API Reference

This section documents the public API of Auto3D.

Core Functions

The main entry points for Auto3D:

Auto3D.auto3D.main(args)	Run the Auto3D conformer generation pipeline.
Auto3D.auto3D.smiles2mols(smiles, args)	Find low-energy conformers for a list of SMILES.

Configuration

Classes for configuring Auto3D:

Auto3D.config.Auto3DOptions([path, k, ...])	Configuration options for Auto3D conformer generation.
Auto3D.config.OptimizationConfig([...])	Configuration for geometry optimization.
Auto3D.config.NNPModel(*args, **kwargs)	Protocol for Neural Network Potential models.

Model Creation

Factory functions and classes for creating neural network potential models:

Auto3D.model_factory.ModelFactory()	Factory for creating and managing NNP model adapters.
Auto3D.model_factory.create_model(name[, ...])	Convenience function to create a model adapter.
Auto3D.model_factory.get_device([gpu_idx, ...])	Get the appropriate torch device.

Isomer Generation

Factory for creating isomer enumeration engines:

Auto3D.isomers.IsomerEngineFactory()

Factory class for creating isomer engine adapters.

Tautomer Enumeration

Functions for tautomer enumeration and selection:

Auto3D.tautomer.get_stable_tautomers(args[, ...])	Get stable tautomers for input molecules.
Auto3D.tautomer.select_tautomers(sdf[, k, ...])	Select and Write the top-k or E <= window tautomers for each input SMILES Only k or window needs to be specified, NOT both.

Utility Functions

Helper functions for energy calculations and analysis:

Auto3D.SPE.calc_spe(path, model_name[, gpu_idx])	Calculates single point energy.
Auto3D.ASE.geometry.opt_geometry(path, ...)	Geometry optimization interface with FIRE optimizer.
Auto3D.ASE.thermo.calc_thermo(path, model_name)	ASE interface for calculating thermo properties using ANI2x, ANI2xt or AIMNET.

Exceptions

Custom exception classes for error handling:

Auto3D.exceptions.Auto3DError	Base exception for all Auto3D errors.
Auto3D.exceptions.ConfigurationError	Raised when there's an invalid configuration.
Auto3D.exceptions.InputValidationError	Raised when input file validation fails.
Auto3D.exceptions.ModelError	Base exception for model-related errors.
Auto3D.exceptions.ModelNotFoundError	Raised when a requested model cannot be found.
Auto3D.exceptions.ModelLoadError	Raised when a model fails to load.
Auto3D.exceptions.NumericalError	Raised when numerical instability is detected.
Auto3D.exceptions.OptimizationError	Base exception for optimization-related errors.
Auto3D.exceptions.ConvergenceError	Raised when geometry optimization fails to converge.
Auto3D.exceptions.IsomerEnumerationError	Raised when stereoisomer enumeration fails.
Auto3D.exceptions.TautomerEnumerationError	Raised when tautomer enumeration fails.
Auto3D.exceptions.FileFormatError	Raised for unsupported or invalid file formats.
Auto3D.exceptions.DependencyError	Raised when a required dependency is not available.
Auto3D.exceptions.GPUError	Raised for GPU-related errors.