Handle hex values for atom and residue numbers

It works as follows.  It first tries to parse all values as decimal.  If it fails on a value, it then tries to parse it as hex.  If that succeeds, it sets a flag indicating that all further values should be parsed as hex.

This correctly interprets the values outputted by VMD, which is different from hybrid-36.  Files using the latter will still load without problem, but there will be a gap in the atom IDs where it jumps from 99999 to A0000 (655360).  
Sorry, I'm in the wrong window...  Meant to be in the MDTraj port of this code.  Please disregard.