The Bsoft molecular object model is an attempt to implement the most general pragmatic molecular structure. Sequence and atomic coordinates are alternative representations of the same molecule. The molecules studied in structural biology are typically proteins or nucleic acids with associated sequence information. In Bsoft, these descriptors of molecules are grouped into one structure with utilities for reconciling alternative descriptions.
A molecule is generally defined as a collection of covalently bound atoms. Exceptions involve cross-links such as disulfide bonds, or covalent bonding between what are considered different molecules. To deal with multiple molecules in a data set, the notion of a "molecule group" is defined in Bsoft. This loose concept can be used for all the molecules in a quaternary structure, or for all the molecules in a complete system (which may include solvent).
Simple molecules are usually small numbers of covalently bound atoms. However, the polymeric macromolecules (such as proteins and nucleic acids) require a hierarchical level between molecule and atom. In Bsoft this intermediate level is a "residue", whether it is an amino acid residue in a protein, a nucleotide in a nucleic acid, or a sugar monomer in a polysaccharide. For simple monomeric molecules, the residue is considered to be the whole molecule.
The molecule group hierarchy is therefore:
Molecule group
Molecule
Residue
Atom