Hi Noel,
On Tue, Apr 22, 2008 at 2:48 PM, Noel O'Boyle <[email protected]> wrote:
> Yes, I should have said - I'm using the latest release on Windows.
>
>
By latest release do you mean the Jan2008 release or did you do a
build of the svn version yourself?
I just tried this with the svn version on windows:
[4] >>> print Chem.MolToMolBlock(Chem.MolFromSmiles("CCCC"))
RDKit
4 3 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
M END
so that looks ok
I can reproduce the error using the Jan2008 release though. The way to
solve the problem with the Jan release is to add 2D coords to the
molecule:
[5] >>> from Chem import AllChem
[6] >>> m = Chem.MolFromSmiles('CCCC')
[7] >>> AllChem.Compute2DCoords(m)
Out[7]: 0
[8] >>> print Chem.MolToMolBlock(m)
4 3 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.5981 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.8971 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
3 4 1 0
M END
-greg
