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
> <[email protected]
> <mailto:[email protected]>> 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
>
>
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>
>
--
Carolina Román Salgado
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