The key terms used within the PatternQuery (PQ) environment are defined below. It is important to establish these terms before moving on the description of the principles on which PQ 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 PQ environment, each atom is uniquely identified in the input file by its atom name, id, chemical element, chain and the residue details the atom belongs to (PDB residue name and PDB id).
The term residues is generally used to refer to any component of a biomolecule. Within the PQ 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.
A pattern is a subset of atoms of the input biomolecule. It can also be understood as an arrangement of either atoms or residues. Therefore, individual atoms and residues can be considered as patterns as well.
A query is a single declarative expression of the PQ language which describes one or more structural patterns inside an input biomolecule.