def test_can_get_string_from_pdb(self, mock_string, mock_dict):
pdb = Pdb()
pdb_dict = Mock()
mock_string.return_value = "filecontents"
mock_dict.return_value = pdb_dict
s = pdb.to_file_string()
mock_dict.assert_called_with(pdb)
mock_string.assert_called_with(pdb_dict)
self.assertEqual(s, "filecontents")
def protonate_pdb(pdb: Pdb) -> Pdb:
"""Hydrogenate a first model of PDB
1. Passes generic molecules to protonate_ligand, ligands which already contain hydrogens are skipped
2. Take H in protonated ligand block and add to existing pdb
3. Pass pdb to protonate_protein
Args:
pdb: The pdb to hydrogenate
Returns:
A pdb with hydrogens added
"""
# Protonate whole pdb
unprotonated_block = pdb.to_file_string()
protonated_block = protonate_protein(unprotonated_block)
protonated_pdb = pdb_dict_to_pdb(
pdb_string_to_pdb_dict(protonated_block[0]))
fill_serial_numbers(protonated_pdb)
return protonated_pdb
