def test_loadall() -> None:
path = os.path.join(molecules.molpath, "1cbr_docking.sdf")
mols = io.loadall(path)
assert len(mols) == 10
def test_loadall_sdf(molfile, natoms: int, nbonds: int) -> None:
ms = io.loadall(os.path.join(molpath, molfile))
assert len(ms) == 10
for m in ms:
assert io.numatoms(m) == natoms
assert io.numbonds(m) == nbonds
def test_loadall_mol2(molfile, natoms: int, nbonds: int) -> None:
try:
ms = io.loadall(os.path.join(molpath, molfile))
assert len(ms) == 10
for m in ms:
assert io.numatoms(m) == natoms
assert io.numbonds(m) == nbonds
except NotImplementedError: # Mol2MolSupplier in RDkit is not supported
pass # TODO: Warning
def test_loadall_pdb_single_model() -> None:
"""
Test load_all function for PDB files when only a single model is present.
"""
try:
ms = io.loadall(os.path.join(molpath, "1a99_ligand.pdb"))
assert len(ms) == 1
assert io.numatoms(ms[0]) == 20
assert io.numbonds(ms[0]) == 19
except NotImplementedError: # PDBMolSupplier in RDkit is not supported
pass # TODO: Warning
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 loadall(fname: str) -> Tuple[List[Any], List[molecule.Molecule]]:
"""
Load all molecule from file.
Parameters
----------
fname: str
Input file name
Returns
-------
Tuple[List[Any], List[molecule.Molecule]]
Loaded molecule as `pybel.Molecule` or `rdkit.Chem.rdchem.Mol` and
`pyrmsd.molecule.Molecule`
"""
fname = os.path.join(molpath, fname)
ms = io.loadall(fname)
mols = [io.to_molecule(m, adjacency=True) for m in ms]
return ms, mols