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
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
