I believe this is an example of the sort of thing that the essay author complained about.
Bit-packing is simple. You spent a lot of time working around problems that shouldn't have existed in the first place. Even when using the approach you described, here is Python code which does what you described:
>>> byte_to_bits = dict((chr(i), bin(i)[2:].zfill(8)) for i in range(256))
>>> byte_to_bits["A"]
'01000001'
>>> as_bits = "".join(byte_to_bits[c] for c in open("benzotriazole.sdf").read())
>>> as_bits[:16]
'0000110100001010'
>>> chr(int(as_bits[:8], 2))
'\r'
>>> chr(int(as_bits[8:16], 2))
'\n'
>>> open("benzotriazole.sdf").read(2)
'\r\n'
This keeps everything in memory, since 300MB is not a lot of memory. If it was in the GB range then I would have written to a file instead of building an in-memory string.
The run-time was small enough that I didn't notice it.
The thing is, you succeeded in solving the problem, and are justly proud of your success. This is how a lot of scientists feel. But a lot of CS people look at the wasted work when there are simpler, better, more maintainable ways.
