def test_featurize_splif(self):
prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file)
lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file)
distance = rgf.compute_pairwise_distances(protein_xyz=prot_xyz,
ligand_xyz=lig_xyz)
bins = [(1, 2), (2, 3)]
dicts = rgf.featurize_splif(prot_xyz,
prot_rdk,
lig_xyz,
lig_rdk,
contact_bins=bins,
pairwise_distances=distance,
ecfp_degree=2)
expected_dicts = [
rgf.compute_splif_features_in_range(prot_rdk,
lig_rdk,
distance,
c_bin,
ecfp_degree=2)
for c_bin in bins
]
self.assertIsInstance(dicts, list)
self.assertEqual(dicts, expected_dicts)
def test_compute_splif_features_in_range(self):
prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file)
lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file)
prot_num_atoms = prot_rdk.GetNumAtoms()
lig_num_atoms = lig_rdk.GetNumAtoms()
distance = rgf.compute_pairwise_distances(
protein_xyz=prot_xyz, ligand_xyz=lig_xyz)
for bins in ((0, 2), (2, 3)):
splif_dict = rgf.compute_splif_features_in_range(
prot_rdk,
lig_rdk,
distance,
bins,
)
self.assertIsInstance(splif_dict, dict)
for (prot_idx, lig_idx), ecfp_pair in splif_dict.items():
for idx in (prot_idx, lig_idx):
self.assertIsInstance(idx, (int, np.int64))
self.assertGreaterEqual(prot_idx, 0)
self.assertLess(prot_idx, prot_num_atoms)
self.assertGreaterEqual(lig_idx, 0)
self.assertLess(lig_idx, lig_num_atoms)
for ecfp in ecfp_pair:
ecfp_idx, ecfp_frag = ecfp.split(',')
ecfp_idx = int(ecfp_idx)
self.assertGreaterEqual(ecfp_idx, 0)
def test_compute_splif_features_in_range(self):
prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file)
lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file)
prot_num_atoms = prot_rdk.GetNumAtoms()
lig_num_atoms = lig_rdk.GetNumAtoms()
distance = rgf.compute_pairwise_distances(protein_xyz=prot_xyz,
ligand_xyz=lig_xyz)
for bins in ((0, 2), (2, 3)):
splif_dict = rgf.compute_splif_features_in_range(
prot_rdk,
lig_rdk,
distance,
bins,
)
self.assertIsInstance(splif_dict, dict)
for (prot_idx, lig_idx), ecfp_pair in splif_dict.items():
for idx in (prot_idx, lig_idx):
self.assertIsInstance(idx, (int, np.int64))
self.assertGreaterEqual(prot_idx, 0)
self.assertLess(prot_idx, prot_num_atoms)
self.assertGreaterEqual(lig_idx, 0)
self.assertLess(lig_idx, lig_num_atoms)
for ecfp in ecfp_pair:
ecfp_idx, ecfp_frag = ecfp.split(',')
ecfp_idx = int(ecfp_idx)
self.assertGreaterEqual(ecfp_idx, 0)
def test_featurize_splif(self):
prot_xyz, prot_rdk = rgf.load_molecule(self.protein_file)
lig_xyz, lig_rdk = rgf.load_molecule(self.ligand_file)
distance = rgf.compute_pairwise_distances(
protein_xyz=prot_xyz, ligand_xyz=lig_xyz)
bins = [(1, 2), (2, 3)]
dicts = rgf.featurize_splif(
prot_xyz,
prot_rdk,
lig_xyz,
lig_rdk,
contact_bins=bins,
pairwise_distances=distance,
ecfp_degree=2)
expected_dicts = [
rgf.compute_splif_features_in_range(
prot_rdk, lig_rdk, distance, c_bin, ecfp_degree=2) for c_bin in bins
]
self.assertIsInstance(dicts, list)
self.assertEqual(dicts, expected_dicts)
