[Biopython-dev] flex, setup.py and Bio.PDB.mmCIF (Bug 2619)

Lenna Peterson arklenna at gmail.com
Thu Feb 14 19:52:54 UTC 2013

On Sat, Feb 9, 2013 at 10:55 PM, Michiel de Hoon <mjldehoon at yahoo.com>wrote:

> Currently lex.yy.c contains lots of code that is generated automatically
> by lex but is not actually needed for the mmCIF parser. I was thinking to
> remove those parts, and to clean up the remainder so that the code is
> understandable (allowing us to fix any bugs, or to convert it to pure
> Python).

Whoops, failed to reply all. Sorry for the double email, Michiel.


But generated C is by definition not understandable or debuggable. The only
function of lex.yy.c is to tokenize the mmCIF input.

All of the communication to Python is handled by MMCIFlexmodule.c, which is
70 lines and a header with 3 statements. In parallel to the PLY version, I
rewrote the C to be object-oriented, which pushed it to 101 lines.



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