On Tue, Apr 26, 2011 at 3:41 PM, seritaka <seritaka@...> wrote:
> I have one question about murckoscaffold.
> When I tried to covert quinones to murcko scaffold,
> Dimethyl cyclohexane was returned, not cyclohexane.
> I want advice.
Can you please provide the exact example that you did, the version of
the RDKit you used, and the output you observed?
On Wed, Apr 27, 2011 at 12:47 PM, takayuki serizawa <seritaka@...> wrote:
> Hi Greg
> Thank you for your mail !
> I send my example file.
> I refer to your code.
> Cyclopentanone converted to methylpentane.
> My RDKit ver. is 2011_03_1 and Python 2.6.6
> Best Regards, Taka
In your code you do the following:
The first call finds the Murcko scaffold and converts cyclopentanone
to cyclopentanone (i.e. no change).
The second call converts that to the generic scaffold, where all atoms
are "C" and all bonds are single.
To demonstrate, here's the output of running your script on your input
file where I've printed :
input_smiles murcko_smiles generic_murcko_smiles
Cc1ccccc1 c1ccccc1 C1CCCCC1
CC1CCCCC1 C1CCCCC1 C1CCCCC1
c1cc(=C)ccc1=C c1cc(=C)ccc1=C CC1CCC(C)CC1
O=C1C=CC(=O)C=C1 O=C1C=CC(=O)C=C1 CC1CCC(C)CC1
CC1CCCC1 C1CCCC1 C1CCCC1
O=C1CCCC1 O=C1CCCC1 CC1CCCC1