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.

Isomer Generation

Factory for creating isomer enumeration engines:

Auto3D.isomers.IsomerEngineFactory()

Factory class for creating isomer engine adapters.

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.