the main thrust of this release adds new support for DOCK6 receptor and DOCKing parameters. The remainder of the changes is mostly logical improvements in the codebase that will (unfortunately) break some client code. The `CalculationData` has been renamed to a `Simulation` and the `CalculationRunner.prepare_and_run()` methods now return the `Result` object rather than the full `Simulation` (as was done previously. This will speed up task distribution for virtual screening purposes but now loses the added information of the `prepared_ligand` and `prepared_receptor` filenames (which will be lost forever if utilizing the `VirtualScreen` interface.) We'll look back into adding this information back, but we don't think any users were actually taking advantage of this information.
Additionally, a full `VirtualScreen` used to crash when handed an invalid molecule. Theoretically, users could always prevent this via pre-filtering what molecules are passed, but now the returned score array just handles them silently and indicates `nan` values in their place. Note that `nan` could also indicate that the molecule failed during simulation itself, which means it could be attempted again and possibly succeed (about 1% of molecules randomly fail.) Now, however a `nan` could mean one of those two things. If this distinction is important, you can do the following:
python
import numpy as np
from rdkit import Chem
import pyscreener as ps
smis: Iterable[str]
vs = ps.virtual_screen(...)
s = vs(smis)
failed_idxs = np.arange(len(s))[np.isnan(s)]
invalid_mol_idxs = set(i for i in failed_idxs if Chem.MolFromSmiles(smis[i]) is None)
failed_sim_idxs = set(failed_idxs) -inavlid_mol_idxs
happy screening!