Guesses residues from existing bonds.

Atoms are split in fragments, where each fragment is mapped to a list of residues. Then, fragments are divided into polymers (e.g., peptide) and non-polymer fragments (e.g., water), where residues assigned to the latter are grouped together by their kind (i.e., protein, ion, solvent, etc.). Finally, polymer fragments and residues grouped by kind are assigned to their own unique chain as long as there are less residue groups than the chain limit (62), otherwise all residues are assigned to the same chain.