[BioPython] Compiling Bio.PDB.mmCIF.MMCIFlex on Windows

[Michiel De Hoon]

> Does Cygwin cope with the Bio.PDB.mmCIF.MMCIFlex extension module?

I don't think it does.

> I tried to compiled BioPython 1.41 with Python 2.3.3 on Windows XP SP2 
> using MSVC 6.0 (Microsoft Visual C++ 6.0).

> There is a problem with unistd.h missing while trying to compile file 
> lex.yy.c into lex.yy.obj as shown below:

On cygwin, there is no problem with unistd.h. However, since
Bio.PDB.mmCIF.MMCIFlex needs flex to be installed, the linking fails:

C:\cygwin\bin\gcc.exe -mno-cygwin -shared -s
build\temp.win32-2.4\Release\bio\pd
b\mmcif\lex.yy.o build\temp.win32-2.4\Release\bio\pdb\mmcif\mmciflexmodule.o
bui
ld\temp.win32-2.4\Release\bio\pdb\mmcif\MMCIFlex.def -Lc:\Python24\libs
-Lc:\Pyt
hon24\PCBuild -lfl -lpython24 -lmsvcr71 -o
build\lib.win32-2.4\Bio\PDB\mmCIF\MMC
IFlex.pyd
/usr/lib/gcc/i686-pc-mingw32/3.4.4/../../../../i686-pc-mingw32/bin/ld: cannot
fi
nd -lfl

This is a recurring problem and is not limited to Windows, but to any machine
without flex installed.
So ... is there a chance of getting Bio.PDB.mmCIF.MMCIFlex rewritten without
relying on flex?

--Michiel.