Noel
This worked fine for me. It was the
"configure --enable-maintainer-mode" step
that I was missing.
After that, everything went without a hitch.
And the Canonical Atom Order is working fine too.
Thanks,
TJ
Noel O'Boyle wrote:
> Sorry - I beg your pardon. The problem is the documentation (which I
> now remember I was supposed to update). If you are using the trunk,
> there is a file missing which you need to create yourself.
>
> You need to do two things:
> (1) install SWIG (we recommend you download the latest version and
> compile it yourself)
> (2) run "configure --enable-maintainer-mode" instead of just
> "configure" (see the last line in
> http://openbabel.org/wiki/Install_%28source_code%29#Advanced_Notes)
>
> When you run 'make' it will create the SWIG bindings as the file
> openbabel_python.cpp. After running "make install", "python setup.py
> build" should hopefully work.
>
> Noel
>
>> wrote:
>> I think it must be those recent, um, improvements to the setup.py.
>> Could you do me a favour and send me (off-list) the output of "ls
>> -alR" in the top openbabel directory (where the ChangeLog and so on
>> are)? This will help me fix this problem. Also, what is your exact
>> operating system? Is that a regular Ubuntu?
>>
>> In the meanwhile, you can just set the environment variable
>> OPENBABEL_INSTALL to the location where you installed OpenBabel, e.g.
>> /usr/local. Then it should work for you.
>>
>>
>> Noel
>>
>>
>> On 21/03/2008, TJ O'Donnell <tj...@ac...> wrote:
>> > Hi Noel - another O'Person :)
>> >
>> > I downloaded the latest via svn. It seems to have compiled and
>> > installed OK. But the python setup fails.
>> >
>> > tj@vmubuntu:~/openbabel/trunk/scripts/python$ python setup.py build
>> > WARNING: Environment variable OPENBABEL_INSTALL is not set
>> > INFO: Looking for library and include files in ../../src and ../../include
>> > running build
>> > running build_py
>> > file openbabel.py (for module openbabel) not found
>> > file openbabel.py (for module openbabel) not found
>> > running build_ext
>> > building '_openbabel' extension
>> > gcc -pthread -fno-strict-aliasing -DNDEBUG -g -O2 -Wall
>> > -Wstrict-prototypes -fPIC -I../../include -I/usr/include/python2.5 -c
>> > openbabel_python.cpp -o build/temp.linux-i686-2.5/openbabel_python.o
>> > gcc: openbabel_python.cpp: No such file or directory
>> > gcc: no input files
>> > error: command 'gcc' failed with exit status 1
>> >
>> > I've attached the configure.out and make.out.
>> >
>> > Can you figure out why python setup is not working?
>> >
>> > Thanks,
>> >
>> > TJ
>> >
>> >
>> >
>> >
>> > > Geoff - it might be a good idea to document these side-effects...I
>> > > wasn't aware of this one.
>> > >
>> > > TJ, from O'person to another:
>> > >
>> > >>>> a = pybel.readstring("smi", "CCCC(=O)")
>> > >>>> a.data.keys()
>> > > []
>> > >>>> print a.write("can")
>> > > CCCC=O
>> > >>>> a.data.keys()
>> > > ['PartialCharges', 'canonical order']
>> > >>>> a.data['canonical order']
>> > > '1 2 3 4 5'
>> > >
>> > >>>> a = pybel.readstring("smi", "C(=O)CCC")
>> > >>>> a.data.keys()
>> > > []
>> > >>>> print a.write("can")
>> > >>>> print b
>> > > CCCC=O
>> > >>>> a.data['canonical order']
>> > > '5 4 3 1 2'
>> > >
>> > > If you have any further questions, please let us know.
>> > >
>> > > - Noel
>> > >
>> > > On 21/03/2008, Geoffrey Hutchison <ge...@ge...> wrote:
>> > >>
>> > >> On Mar 21, 2008, at 2:05 PM, TJ O'Donnell wrote:
>> > >>
>> > >> > Is it possible to get the canonical atom re-ordering,
>> > >> > say as an int vector, after conversion to canonical smiles?
>> > >>
>> > >>
>> > >> As a matter of fact, yes. The current SVN trunk has this feature --
>> > >> after conversion to canonical SMILES, the ordering is available as an
>> > >> OBPairData called "Canonical Atom Order"
>> > >>
>> > >> For a C++ example, of this, check out tools/obfragment.cpp.
>> > >>
>> > >> This should be accessible from Python directly, although I defer to
>> > >> Noel on the Pybel syntax for this.
>> > >>
>> > >> Cheers,
>> > >> -Geoff
>> > >>
>> > >>
>> > >> -------------------------------------------------------------------------
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>> > >> Defy all challenges. Microsoft(R) Visual Studio 2008.
>> > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/
>> > >> _______________________________________________
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>> > >>
>> > >
>> >
>> >
>>
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