UFFOptimizeMoleculesConfs#

nvmolkit.uffOptimization.UFFOptimizeMoleculesConfs(
molecules: list['Mol'],
maxIters: int = 1000,
vdwThreshold: float | Sequence[float] = 10.0,
ignoreInterfragInteractions: bool | Sequence[bool] = True,
hardwareOptions: HardwareOptions | None = None,
output: Literal[CoordinateOutput.RDKIT_CONFORMERS] = CoordinateOutput.RDKIT_CONFORMERS,
targetGpu: int = -1,
) → list[list[float]]#
nvmolkit.uffOptimization.UFFOptimizeMoleculesConfs(
molecules: list['Mol'],
maxIters: int = 1000,
vdwThreshold: float | Sequence[float] = 10.0,
ignoreInterfragInteractions: bool | Sequence[bool] = True,
hardwareOptions: HardwareOptions | None = None,
*,
output: Literal[CoordinateOutput.DEVICE],
targetGpu: int = -1,
) → Device3DResult

Optimize conformers for multiple molecules using the UFF force field.

Parameters:

  • molecules – List of RDKit molecules to optimize. Each molecule should already contain conformers.

  • maxIters – Maximum number of UFF minimization iterations.

  • vdwThreshold – Van der Waals threshold used when constructing the UFF force field. May be provided as a scalar or per-molecule sequence.

  • ignoreInterfragInteractions – If True, omit non-bonded terms between fragments. May be provided as a scalar or per-molecule sequence.

  • hardwareOptions – Configures CPU and GPU batching, threading, and device selection. Defaults are chosen automatically when omitted.

  • output – RDKIT_CONFORMERS (default) writes optimized coordinates back into RDKit conformers and returns nested host energy lists. DEVICE keeps optimized coordinates and energies on GPU and returns a Device3DResult.

  • targetGpu – In DEVICE mode, the GPU to consolidate the result onto. -1 selects the first configured execution GPU.

Returns:

list of lists of optimized conformer energies. For DEVICE: a Device3DResult with values (positions), energies, converged, and CSR indices.

Return type:

For RDKIT_CONFORMERS

Raises:

ValueError – If molecules contains None entries or molecules lacking UFF atom types. e.args[1] contains keys "none" and "no_params".