User Guide# The user guide of EncoderMap is organized into topics. Each section introduces a topic and contains examples. Code examples Cube example Cube example distance analysis Dihedral to cartesian diubi Dihedral to cartesian diubi analysis Trp cage Starter notebooks Cube Example - Basic Usage Asp7 Example - Advanced Usage Your Data Learn how to Customize EncoderMap Learning Rate Scheduler Logging Custom Images Writing Custom Loss Functions Logging Custom Scalars Intermediate notebooks Training with different topologies Learn how EncoderMap handles MD data and trajectory ensembles