Re: [Rdkit-discuss] RuntimeError creating MolBlock

[Greg L. <gre...@gm...>]

Hi Noel,

On Tue, Apr 22, 2008 at 2:48 PM, Noel O'Boyle <bao...@gm...> 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