Create tutorial for ML usage

Combine pieces from the examples (Datasets in AtomWorks, Creating Custom Ligand Transforms) to create an ML tutorial.

Tutorial should have:

• Clear learning objective(s)
• Instructions on how to obtain any necessary input files
• Example output files for comparison
• List of prerequisites (dependencies that need to be installed, folders that need to be created, etc.)
• An ordered list of steps with concise explanations
• Images wherever appropriate
• Tested on various systems and by several users