline == eline, i