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Update Python wf
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@gbayarri
gbayarri committed Jan 15, 2025
1 parent 2d2f251 commit 49bf7b5
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Binary file added biobb_wf_flexserv/tests/python/Files/1a32.MoDEL.pcz
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573 changes: 573 additions & 0 deletions biobb_wf_flexserv/tests/python/biobb_wf_flexserv.py
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27 changes: 27 additions & 0 deletions biobb_wf_flexserv/tests/python/conftest.py
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import pytest
import shutil
import os


def pytest_addoption(parser):
parser.addoption("--config", action="store", default=None, help="Path to the config file")
parser.addoption("--remove", action="store_true", default=False, help="Remove working directory after tests")


@pytest.fixture
def config_path(request):
return request.config.getoption("--config")


@pytest.fixture
def remove_flag(request):
return request.config.getoption("--remove")


@pytest.fixture(scope="session", autouse=True)
def cleanup():
yield
# This code will run after all tests are completed
pycache_dir = os.path.join(os.path.dirname(__file__), '__pycache__')
if os.path.exists(pycache_dir):
shutil.rmtree(pycache_dir)
85 changes: 85 additions & 0 deletions biobb_wf_flexserv/tests/python/reference/step0_extract_atoms/structure_ca.pdb
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ATOM 2 CA LEU A 2 -9.711 -13.341 53.419 1.00 48.40 C
ATOM 10 CA THR A 3 -10.405 -9.634 52.826 1.00 40.93 C
ATOM 17 CA GLN A 4 -10.626 -8.238 49.277 1.00 39.77 C
ATOM 26 CA GLU A 5 -7.621 -6.033 50.061 1.00 37.91 C
ATOM 35 CA ARG A 6 -5.427 -8.959 51.040 1.00 30.57 C
ATOM 46 CA LYS A 7 -6.912 -11.114 48.265 1.00 22.90 C
ATOM 55 CA ARG A 8 -6.112 -8.471 45.620 1.00 17.48 C
ATOM 66 CA GLU A 9 -2.714 -7.768 47.141 1.00 17.18 C
ATOM 75 CA ILE A 10 -1.785 -11.469 47.052 1.00 18.54 C
ATOM 83 CA ILE A 11 -2.976 -11.579 43.426 1.00 21.84 C
ATOM 91 CA GLU A 12 -0.568 -8.955 42.089 1.00 28.60 C
ATOM 100 CA GLN A 13 2.151 -9.801 44.614 1.00 28.21 C
ATOM 109 CA PHE A 14 2.263 -13.377 43.256 1.00 22.26 C
ATOM 120 CA LYS A 15 1.514 -13.005 39.545 1.00 39.69 C
ATOM 129 CA VAL A 16 4.805 -13.772 37.807 1.00 58.66 C
ATOM 136 CA HIS A 17 5.955 -11.273 35.090 1.00 70.47 C
ATOM 146 CA GLU A 18 6.919 -7.716 34.036 1.00 76.81 C
ATOM 155 CA ASN A 19 5.327 -4.306 34.774 1.00 75.85 C
ATOM 163 CA ASP A 20 8.320 -3.607 36.994 1.00 64.41 C
ATOM 171 CA THR A 21 10.141 -0.845 35.066 1.00 52.69 C
ATOM 178 CA GLY A 22 10.679 1.055 38.316 1.00 31.92 C
ATOM 182 CA SER A 23 14.352 1.433 37.402 1.00 25.24 C
ATOM 188 CA PRO A 24 15.855 4.567 35.775 1.00 22.02 C
ATOM 195 CA GLU A 25 17.948 2.317 33.513 1.00 20.44 C
ATOM 204 CA VAL A 26 14.971 0.165 32.445 1.00 15.30 C
ATOM 211 CA GLN A 27 12.828 3.267 31.740 1.00 18.96 C
ATOM 220 CA ILE A 28 15.669 4.788 29.713 1.00 17.74 C
ATOM 228 CA ALA A 29 16.137 1.495 27.816 1.00 15.20 C
ATOM 233 CA ILE A 30 12.434 0.941 27.100 1.00 15.68 C
ATOM 241 CA LEU A 31 12.212 4.490 25.731 1.00 20.56 C
ATOM 249 CA THR A 32 15.376 4.042 23.652 1.00 22.97 C
ATOM 256 CA GLU A 33 13.924 0.863 22.127 1.00 23.01 C
ATOM 265 CA GLN A 34 10.721 2.711 21.215 1.00 24.17 C
ATOM 274 CA ILE A 35 12.619 5.750 19.913 1.00 20.78 C
ATOM 282 CA ASN A 36 14.819 3.444 17.790 1.00 23.54 C
ATOM 290 CA ASN A 37 11.846 1.479 16.489 1.00 28.70 C
ATOM 298 CA LEU A 38 9.882 4.630 15.644 1.00 25.71 C
ATOM 306 CA ASN A 39 12.891 6.144 13.854 1.00 21.34 C
ATOM 314 CA GLU A 40 13.409 2.984 11.758 1.00 27.93 C
ATOM 323 CA HIS A 41 9.684 3.244 10.990 1.00 28.98 C
ATOM 333 CA LEU A 42 9.824 6.899 9.852 1.00 27.50 C
ATOM 341 CA ARG A 43 12.885 5.891 7.844 1.00 28.13 C
ATOM 352 CA VAL A 44 10.637 3.983 5.442 1.00 37.69 C
ATOM 359 CA HIS A 45 7.543 6.158 5.963 1.00 35.91 C
ATOM 369 CA LYS A 46 8.855 9.656 5.123 1.00 39.03 C
ATOM 378 CA LYS A 47 5.290 10.888 4.454 1.00 38.60 C
ATOM 387 CA ASP A 48 4.175 10.326 8.072 1.00 41.09 C
ATOM 395 CA HIS A 49 3.026 13.280 10.212 1.00 49.40 C
ATOM 405 CA HIS A 50 1.220 11.709 13.170 1.00 47.52 C
ATOM 415 CA SER A 51 4.184 9.809 14.662 1.00 34.76 C
ATOM 421 CA ARG A 52 6.326 12.964 14.728 1.00 33.65 C
ATOM 432 CA ARG A 53 4.785 14.455 17.878 1.00 36.34 C
ATOM 443 CA GLY A 54 4.964 11.145 19.710 1.00 26.13 C
ATOM 447 CA LEU A 55 8.661 10.698 18.958 1.00 26.58 C
ATOM 455 CA LEU A 56 9.451 14.183 20.251 1.00 30.02 C
ATOM 463 CA LYS A 57 7.656 13.453 23.539 1.00 30.56 C
ATOM 472 CA MET A 58 9.642 10.232 24.051 1.00 22.98 C
ATOM 480 CA VAL A 59 12.921 11.984 23.299 1.00 14.94 C
ATOM 487 CA GLY A 60 12.071 14.694 25.845 1.00 18.07 C
ATOM 491 CA LYS A 61 10.965 12.236 28.502 1.00 17.69 C
ATOM 500 CA ARG A 62 14.275 10.376 28.007 1.00 14.84 C
ATOM 511 CA ARG A 63 16.389 13.552 28.361 1.00 17.28 C
ATOM 522 CA ARG A 64 14.581 14.150 31.638 1.00 21.15 C
ATOM 533 CA LEU A 65 15.199 10.611 32.914 1.00 18.67 C
ATOM 541 CA LEU A 66 18.851 10.778 31.824 1.00 19.80 C
ATOM 549 CA ALA A 67 19.287 14.157 33.528 1.00 20.75 C
ATOM 554 CA TYR A 68 17.836 12.601 36.646 1.00 18.99 C
ATOM 566 CA LEU A 69 20.291 9.659 36.642 1.00 14.26 C
ATOM 574 CA ARG A 70 23.255 11.931 35.820 1.00 24.85 C
ATOM 585 CA ASN A 71 22.633 13.977 38.958 1.00 31.70 C
ATOM 593 CA LYS A 72 21.801 11.047 41.202 1.00 30.21 C
ATOM 602 CA ASP A 73 24.704 8.787 40.263 1.00 24.03 C
ATOM 610 CA VAL A 74 27.246 9.557 37.514 1.00 25.95 C
ATOM 617 CA ALA A 75 28.539 5.962 37.486 1.00 21.67 C
ATOM 622 CA ARG A 76 25.093 4.503 36.781 1.00 15.53 C
ATOM 633 CA TYR A 77 24.436 7.366 34.345 1.00 21.31 C
ATOM 645 CA ARG A 78 27.485 6.712 32.128 1.00 27.43 C
ATOM 656 CA GLU A 79 27.155 2.926 32.383 1.00 17.69 C
ATOM 665 CA ILE A 80 23.632 3.043 30.869 1.00 18.33 C
ATOM 673 CA VAL A 81 24.507 5.678 28.248 1.00 23.86 C
ATOM 680 CA GLU A 82 27.387 3.449 27.208 1.00 31.18 C
ATOM 689 CA LYS A 83 25.278 0.286 27.040 1.00 28.71 C
ATOM 698 CA LEU A 84 22.526 1.872 24.940 1.00 25.97 C
ATOM 706 CA GLY A 85 25.013 3.568 22.598 1.00 29.63 C
ATOM 710 CA LEU A 86 23.705 7.068 23.281 1.00 38.81 C
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