def molecules(request):
system = request.param
fref = os.path.join(molpath, system, f"{system}_ligand.sdf")
fmols = os.path.join(molpath, system, f"{system}_dock.sdf")
ref = io.load(os.path.join(molpath, fref))
mols = io.loadall(os.path.join(molpath, fmols))
ref = io.to_molecule(ref)
mols = [io.to_molecule(mol) for mol in mols]
ref.strip()
for mol in mols:
mol.strip()
return ref, mols, system
def load(fname: str) -> Tuple[Any, molecule.Molecule]:
"""
Load molecule from file.
Parameters
----------
fname: str
Input file name
Returns
-------
Tuple[Any, molecule.Molecule]
Loaded molecule as `pybel.Molecule` or `rdkit.Chem.rdkem.Mol` and
`pyrmsd.molecule.Molecule`
"""
fname = os.path.join(molpath, fname)
m = io.load(fname)
mol = io.to_molecule(m, adjacency=True)
return m, mol
def test_load_pdb(molfile, natoms: int, nbonds: int) -> None:
m = io.load(os.path.join(molpath, molfile))
assert io.numatoms(m) == natoms
assert io.numbonds(m) == nbonds