To follow-up what David suggests, just replace your current pybel.py by the
file at:
https://raw.githubusercontent.com/openbabel/openbabel/df59c4a630cf753723d1318c40479d48b7507e1c/scripts/python/pybel.py
This can this problem corrected so that your original code will work
unchanged.
Regards,
Noel
On 12 April 2014 00:32, David Hall <li...@cowsandmilk.net> wrote:
> Hi Carolina,
>
> Try making a change like shown in this commit to the draw function in
> pybel.py :
>
>
> https://github.com/openbabel/openbabel/commit/df59c4a630cf753723d1318c40479d48b7507e1c
>
> Then, your original python code will hopefully work.
>
> -David
>
>
>
>
> On Fri, Apr 11, 2014 at 6:58 PM, Carolina Román Salgado <
> carolina.roman.salg...@gmail.com> wrote:
>
>> Hi Noel
>>
>> I tried replacing
>>
>> pybel.readstring('smi', str(v_name)).draw(show=False, filename=img_path)
>>
>> with
>>
>> pybel.readstring('smi', str(v_name)).draw(show=False, filename=img_path,
>> formatok=obConversion.SetOutFormat("_png2"))
>>
>> but I got the error "draw() got an unexpected keyword argument
>> 'formatok'". I expected it, because there is no formatok argument in the
>> documentation for draw [1].
>>
>> I also tried calling formatok = obconversion.SetOutFormat("_png2")
>> before draw, but I got the original error:
>>
>> ImportError: PNG output format not found. You should compile Open Babel
>> with PNG support. See installation instructions for more information.
>>
>> Could you explain to me how/where should I use formatok?
>>
>> Thanks
>>
>> Carolina
>>
>> [1]
>>
>> http://openbabel.org/docs/2.3.1/UseTheLibrary/Python_PybelAPI.html#pybel.Molecule.draw
>>
>>
>> On 04/02/2014 11:54 AM, Noel O'Boyle wrote:
>> > It's a bug in the Pybel release. Change the line in "draw" to
>> >
>> > formatok = obconversion.SetOutFormat("_png2")
>> >
>> > - Noel
>> >
>> >
>> > On 2 April 2014 16:44, Carolina Román-Salgado
>> > <carolina.roman.salg...@gmail.com
>> > <mailto:carolina.roman.salg...@gmail.com>> wrote:
>> >
>> > Hi
>> >
>> > I'm trying to get Pybel (OpenBabel 2.3.2) to export to PNG format in
>> > Centos 6.5.
>> >
>> > As I understood from the the docs, I just need to install Cairo; the
>> > packages for Centos are cairo and cairo-devel. I also installed
>> libpng
>> > and libpng-devel.
>> >
>> > This is the compilation command and (relevant) output:
>> >
>> > [yo@mol build]$ cmake ../openbabel-2.3.2 -DPYTHON_BINDINGS=ON
>> >
>> -DEIGEN2_INCLUDE_DIR=/home/yo/openbabel_compilation/eigen-eigen-b23437e61a07/
>> >
>> -DEIGEN3_INCLUDE_DIR=/home/yo/openbabel_compilation/eigen-eigen-6b38706d90a9/
>> >
>> > -- Using included inchi library.
>> > -- Could NOT find wxWidgets (missing: wxWidgets_FOUND)
>> > -- Cairo found. PNG output will be supported.
>> > -- Attempting to build the GUI
>> > -- wxWidgets not found => GUI will not be built
>> > -- Python bindings will be compiled
>> > -- Configuring done
>> > -- Generating done
>> > -- Build files have been written to:
>> > /home/yo/openbabel_compilation/build
>> >
>> >
>> > It says "Cairo found. PNG output will be supported.". Indeed, I get
>> a
>> > png if I run:
>> >
>> > /usr/local/bin/obabel -:"CC(=O)Cl" -O mymol.png -xO smi
>> >
>> >
>> > But when I try to run my code using pybel
>> >
>> > [yo@mol MDB]$ python get_data.py
>> >
>> > Traceback (most recent call last):
>> > File "get_data.py", line 30, in name_to_img
>> > pybel.readstring('smi', str(v_name)).draw(show=False,
>> > filename=img_path)
>> > File "/usr/lib64/python2.6/site-packages/pybel.py", line 502, in
>> > draw
>> > raise ImportError(errormessage)
>> > ImportError: PNG output format not found. You should compile Open
>> Babel
>> > with PNG support. See installation instructions for more
>> information.
>> >
>> >
>> > I can export to PNG using a script sample for Cairo and using obabel
>> > directly, so in this point I don't even understand the error from
>> pybel.
>> > How do I get PNG support or at least understand where the problem
>> is?
>> >
>> > Thank you
>> >
>> > Carolina
>> >
>> >
>> ------------------------------------------------------------------------------
>> > _______________________________________________
>> > OpenBabel-discuss mailing list
>> > OpenBabel-discuss@lists.sourceforge.net
>> > <mailto:OpenBabel-discuss@lists.sourceforge.net>
>> > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
>> >
>> >
>>
>>
>> --
>> Carolina Román Salgado
>>
>>
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>
>
>
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