Fix rebase issue (6c0f41d5) · Commits · 钟慕尧 / deepchem

deepchem/utils/test/test_rdkit_util.py

+1 −27

Original line number	Diff line number	Diff line
		@@ -88,7 +88,7 @@ class TestRdkitUtil(unittest.TestCase):
		atom = mol.GetAtoms()[atom_idx]
		if atom.GetAtomicNum() == 1:
		after_hydrogen_count += 1
		assert_true(after_hydrogen_count >= original_hydrogen_count)
		assert after_hydrogen_count >= original_hydrogen_count

		def test_compute_charges(self):
		current_dir = os.path.dirname(os.path.realpath(__file__))
		@@ -132,32 +132,6 @@ class TestRdkitUtil(unittest.TestCase):
		atom2 = mol.GetAtoms()[atom_idx]
		assert atom1.GetAtomicNum() == atom2.GetAtomicNum()

		def test_pdbqt_to_pdb(self):
		current_dir = os.path.dirname(os.path.realpath(__file__))
		protein_file = os.path.join(current_dir,
		"../../dock/tests/1jld_protein.pdb")
		xyz, mol = rdkit_util.load_molecule(
		protein_file, calc_charges=False, add_hydrogens=False)
		with tempfile.TemporaryDirectory() as tmp:
		out_pdb = os.path.join(tmp, "mol.pdb")
		out_pdbqt = os.path.join(tmp, "mol.pdbqt")

		rdkit_util.write_molecule(mol, out_pdb)
		rdkit_util.write_molecule(mol, out_pdbqt, is_protein=True)

		pdb_block = rdkit_util.pdbqt_to_pdb(out_pdbqt)
		from rdkit import Chem
		pdb_mol = Chem.MolFromPDBBlock(pdb_block, sanitize=False, removeHs=False)

		xyz, pdbqt_mol = rdkit_util.load_molecule(
		out_pdbqt, add_hydrogens=False, calc_charges=False)

		assert pdb_mol.GetNumAtoms() == pdbqt_mol.GetNumAtoms()
		for atom_idx in range(pdb_mol.GetNumAtoms()):
		atom1 = pdb_mol.GetAtoms()[atom_idx]
		atom2 = pdbqt_mol.GetAtoms()[atom_idx]
		assert atom1.GetAtomicNum() == atom2.GetAtomicNum()

		def test_merge_molecules_xyz(self):
		current_dir = os.path.dirname(os.path.realpath(__file__))
		ligand_file = os.path.join(current_dir, "../../dock/tests/1jld_ligand.sdf")

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