If you read all from tutorial you will find a example:
>>> suppl = Chem.SDMolSupplier('data/cdk2.sdf')>>> ms = [x for x in suppl if x
>>> is not None]>>> for m in ms: tmp=AllChem.Compute2DCoords(m)>>> from
>>> rdkit.Chem import Draw>>> Draw.MolToFile(ms[0],'images/cdk2_mol1.png')>>>
>>> Draw.MolToFile(ms[1],'images/cdk2_mol2.png')
for this example with you pasted you can just write mol to file:
>>> from rdkit.Chem import AllChem
>>> from rdkit import Chem
>>> m = Chem.MolFromSmiles('c1nccc2n1ccc2')
>>> AllChem.Compute2DCoords(m)
Draw.MolToFile(m,'example.png')
pozdrawiam
Adrian Jasiński
2014-02-17 18:34 GMT+01:00 Yingfeng Wang <ywang...@gmail.com>:
> I want to draw a 2D figure of a compound. And I follow the example given
> at the following link,
>
> http://www.rdkit.org/docs/GettingStartedInPython.html
>
> My code is given as follows,
>
> >>> from rdkit.Chem import AllChem
> >>> from rdkit import Chem
> >>> m = Chem.MolFromSmiles('c1nccc2n1ccc2')
> >>> AllChem.Compute2DCoords(m)
> 0
> >>> template = Chem.MolFromSmiles('c1nccc2n1ccc2')
> >>> AllChem.Compute2DCoords(template)
> 0
> >>> AllChem.GenerateDepictionMatching2DStructure(m,template)
> >>>
>
>
> However, I got nothing. I am wondering what the correct way is to generate
> the 2D figure of "c1nccc2n1ccc2". Thanks.
>
> Yingfeng
>
>
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