This guide aims to provide an outline of the purpose, capabilities, and interaction of the various parts of the code in GMML2 from a developer perspective. For learning about specific functions and data structures we refer to the code itself.
In molecular structures, atoms are often grouped into residues (e.g monosaccharides or amino acids), and residues grouped into molecules (e.g a carbohydrate or a protein chain).
Molecules can further be assembled into larger structures (e.g multi-chain proteins or glycoproteins), known as macromolecular assemblies. We simply call these assemblies. Most functionality in gmml2 follows this model. The exception is the sequence code, which deals exclusively with residues.