def __getitem__(self, index):
pocket_pdbqt_file = protein_file
if os.path.exists(pocket_pdbqt_file):
pocket = GridPDB(pocket_pdbqt_file)
else:
raise Error("Please preprocess PDB files")
# pocket = GridPDB(pocketfile)
ligand_pdbqt_file = ligand_file
if os.path.exists(ligand_pdbqt_file):
ligand = GridPDB(ligand_pdbqt_file)
else:
raise Error("Please preprocess ligand files")
# ligand = GridPDB(ligandfile)
sample = {
'code': '',
'pdbfile': '',
'pocket': GridPDB(pocket_pdbqt_file),
'ligand': GridPDB(ligand_pdbqt_file),
'channels': [],
'pose': 1,
'affinity': 1
}
if self.transform:
sample = self.transform(sample)
return sample
def test_smina_type():
ligfile = 'test/fixtures/4rdn_ligand.pdbqt'
lig = GridPDB(ligfile)
atom_data = AtomData()
ref_atom_types = [4, 4, 4, 4, 14, 7, 6, 10, 6, 10, 6, 6, 10, 6, 8, 2, 4, 13, 2, 13, 2, 4, 13, 2]
test_atom_types = []
for i in range(lig.natom):
data_i = atom_data[lig.atomdata[i]]
test_atom_types.append(data_i['smina_type'])
assert ref_atom_types == test_atom_types
def run(self):
lig = GridPDB(self.input().path)
lig.to_h5(self.output().path)
def run(self):
pdb = GridPDB(self.input().path)
pdb.to_h5(self.output().path)