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
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
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
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
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
