Preparation layer

The first layer of the library provides utilities for preparing the simulation by loading the requisite files, modifying them and outputting results. The layer is independent of the simulation layers; more appropriate storage formats can be used in the simulation layer without having to modify any of the files here.

Modules

• Contact map files
• Sequence files
• PDB objects and parsing
  • PDB file records
  • Raw PDB data
  • PDB atomic model
  • PDB parsing framework
• Model
• Parameter files