Re: [OpenBabel-scripting] Graph Kernels

[Noel O'B. <no...@ca...>]

The install procedure is as follows. Please let me know if this is
confusing, if you have any problems, or if you do not have root access.

(1) You should download OpenBabel 2.0.2 for Linux by clicking on
"Download" under the picture of the fish on
http://openbabel.sourceforge.net/wiki/Main_Page and choose
openbabel-2.0.2.tar.gz. You should save this into a folder called
'openbabel' somewhere on your computer.

(2) Open a command window, change directory into 'openbabel', and
decompress the downloaded file with following command:

tar zxvf openbabel-2.0.2.tar.gz

This will create a folder called 'openbabel-2.0.2'.

(3) You now need to configure and compile openbabel. To do this, change
directory into 'openbabel-2.0.2'. Run the following commands, one after
the other

./configure | tee configure.out
make | tee make.out

If there are any errors at this point, send an email to the
openbabel-discuss mailing list (ope...@li...)
and attach the files 'configure.out' and 'make.out'.

(4) If you have root permissions, you should install openbabel globally.
As root, run the following command:

make install

(5) You now need to compile the python extension. Change directory to
'openbabel-2.0.2/scripts/python' and run:

python setup.py build

(6) To install the python interface globally, as root type:

python setup.py install

(7) It's all done. Test out the 'openbabel' module by trying some of the
Python code at:
http://openbabel.sourceforge.net/wiki/Python#The_openbabel_module

Hope this helps,
   Noel



On Tue, 2006-08-08 at 10:57 -0400, Geoffrey Hutchison wrote:
> > Openbabel is more of a molecule parsing program then a graph kernel
> > program.
> 
> Not!
> 
> >> Regarding DFS specifically, I believe it is present but I am not sure
> >> where. I'm sure that Geoff can comment on this.
> 
> There are both DFS and BFS iterators in the 2.1 development code,  
> which incidentally is the only version with PyOpenBabel.
> 
> >> Regarding installation, we should have an install page on the web  
> >> site.
> >> At the moment we don't have one, but I will write one as soon as
> >> possible. What operating system do you use? If you are using  
> >> Windows, I
> >> am afraid you will not be able to use Python to access OpenBabel, you
> >> can only use C++.
> 
> Well, that's not quite correct. In principle, you can use Windows to  
> access Python -- however, since there aren't many currently active  
> developers on Open Babel who use Windows, it's currently not  
> available. There's absolutely nothing technically holding back the  
> Python interface through SWIG -- I just don't have time to figure out  
> what needs to be linked.
> 
> I'm not particularly versed on "tanimoto" vs. "hybrid". There is  
> already support for Tanimoto based on various fingerprint methods:
> http://openbabel.sourceforge.net/wiki/Tutorial:Fingerprints
> 
> These should already be available via the Python SWIG interface -- I  
> don't know if that's true of PyOpenBabel or not.
> 
> Cheers,
> -Geoff
> 
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