def test_rmsd(idx, download, path, minimize):
id = download[idx]
p = path_from_id(id, path)
try:
ref = io.loadmol(os.path.join(p, f"{id}_ligand.sdf"))
mols = io.loadallmols(os.path.join(p, f"{id}_dock.sdf"))
# Load results obtained with OpenBabel
results = np.loadtxt(
os.path.join(p, "obrms-min.dat" if minimize else "obrms.dat"))
except OSError: # Docking didn't find any configuration for some systems
pytest.xfail("Problems loading PDB ID {id}.")
# Some molecules in the dataset give errors when parsed with RDKit
if ref is None or None in mols:
pytest.xfail("Problems loading PDB ID {id}.")
rmsds = rmsd.rmsdwrapper(ref, mols, minimize=minimize, strip=True)
assert np.allclose(rmsds, results)
def test_loadmol_mol2(molfile, natoms: int) -> None:
m = io.loadmol(os.path.join(molpath, molfile))
assert len(m) == natoms
parser.add_argument("-c",
"--center",
action="store_true",
help="Center molecules at origin")
parser.add_argument("--hydrogens",
action="store_true",
help="Keep hydrogen atoms")
parser.add_argument("-n",
"--nosymm",
action="store_false",
help="No graph isomorphism")
args = parser.parse_args()
try:
ref = io.loadmol(args.reference)
except OSError:
print("ERROR: Reference file not found.", file=sys.stderr)
exit(-1)
# Load all molecules
try:
mols = [
mol for molfile in args.molecules
for mol in io.loadallmols(molfile)
]
except OSError:
print("ERROR: Molecule file(s) not found.", file=sys.stderr)
exit(-1)
# Loop over molecules within fil