Auto3D

class rush.auto3d.Auto3DResult(conformer: TRC, stats: Auto3DStats)[source]

Bases: object

Parameters:
conformer: TRC
stats: Auto3DStats
class rush.auto3d.Auto3DStats(f_max: float, converged: bool, e_rel_kcal_mol: float, e_tot_hartrees: float)[source]

Bases: object

Parameters:

  • f_max (float)

  • converged (bool)

  • e_rel_kcal_mol (float)

  • e_tot_hartrees (float)

converged: bool
e_rel_kcal_mol: float
e_tot_hartrees: float
f_max: float
rush.auto3d.auto3d(smis, k=1, batchsize_atoms=1024, capacity=40, convergence_threshold=0.003, enumerate_isomer=True, enumerate_tautomer=False, max_confs=None, opt_steps=5000, patience=1000, threshold=0.3, run_spec=RunSpec(), run_opts=RunOpts(), collect=False)[source]

Runs Auto3D on a list of SMILES strings, returning either the TRC structure or an error string.

Parameters:

  • smis (list[str])

  • k (int)

  • batchsize_atoms (int)

  • capacity (int)

  • convergence_threshold (float)

  • enumerate_isomer (bool)

  • enumerate_tautomer (bool)

  • max_confs (int | None)

  • opt_steps (int)

  • patience (int)

  • threshold (float)

  • run_spec (RunSpec)

  • run_opts (RunOpts)

rush.auto3d.save_outputs(res)[source]

Download output files from an auto3d run.

The auto3d rex computation returns a Rush object store pointers for TRCs and stats for each conformer generated. There are up to k conformers per input. Each input can either succeed, in which case a Iterator[Auto3DResult] is returned that downloads and packages each conformer on the fly, or fail, in which case the run error is returned.

If collect=False was used, the input will be a run ID string, which is returned as-is for later collection by the caller.

Parameters:

res – Either: - A run ID string (if collect=False was used) - The successful output from auto3d() - A RunError Each VirtualObject dict has keys: ‘path’, ‘size’, ‘format’.

Returns:

  • A run ID string (if input was a run ID)

  • list[Iterator[Auto3DResult] | RunError], if the run succeeded

  • RunError if input is an error

Return type:

Either