On Fri, Apr 30, 2010 at 12:56 PM, Greg Landrum <[email protected]> wrote:
>
> I don't see any problems in your script, so I have to assume that it's
> a problem with the binary you're using. I'm travelling and don't have
> a windows machine handy, so this will have to wait until I'm back home
> this weekend.
Ok, I was able to reproduce this on my windows box. It's clearly a
problem with the windows build:
In [29]: m = Chem.MolFromSmiles('OC(=O)C1CCCC1')
In [30]: AllChem.Compute2DCoords(m)
Out[30]: 0
In [31]: print Chem.MolToMolBlock(m)
-------> print(Chem.MolToMolBlock(m))
RDKit 2D
8 8 0 0 0 0 0 0 0 0999 V2000
-1.#IND 1.#QNB 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.#IND 1.#QNB 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.#IND 1.#QNB 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.#IND 1.#QNB 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.#IND 1.#QNB 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.#IND 1.#QNB 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.#IND 1.#QNB 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.#IND 1.#QNB 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 3
2 4 1 0
4 5 1 0
5 6 1 0
6 7 1 0
7 8 1 0
8 4 1 0
M END
I will look into this and see where the problem lies.
Note: whatever is going on here doesn't affect every depiction; other
molecules do end up with correct coordinates.
Best Regards,
-greg
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