Large structures and hexadecimal serials

The legacy PDB format allots five columns to the atom serial number, so it can only count up to 99999. Structures with more atoms than that continue the count in hexadecimal (100000 is written 186A0), a widely used convention that a naive integer parse would get wrong.

pidibble handles this automatically — there is nothing you need to configure. Each PDBParser owns an AtomSerialParser that watches the atom serial column and switches to hexadecimal parsing at the right moment, so serial (and the serial references in CONECT, TER and ANISOU) stay correct past 99999:

p = PDBParser(source_db='rcsb', source_id='<large-entry>').parse()
p.parsed['ATOM'][100000].serial      # a correct integer, not a mis-parsed hex string

How the switch is detected

The transition to hexadecimal is recognized two ways, so it works whether or not the early serial numbers happen to contain the digits a–f:

• By content — as soon as a serial contains a hexadecimal letter, subsequent serials are read as hexadecimal.

• By magnitude — if the running value exceeds 99999, the parser trips into hexadecimal mode even for an all-numeric field.

The switch is latching: once tripped it stays in hexadecimal mode for the rest of the parse. Because the state lives on the parser instance (not in a global), parsing several structures in the same program — or in several threads — never lets one file’s numbering leak into another’s.

Note

Hexadecimal detection is applied only to atom-serial fields. Ordinary integer fields (residue sequence numbers, counts, and the like) are always read as decimal, including legitimately negative values.