I quite agree with Andrew that bzip2 support seems a rather less than
urgent priority.
However, if you'd like to compile for Windows here are the instructions
for MinGW compiler - they work for 2.3.0, 2.3.1 and with one exception
for 2.3.2:
Compiling OpenBabel version 2.3.0: First make sure zlib, eigen2, and
libxml2 are installed. For libxml2 I used the following options for
configure: --without-threads --disable-shared;
Run cmake with the following options:
cmake.exe -G"MSYS Makefiles"
-DZLIB_LIBRARY=/usr/local/lib/libz.a
-DZLIB_INCLUDE_DIR=/usr/local/inclulde
-DEIGEN2_INCLUDE_DIR=/usr/local/include/eigen2
-DLIBXML2_LIBRARIES=/usr/local/lib/libxml2.a
-DLIBXML2_INCLUDE_DIR=/usr/local/include/libxml2
-DCMAKE_INSTALL_PREFIX=/usr/local/
-DBUILD_SHARED=OFF -DCMAKE_CXX_FLAGS=-DLIBXML_STATIC
-DCMAKE_C_FLAGS=-DLIBXML_STATIC
-DCMAKE_CXX_STANDARD_LIBRARIES=-lws2_32 ../
make
make install
The one exception for 2.3.2 is InChI format - it doesn't get compiled
with the above procedure. If you'd like to make a contribution resolving
this problem with InChI would be greatly appreciated.
Best regards,
Igor
On Fri, 2013-01-18 at 03:13 +0100, Andrew Dalke wrote:
> On Jan 17, 2013, at 6:20 PM, Kirill Okhotnikov wrote:
> > I decided to implement bzip2 pack/unpack functionality in open-babel
> > (#91 bzip2 compression/decompression).
>
> What does the "#91" mean? It's not the Open Babel bug id, and a search
> of the mailing list finds nothing matching "bzip" or "bzip2".
>
> I do not think bzip2 support is important. I have rarely come across
> people using it for cheminformatics data. For example, while PubChem,
> ChEMBL and others release their data sets with gzip compression, I
> don't know of anyone who releases bzip2 files.
>
> Which data sets do you use which are big enough that the better
> bzip2 compression becomes worthwhile?
>
> As you found out, bzip2 doesn't support random seeking. It *can*
> be emulated, which Python's bz2 module does, but "depending on
> the parameters the operation may be extremely slow."
>
>
> Personally, I think bzip is no longer a useful format. If you're
> willing to take the extra CPU time then use the LZMA-based methods,
> like .xz. Here's how the Python source distribution compresses
> with each of the three methods:
>
> • Gzipped source tar ball ~ 16 MB
> • Bzipped source tar ball ~ 14 MB
> • XZ compressed source tar ball ~ 11 MB
>
>
> I also think that supporting Boost is a nuisance. However, if
> only some Boost functionality is needed, why not just include its
> header files?
>
>
> > I think, that it will be good idea to have boost library to be required by
> > the project (connected permanently). Some other boost libraries can be
> > useful. For example, Program Options, Geometry, RegExp. In the future
> > developers can easily use this powerful well known library.
>
> Developers can already use Boost, by installing it themselves.
>
> The only reason for switching to Boost is if Open Babel would make
> effective use of what Boost provides. But the examples you list aren't
> things which would easily change:
>
> - who would rewrite the options parser to use the Boost one?
>
> - why replace the existing geometry code with an alternative?
>
> - what advantages does RegExp have over C++'s <regex>? (I see
> that src/formats/gamessukformat.cpp already uses that
> the regex library that the C++ compiler provides.)
>
> - how much code would break?
>
> Now, there are answers to this. For example, perhaps the Boost
> geometry code makes parts of Open Babel 3x faster, or perhaps
> 20 of the format parsers could be shortened by 90% while being
> more maintainable. But given the known work in rewriting those
> parts of the code, and the known difficulty of supporting
> Boost - something I've experienced myself - it's not as easy as
> saying that other people might find it useful.
>
> > 3) Can somebody help me to compile and test the system under MS Windows?
>
> If all else fails, you might look into using an Amazon instance
> running MS Windows, then install Visual Studio Express to compile
> C++ code from the command-line.
>
> Cheers,
>
> Andrew
> da...@dalkescientific.com
>
>
>
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