On Oct 29, 2011, at 2:29 PM, Greg Landrum wrote:
> A colleague pointed me to the new version of IPython, which includes a
> really useful interactive qt-based graphical console.
>
> Since it's easy to do so and the results are actually useful, I added
> a bit of RDKit integration to this:
> http://code.google.com/p/rdkit/wiki/IPythonIntegration
Okay, I've decided to give this a go on my Mac. It appears I'm missing
something because I don't get an image from the following.
import rdkit.Chem.Draw.IPythonConsole
from rdkit import Chem
Chem.MolFromSmiles("C")
It looks like it's perhaps to do with my lack of PIL. I installed
Pillow ('Pillow is the "friendly" PIL fork.') but that didn't work.
I then installed PIL 1.1.7 and that did a bit better, in that
it inserted an image with this URL.
data:image/png;base64,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
However, it was completely blank.
The PIL installation says:
--- TKINTER support available
*** JPEG support not available
--- ZLIB (PNG/ZIP) support available
*** FREETYPE2 support not available
*** LITTLECMS support not available
Also, I did
from rdkit.Chem import Draw
Draw.MolToImageFile(mol,'test.png')
and got the same blank result, when I did the code in the
IPython browser.
But on the command-line,
[xebulon:~] dalke% python
Python 2.7.1 (r271:86832, Jul 31 2011, 19:30:53)
[GCC 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2335.15.00)] on darwin
Type "help", "copyright", "credits" or "license" for more information.
>>> from rdkit.Chem import Draw
>>> from rdkit import Chem
>>> Chem.MolFromSmiles("c1ccccc1O")
<rdkit.Chem.rdchem.Mol object at 0x10faaf980>
>>> mol = _
>>> Draw.MolToImageFile(mol, "test.png")
>>>
This gives a "test.png" with visible graphics.
Also, the ipython notebook and the command-line versions are
using the same Python:
In [4]: import sys
sys.version
Out[4]:
'2.7.1 (r271:86832, Jul 31 2011, 19:30:53) \n[GCC 4.2.1 (Based on Apple Inc.
build 5658) (LLVM build 2335.15.00)]'
Any clues?
Andrew
[email protected]
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