ChargeCalculator:Terminology

Structural elements

Any input file containing structures is parsed and interpreted at several levels.

Molecule

In the ACC environment, a molecule represents the sum of all structural elements in the input file, regardless of other annotations within the file (e.g., ATOM vs HETATM records, chain identifiers marking different components of a complex, etc.). In other words, molecule is used here as an umbrella term for everything from simple compounds to biomacromolecular complexes made up of proteins, nucleic acids, ligands, ions, water, etc. ACC thus assigns a unique identifier (molecule ID) to each molecule according to the input file name.

Atom

Each molecule is made up of a set of atoms. In the ACC environment, each atom is uniquely identified in the input file by its chemical element and atom serial number. Additional useful information can be used in the characterization of each atom, if such information is available in the input file (atom name and residue details).

Residue

We generally use the term residue to refer to any component of a biomacromolecule. Within the ACC 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 annotation (3-letter code) and residue identifier (residue serial number). Not all file formats include residue information, but this has no bearing over the charge calculation procedure in ACC.