The key terms used within the MotiveQuery (MQ) environment are defined below. It is important to establish these terms before moving on the description of the principles on which MQ is built. Any input file containing biomolecular structures is parsed and interpreted at several levels. Any of them can be successfully used when creating queries.
All biomolecules are made up of a set of atoms. In the MQ environment, each atom is uniquely identified in the input file by its atom name, id, chemical element, chain and a residue details the atom belong to (residue name and id).
We generally use the term residue to refer to any component of a biomolecule. Within the MQ environment, any collection of atoms bound by chemical bonds (covalent, coordinative or ionic) is considered a residue if this fact is appropriately indicated in the input file. Specifically, all the atoms that make up a residue should have the same residue name (3-letter code) , residue serial number and chain identifier.
Fragment is a subset of biomolecule defined by a query. Basically, it is any arrangement of either atoms or residues. Therefore, both atoms and also residues can be considered as fragments too.
By a query we mean a single declarative expression of MQ language which denotes a structural fragment.