haddock3/integration_tests/test_topoaa.py at 38bb99b82ddf685e8f56d2da13e007821cbf6638 · haddocking/haddock3 · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
import tempfile
import pytest
from pathlib import Path
from shutil import copyfile

from haddock.core.defaults import DATA_DIRNAME
from haddock.libs.libio import working_directory
from haddock.modules.topology.topoaa import (
    DEFAULT_CONFIG as DEFAULT_TOPOAA_CONFIG,
    HaddockModule as TopoaaModule,
    )

from . import CNS_EXEC, DATA_DIR, has_cns


@pytest.fixture
def molecules():
    return [
        Path(DATA_DIR, "docking-protein-protein/data/e2aP_1F3G.pdb"),
        Path(DATA_DIR, "docking-protein-protein/data/hpr_ensemble.pdb"),
        ]


@pytest.fixture
def prepare_topoaa_run(molecules):
    with tempfile.TemporaryDirectory() as tmpdir:
        with working_directory(tmpdir):
            modulename_path = Path("0_topoaa")
            modulename_path.mkdir(parents=True)
            input_dir_path = Path(DATA_DIRNAME, modulename_path)
            input_dir_path.mkdir(parents=True)
            mol_copies = [
                copyfile(mol, Path(input_dir_path, mol.name))
                for mol in molecules
                ]
            yield modulename_path, mol_copies


@pytest.fixture
def topoaa_module(prepare_topoaa_run):
    modulename_path = prepare_topoaa_run[0]
    mol_copies = prepare_topoaa_run[1]
    topoaa = TopoaaModule(
        order=0,
        path=modulename_path,
        initial_params=DEFAULT_TOPOAA_CONFIG,
        )
    #topoaa.__init__(path=modulename_path, order=0)
    topoaa.params["molecules"] = mol_copies
    topoaa.params["mol1"] = {"prot_segid": "A"}
    topoaa.params["mol2"] = {"prot_segid": "B"}

    topoaa.params["cns_exec"] = CNS_EXEC

    yield topoaa


@has_cns
def test_topoaa_default(topoaa_module):
    """Test the topoaa module."""

    topoaa_module.run()

    expected_inp = Path(topoaa_module.path, "e2aP_1F3G.inp")
    expected_psf = Path(topoaa_module.path, "e2aP_1F3G_haddock.psf")
    expected_pdb = Path(topoaa_module.path, "e2aP_1F3G_haddock.pdb")
    expected_gz = Path(topoaa_module.path, "e2aP_1F3G.out.gz")

    assert expected_inp.exists(), f"{expected_inp} does not exist"
    assert expected_psf.exists(), f"{expected_psf} does not exist"
    assert expected_gz.exists(), f"{expected_gz} does not exist"
    assert expected_pdb.exists(), f"{expected_pdb} does not exist"

    assert expected_inp.stat().st_size > 0, f"{expected_inp} is empty"

    for i in range(1, 10 + 1):
        expected_inp = Path(topoaa_module.path, f"hpr_ensemble_{i}.inp")
        expected_psf = Path(topoaa_module.path, f"hpr_ensemble_{i}_haddock.psf")
        expected_pdb = Path(topoaa_module.path, f"hpr_ensemble_{i}_haddock.pdb")
        expected_gz = Path(topoaa_module.path, f"hpr_ensemble_{i}.out.gz")

        assert expected_inp.exists(), f"{expected_inp} does not exist"
        assert expected_psf.exists(), f"{expected_psf} does not exist"
        assert expected_pdb.exists(), f"{expected_pdb} does not exist"
        assert expected_gz.exists(), f"{expected_gz} does not exist"

        assert expected_inp.stat().st_size > 0, f"{expected_inp} is empty"
        assert expected_psf.stat().st_size > 0, f"{expected_psf} is empty"
        assert expected_pdb.stat().st_size > 0, f"{expected_pdb} is empty"
        assert expected_gz.stat().st_size > 0, f"{expected_gz} is empty"