The configuration files read by freesasa_classifier_from_file() or the command-line option -c should have two sections: types: and atoms:.

The types-section defines what types of atoms are available (aliphatic, aromatic, hydroxyl, ...), what the radius of that type is and what class a type belongs to (polar, apolar, ...). The types are just shorthands to associate an atom with a given combination of class and radius. The user is free to define as many types and classes as necessary.

The atoms-section consists of triplets of residue-name, atom-name (as in the corresponding PDB entries) and type. A prototype file would be

 types:
 C_ALIPHATIC 2.00 apolar
 C_AROMATIC  1.75 apolar
 N 1.55 polar
 
 atoms:
 ANY N  N             
 ANY CA C_ALIPHATIC
 ANY CB C_ALIPHATIC
 
 ARG CG C_ALIPHATIC
 
 PRO CB C_AROMATIC  # overrides ANY CB

The residue type ANY can be used for atoms that are the same in all or most residues (such as backbone atoms). If there is an exception for a given amino acid this can be overridden as is shown for PRO CB in the example.

A few example configurations are available in the directory share/. The configuration-file protor.config is a copy of the default classifier, and can be used to add extra atoms that need to be classified, while keeping the defaults for the standard residues (also see the file scripts/chemcomp2config.pl for instructions on how to generate configurations for new chemical components semi-automatically). If something common is missing in the default classifier, create an issue on Github so that it can be added.

FreeSASA also ships with some configuration-files that mimic other popular programs, such as NACCESS and DSSP.