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

[Peter]

Dear all,

Back in Feb 2006 (shortly before Biopython 1.42), in CVS revision
1.109 setup.py was modified to comment out building & installation of
the Bio.PDB.mmCIF module which requires flex to be installed.

For background see:
http://lists.open-bio.org/pipermail/biopython/2006-February/002923.html
http://lists.open-bio.org/pipermail/biopython-dev/2006-February/002280.html

This issue was recently re-opened with Bug 2619:
http://bugzilla.open-bio.org/show_bug.cgi?id=2619

I looks like Bio.PDB.mmCIF didn't (and probably still doesn't) compile
on Windows, but should compile on Unix provided flex is installed.
Ideally setup.py would check the platform and if flex is installed,
and if so install Bio.PDB.mmCIF - rather than the current situation
never installing it (unless the user edits setup.py by hand).
Alternatively, we could have a simple prompt (on Unix) asking if we
should try and build/install Bio.PDB.mmCIF (like the ugly KDTree
prompt when that was written in C++)?

Does anyone have any code handy for checking if flex is installed from
within python?

Perhaps ideally we could replace the flex version of Bio.PDB.mmCIF
with pure python - but this is a big job.

Peter