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/tests/test_rdkitfixer.py
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--- a +++ b/tests/test_rdkitfixer.py @@ -0,0 +1,594 @@ +import os +import tempfile + +from numpy.testing import assert_array_equal, assert_almost_equal +import pytest + +try: + import rdkit + from rdkit import Chem +except ImportError: + rdkit = None + +if rdkit is not None: + from oddt.toolkits.extras.rdkit.fixer import (AtomListToSubMol, + PreparePDBMol, + ExtractPocketAndLigand, + IsResidueConnected, + FetchStructure, + PrepareComplexes) + +test_data_dir = os.path.dirname(os.path.abspath(__file__)) +test_dir = os.path.join(test_data_dir, 'data', 'pdb') + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_atom_list_to_submol(): + mol = Chem.MolFromSmiles('CCCCC(=O)O') + submol = AtomListToSubMol(mol, range(3, 7)) + assert submol.GetNumAtoms() == 4 + assert submol.GetNumAtoms() == 4 + assert submol.GetNumBonds() == 3 + assert submol.GetBondBetweenAtoms(1, 2).GetBondType() == rdkit.Chem.rdchem.BondType.DOUBLE + + molfile = os.path.join(test_dir, '2qwe_Sbridge.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + assert mol.GetConformer().Is3D() + submol = AtomListToSubMol(mol, range(6), includeConformer=True) + assert submol.GetConformer().Is3D() + + # submol has residue info + atom = submol.GetAtomWithIdx(0) + info = atom.GetPDBResidueInfo() + assert info.GetResidueName() == 'CYS' + assert info.GetResidueNumber() == 92 + + # test multiple conformers + mol.AddConformer(mol.GetConformer()) + assert mol.GetNumConformers() == 2 + submol = AtomListToSubMol(mol, range(6), includeConformer=True) + assert submol.GetNumConformers() == 2 + + # FIXME: Newer RDKit has GetPositions, 2016.03 does not + mol_conf = mol.GetConformer() + submol_conf = submol.GetConformer() + assert_array_equal([submol_conf.GetAtomPosition(i) + for i in range(submol_conf.GetNumAtoms())], + [mol_conf.GetAtomPosition(i) for i in range(6)]) + + submol2 = AtomListToSubMol(submol, range(3), includeConformer=True) + submol2_conf = submol2.GetConformer() + assert submol2.GetNumConformers() == 2 + assert_array_equal([submol2_conf.GetAtomPosition(i) + for i in range(submol2_conf.GetNumAtoms())], + [mol_conf.GetAtomPosition(i) for i in range(3)]) + + +@pytest.mark.skipif(rdkit is None or rdkit.__version__ < '2017.03', reason="RDKit required") +def test_multivalent_Hs(): + """Test if fixer deals with multivalent Hs""" + + # TODO: require mol without Hs in the future (rdkit v. 2018) + molfile = os.path.join(test_dir, '2c92_hypervalentH.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol, residue_whitelist=[], removeHs=False) + + atom = mol.GetAtomWithIdx(84) + assert atom.GetAtomicNum() == 1 # is it H + assert atom.GetDegree() == 1 # H should have 1 bond + + for n in atom.GetNeighbors(): # Check if neighbor is from the same residue + assert atom.GetPDBResidueInfo().GetResidueName() == n.GetPDBResidueInfo().GetResidueName() + + # mol can be sanitized + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_HOH_bonding(): + """Test if fixer unbinds HOH""" + + molfile = os.path.join(test_dir, '2vnf_bindedHOH.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + # don't use templates and don't remove waters + mol = PreparePDBMol(mol, removeHOHs=False) + + atom = mol.GetAtomWithIdx(5) + assert atom.GetPDBResidueInfo().GetResidueName() == 'HOH' + assert atom.GetDegree() == 0 # HOH should have no bonds + + # mol can be sanitized + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_metal_bonding(): + """Test if fixer disconnects metals""" + + molfile = os.path.join(test_dir, '1ps3_zn.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + + mol = PreparePDBMol(mol) + + atom = mol.GetAtomWithIdx(36) + assert atom.GetAtomicNum() == 30 # is it Zn + assert atom.GetDegree() == 0 # Zn should have no bonds + assert atom.GetFormalCharge() == 2 + assert atom.GetNumExplicitHs() == 0 + + # mol can be sanitized + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_interresidue_bonding(): + """Test if fixer removes wrong connections between residues""" + + molfile = os.path.join(test_dir, '4e6d_residues.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + + mol = PreparePDBMol(mol) + + # check if O from PRO + atom1 = mol.GetAtomWithIdx(11) + assert atom1.GetAtomicNum() == 8 + assert atom1.GetPDBResidueInfo().GetResidueName() == 'PRO' + # ...and N from GLN + atom2 = mol.GetAtomWithIdx(22) + assert atom2.GetAtomicNum() == 7 + assert atom2.GetPDBResidueInfo().GetResidueName() == 'GLN' + # ...are not connected + assert mol.GetBondBetweenAtoms(11, 22) is None + + # mol can be sanitized + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_intraresidue_bonding(): + """Test if fixer removes wrong connections within single residue""" + + molfile = os.path.join(test_dir, '1idg_connectivity.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol) + + # check if N and C from GLU20 are not connected + atom1 = mol.GetAtomWithIdx(11) + assert atom1.GetAtomicNum() == 7 + assert atom1.GetPDBResidueInfo().GetResidueName() == 'GLU' + assert atom1.GetPDBResidueInfo().GetResidueNumber() == 20 + atom2 = mol.GetAtomWithIdx(13) + assert atom2.GetAtomicNum() == 6 + assert atom2.GetPDBResidueInfo().GetResidueName() == 'GLU' + assert atom2.GetPDBResidueInfo().GetResidueNumber() == 20 + + assert mol.GetBondBetweenAtoms(11, 13) is None + + # mol can be sanitized + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_bondtype(): + """Test if fixer deals with non-standard residue and fixes bond types""" + + molfile = os.path.join(test_dir, '3rsb_bondtype.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol) + + # check if there is double bond between N and C from MSE + atom1 = mol.GetAtomWithIdx(13) + assert atom1.GetAtomicNum() == 6 + assert atom1.GetPDBResidueInfo().GetResidueName() == 'MSE' + atom2 = mol.GetAtomWithIdx(14) + assert atom2.GetAtomicNum() == 8 + assert atom2.GetPDBResidueInfo().GetResidueName() == 'MSE' + + # there is a bond and it is double + bond = mol.GetBondBetweenAtoms(13, 14) + assert bond is not None + assert_almost_equal(bond.GetBondTypeAsDouble(), 2.0) + + # mol can be sanitized + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_ring(): + """Test if fixer adds missing bond in ring""" + + molfile = os.path.join(test_dir, '4yzm_ring.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol) + + # check if there is double bond between N and C from MSE + atom1 = mol.GetAtomWithIdx(12) + assert atom1.GetAtomicNum() == 6 + assert atom1.GetPDBResidueInfo().GetResidueName() == 'PHE' + atom2 = mol.GetAtomWithIdx(13) + assert atom2.GetAtomicNum() == 6 + assert atom2.GetPDBResidueInfo().GetResidueName() == 'PHE' + + # there is a bond and it is aromatic + bond = mol.GetBondBetweenAtoms(12, 13) + assert bond is not None + assert_almost_equal(bond.GetBondTypeAsDouble(), 1.5) + + # mol can be sanitized + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_sulphur_bridge(): + """Test sulphur bridges retention""" + + molfile = os.path.join(test_dir, '2qwe_Sbridge.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + + mol = PreparePDBMol(mol) + + atom1 = mol.GetAtomWithIdx(5) + atom2 = mol.GetAtomWithIdx(11) + bond = mol.GetBondBetweenAtoms(atom1.GetIdx(), atom2.GetIdx()) + assert atom1.GetPDBResidueInfo().GetName().strip() == 'SG' + assert atom1.GetPDBResidueInfo().GetResidueNumber() == 92 + assert atom2.GetPDBResidueInfo().GetName().strip() == 'SG' + assert atom2.GetPDBResidueInfo().GetResidueNumber() == 417 + assert bond is not None + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_pocket_extractor(): + """Test extracting pocket and ligand""" + + molfile = os.path.join(test_dir, '5ar7.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + + # there should be no pocket at 1A + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=1.) + assert pocket.GetNumAtoms() == 0 + assert ligand.GetNumAtoms() == 26 + + # small pocket of 5A + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=12.) + assert pocket.GetNumAtoms() == 928 + assert ligand.GetNumAtoms() == 26 + + # check if HOH is in pocket + atom = pocket.GetAtomWithIdx(910) + assert atom.GetAtomicNum() == 8 + assert atom.GetPDBResidueInfo().GetResidueName() == 'HOH' + + # Prepare and sanitize pocket and ligand + pocket = PreparePDBMol(pocket) + ligand = PreparePDBMol(ligand) + assert Chem.SanitizeMol(pocket) == Chem.SanitizeFlags.SANITIZE_NONE + assert Chem.SanitizeMol(ligand) == Chem.SanitizeFlags.SANITIZE_NONE + + # Check atom/bond properies for both molecules + bond = pocket.GetBondWithIdx(39) + assert bond.GetIsAromatic() + assert bond.GetBeginAtom().GetPDBResidueInfo().GetResidueName() == 'TYR' + + atom = ligand.GetAtomWithIdx(22) + assert atom.GetAtomicNum() == 7 + assert atom.GetIsAromatic() + assert atom.GetPDBResidueInfo().GetResidueName() == 'SR8' + + # test if metal is in pocket + molfile = os.path.join(test_dir, '4p6p_lig_zn.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + assert mol.GetNumAtoms() == 176 + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=5.) + assert pocket.GetNumAtoms() == 162 + assert ligand.GetNumAtoms() == 14 + + atom = pocket.GetAtomWithIdx(153) + assert atom.GetPDBResidueInfo().GetResidueName().strip() == 'ZN' + atom = pocket.GetAtomWithIdx(160) + assert atom.GetPDBResidueInfo().GetResidueName() == 'HOH' + + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=5., expandResidues=False) + assert pocket.GetNumAtoms() == 74 + assert ligand.GetNumAtoms() == 14 + + atom = pocket.GetAtomWithIdx(65) + assert atom.GetPDBResidueInfo().GetResidueName().strip() == 'ZN' + atom = pocket.GetAtomWithIdx(73) + assert atom.GetPDBResidueInfo().GetResidueName() == 'HOH' + + # ligand and protein white/blacklist + molfile = os.path.join(test_dir, '1dy3_2LIG.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + + # by default the largest ligand - ATP + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=20.) + assert pocket.GetNumAtoms() == 304 + assert ligand.GetNumAtoms() == 31 + + atom = ligand.GetAtomWithIdx(0) + assert atom.GetPDBResidueInfo().GetResidueName() == 'ATP' + + # blacklist APT to get other largest ligand - 87Y + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=20., + ligand_residue_blacklist=['ATP']) + assert pocket.GetNumAtoms() == 304 + assert ligand.GetNumAtoms() == 23 + + atom = ligand.GetAtomWithIdx(0) + assert atom.GetPDBResidueInfo().GetResidueName() == '87Y' + + # point to 87Y explicitly + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=20., + ligand_residue='87Y') + assert pocket.GetNumAtoms() == 304 + assert ligand.GetNumAtoms() == 23 + + atom = ligand.GetAtomWithIdx(0) + assert atom.GetPDBResidueInfo().GetResidueName() == '87Y' + + # include APT in pocket to get other largest ligand - 87Y + pocket, ligand = ExtractPocketAndLigand(mol, cutoff=20., + append_residues=['ATP']) + assert pocket.GetNumAtoms() == 304+31 + assert ligand.GetNumAtoms() == 23 + + atom = ligand.GetAtomWithIdx(0) + assert atom.GetPDBResidueInfo().GetResidueName() == '87Y' + + atom = pocket.GetAtomWithIdx(310) + assert atom.GetPDBResidueInfo().GetResidueName() == 'ATP' + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_aromatic_ring(): + """Test aromaticity for partial matches""" + + # ring is complete and should be aromatic + molfile = os.path.join(test_dir, '5ar7_HIS.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol) + + atom = mol.GetAtomWithIdx(6) + assert atom.GetAtomicNum() == 7 + info = atom.GetPDBResidueInfo() + assert info.GetResidueName() == 'HIS' + assert info.GetResidueNumber() == 246 + assert info.GetName().strip() == 'ND1' + assert atom.GetIsAromatic() + + atom = mol.GetAtomWithIdx(9) + assert atom.GetAtomicNum() == 7 + info = atom.GetPDBResidueInfo() + assert info.GetResidueName() == 'HIS' + assert info.GetResidueNumber() == 246 + assert info.GetName().strip() == 'NE2' + assert atom.GetIsAromatic() + + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + # there is only one atom from the ring and it shouldn't be aromatic + molfile = os.path.join(test_dir, '3cx9_TYR.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol) + + atom = mol.GetAtomWithIdx(14) + assert atom.GetAtomicNum() == 6 + info = atom.GetPDBResidueInfo() + assert info.GetResidueName() == 'TYR' + assert info.GetResidueNumber() == 138 + assert info.GetName().strip() == 'CG' + assert not atom.GetIsAromatic() + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_many_missing(): + """Test parsing residues with **many** missing atoms and bonds""" + + molfile = os.path.join(test_dir, '2wb5_GLN.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol) + + assert mol.GetNumAtoms() == 5 + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + assert mol.GetAtomWithIdx(4).GetDegree() == 0 + + # test if removal works + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol, remove_incomplete=True) + + assert mol.GetNumAtoms() == 0 + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_remove_incomplete(): + """Test removing residues with missing atoms""" + + molfile = os.path.join(test_dir, '3cx9_TYR.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + + # keep all residues + new_mol = PreparePDBMol(mol, remove_incomplete=False) + assert new_mol.GetNumAtoms() == 23 + residues = set() + for atom in new_mol.GetAtoms(): + residues.add(atom.GetPDBResidueInfo().GetResidueNumber()) + assert residues, {137, 138 == 139} + assert Chem.SanitizeMol(new_mol) == Chem.SanitizeFlags.SANITIZE_NONE + + # remove residue with missing sidechain + new_mol = PreparePDBMol(mol, remove_incomplete=True) + assert new_mol.GetNumAtoms() == 17 + residues = set() + for atom in new_mol.GetAtoms(): + residues.add(atom.GetPDBResidueInfo().GetResidueNumber()) + assert residues, {137 == 139} + assert Chem.SanitizeMol(new_mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_custom_templates(): + """Test using custom templates""" + + molfile = os.path.join(test_dir, '3cx9_TYR.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + + templates = { + 'TYR': 'CCC(N)C=O', + 'LYS': 'NC(C(O)=O)CCCCN', + 'LEU': 'CC(C)CC(N)C(=O)O', + } + + mol_templates = {resname: Chem.MolFromSmiles(smi) + for resname, smi in templates.items()} + + for kwargs in ({'custom_templates': {'TYR': 'CCC(N)C=O'}}, + {'custom_templates': {'TYR': Chem.MolFromSmiles('CCC(N)C=O')}}, + {'custom_templates': templates, 'replace_default_templates': True}, + {'custom_templates': mol_templates, 'replace_default_templates': True}): + + # use TYR without sidechain - all matches should be complete + new_mol = PreparePDBMol(mol, remove_incomplete=True, **kwargs) + assert new_mol.GetNumAtoms() == 23 + residues = set() + for atom in new_mol.GetAtoms(): + residues.add(atom.GetPDBResidueInfo().GetResidueNumber()) + assert residues, {137, 138 == 139} + assert Chem.SanitizeMol(new_mol) == Chem.SanitizeFlags.SANITIZE_NONE + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_add_missing_atoms(): + # add missing atom at tryptophan + molfile = os.path.join(test_dir, '5dhh_missingatomTRP.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=True) + mol = Chem.RemoveHs(mol, sanitize=False) + + assert mol.GetNumAtoms() == 26 + mol = PreparePDBMol(mol, add_missing_atoms=True) + assert mol.GetNumAtoms() == 27 + + atom = mol.GetAtomWithIdx(21) + assert atom.GetAtomicNum() == 6 + info = atom.GetPDBResidueInfo() + assert info.GetResidueName() == 'TRP' + assert info.GetResidueNumber() == 175 + assert info.GetName().strip() == 'C9' + assert atom.IsInRing() + assert atom.GetIsAromatic() + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + # add whole ring to tyrosine + molfile = os.path.join(test_dir, '3cx9_TYR.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=True) + mol = Chem.RemoveHs(mol, sanitize=False) + + assert mol.GetNumAtoms() == 23 + mol = PreparePDBMol(mol, add_missing_atoms=True) + assert mol.GetNumAtoms() == 29 + + atom = mol.GetAtomWithIdx(17) + assert atom.GetAtomicNum() == 6 + info = atom.GetPDBResidueInfo() + assert info.GetResidueName() == 'TYR' + assert info.GetResidueNumber() == 138 + assert info.GetName().strip() == 'C6' + assert atom.IsInRing() + assert atom.GetIsAromatic() + assert Chem.SanitizeMol(mol) == Chem.SanitizeFlags.SANITIZE_NONE + + # missing protein backbone atoms + molfile = os.path.join(test_dir, '5ar7_HIS.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False) + mol = Chem.RemoveHs(mol, sanitize=False) + + assert mol.GetNumAtoms() == 21 + assert mol.GetNumBonds() == 19 + mol = PreparePDBMol(mol, add_missing_atoms=True) + assert mol.GetNumAtoms() == 25 + assert mol.GetNumBonds() == 25 + + # missing nucleotide backbone atoms + molfile = os.path.join(test_dir, '1bpx_missingBase.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False) + mol = Chem.RemoveHs(mol, sanitize=False) + + assert mol.GetNumAtoms() == 301 + assert mol.GetNumBonds() == 333 + mol = PreparePDBMol(mol, add_missing_atoms=True) + assert mol.GetNumAtoms() == 328 + assert mol.GetNumBonds() == 366 + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_connected_residues(): + molfile = os.path.join(test_dir, '4p6p_lig_zn.pdb') + mol = Chem.MolFromPDBFile(molfile, sanitize=False, removeHs=False) + mol = PreparePDBMol(mol) # we need to use fixer with rdkit < 2018 + + # residue which has neighbours + assert IsResidueConnected(mol, range(120, 127)) + + # ligand + assert not IsResidueConnected(mol, range(153, 167)) + + # fragments of two residues + with pytest.raises(ValueError): + IsResidueConnected(mol, range(5, 15)) + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_fetch_structures(): + pdbid = '3ws8' + tmpdir = tempfile.mkdtemp() + + mol1 = FetchStructure(pdbid) + mol2 = FetchStructure(pdbid, cache_dir=tmpdir) + mol3 = FetchStructure(pdbid, cache_dir=tmpdir) + assert mol1.GetNumAtoms() == mol2.GetNumAtoms() + assert mol1.GetNumAtoms() == mol3.GetNumAtoms() + + +@pytest.mark.skipif(rdkit is None, reason="RDKit required") +def test_prepare_complexes(): + ids = [ + '3WS9', # simple case with everything fine + '3HLJ', # ligand not in report + '3BYM', # non-existing ligand and backbone residue in report + '2PIN', # two ligands with binding affinities + '3CYU', # can't parse ligands properly + '1A28', # multiple affinity types + ] + + tmpdir = tempfile.mkdtemp() + complexes = PrepareComplexes(ids, cache_dir=tmpdir) + expected_values = { + '3WS9': {'X4D': {'IC50': 92.0}}, + '3BYM': {'AM0': {'IC50': 6.0}}, + '2PIN': {'LEG': {'IC50': 1500.0}}, + '3CYU': {'0CR': {'Kd': 60.0}}, + '1A28': {'STR': {'Ki': 5.1}}, + } + + values = {} + for pdbid, pairs in complexes.items(): + values[pdbid] = {} + for resname, (_, ligand) in pairs.items(): + values[pdbid][resname] = {k: float(v) for k, v + in ligand.GetPropsAsDict().items()} + + assert expected_values.keys() == values.keys() + + for pdbid in expected_values: + assert values[pdbid].keys() == expected_values[pdbid].keys() + for resname in values[pdbid]: + assert values[pdbid][resname].keys() == expected_values[pdbid][resname].keys() + for key, val in values[pdbid][resname].items(): + assert key in expected_values[pdbid][resname] + assert_almost_equal(expected_values[pdbid][resname][key], val) + for idx in expected_values: + assert os.path.exists(os.path.join(tmpdir, idx, + '%s.pdb' % idx))