In an ideal world each individual residue and atom would have a standard, distinct name. Unfortunately several naming schemes for atoms exist, particularly for hydrogens. As such, in order to detect the presence/absence of atoms in a protein, an internal canonical naming scheme is used. The naming scheme used in PDB2PQR is the one recommended by the PDB itself, and derives from the IUPAC naming recommendations found in

This canonical naming scheme is used as the default PDB2PQR output. For a list of standard residue/atom name pairs, please see the PDB Change Advisory Notice regarding the naming scheme.

All conversions in PDB2PQR use the internal canonical naming scheme to determine distinct atom names. In previous versions of PDB2PQR these conversions were stored in long lists of if statements, but for transparency and editing this is a bad thing. Instead, all conversions can now be found in the various XML files found in PDB2PQR - for more discussion on the XML files see the XML section of the Programmer Guide.

There are a few additions to the canonical naming scheme, mirrored after the AMBER naming scheme (chosen since for the most part it follows the IUPAC recommendations). These changes are made in PATCHES.xml, and allow any of the following to be patched as necessary as well as detected on input: